-- dump date 20120504_140831 -- class Genbank::misc_feature -- table misc_feature_note -- id note 340054000001 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340054000002 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 340054000003 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 340054000004 substrate binding pocket [chemical binding]; other site 340054000005 membrane-bound complex binding site; other site 340054000006 hinge residues; other site 340054000007 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340054000008 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 340054000009 dimer interface [polypeptide binding]; other site 340054000010 conserved gate region; other site 340054000011 putative PBP binding loops; other site 340054000012 ABC-ATPase subunit interface; other site 340054000013 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 340054000014 dimer interface [polypeptide binding]; other site 340054000015 conserved gate region; other site 340054000016 putative PBP binding loops; other site 340054000017 ABC-ATPase subunit interface; other site 340054000018 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 340054000019 DNA binding site [nucleotide binding] 340054000020 Helix-turn-helix domains; Region: HTH; cl00088 340054000021 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 340054000022 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 340054000023 dimer interface [polypeptide binding]; other site 340054000024 putative anticodon binding site; other site 340054000025 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 340054000026 motif 1; other site 340054000027 active site 340054000028 motif 2; other site 340054000029 motif 3; other site 340054000030 peptide chain release factor 2; Validated; Region: prfB; PRK00578 340054000031 RF-1 domain; Region: RF-1; cl02875 340054000032 RF-1 domain; Region: RF-1; cl02875 340054000033 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 340054000034 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: AlaRS_core; cd00673 340054000035 motif 1; other site 340054000036 active site 340054000037 motif 2; other site 340054000038 motif 3; other site 340054000039 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 340054000040 DHHA1 domain; Region: DHHA1; pfam02272 340054000041 Global regulator protein family; Region: CsrA; cl00670 340054000042 potassium/proton antiporter; Reviewed; Region: PRK05326 340054000043 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 340054000044 Transporter associated domain; Region: CorC_HlyC; cl08393 340054000045 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 340054000046 septum formation inhibitor; Reviewed; Region: minC; PRK03511 340054000047 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 340054000048 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 340054000049 cell division inhibitor MinD; Provisional; Region: PRK10818 340054000050 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 340054000051 Switch I; other site 340054000052 Switch II; other site 340054000053 Septum formation topological specificity factor MinE; Region: MinE; cl00538 340054000054 glyceraldehyde-3-phosphate dehydrogenase A; Provisional; Region: gapA; PRK15425 340054000055 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054000056 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 340054000057 Domain of unknown function DUF20; Region: UPF0118; pfam01594 340054000058 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 340054000059 recombinase A; Provisional; Region: recA; PRK09354 340054000060 RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange; Region: recA; cd00983 340054000061 hexamer interface [polypeptide binding]; other site 340054000062 Walker A motif; other site 340054000063 ATP binding site [chemical binding]; other site 340054000064 Walker B motif; other site 340054000065 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340054000066 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054000067 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 340054000068 exoribonuclease II; Provisional; Region: PRK05054 340054000069 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 340054000070 RNB domain; Region: RNB; pfam00773 340054000071 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 340054000072 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 340054000073 Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the...; Region: Riboflavin_deaminase-reductase; cd01284 340054000074 catalytic motif [active] 340054000075 Zn binding site [ion binding]; other site 340054000076 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 340054000077 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 340054000078 ATP cone domain; Region: ATP-cone; pfam03477 340054000079 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 340054000080 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054000081 Family description; Region: UvrD_C_2; cl15862 340054000082 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 340054000083 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 340054000084 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 340054000085 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 340054000086 Prepilin peptidase dependent protein C term (DUF3728); Region: DUF3728; pfam12528 340054000087 Protein of unknown function (DUF2509); Region: DUF2509; cl11672 340054000088 hypothetical protein; Provisional; Region: PRK10557 340054000089 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 340054000090 hypothetical protein; Provisional; Region: PRK10506 340054000091 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054000092 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 340054000093 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 340054000094 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 340054000095 active site 340054000096 tetramer interface; other site 340054000097 putative assembly protein; Provisional; Region: PRK10833 340054000098 AsmA-like C-terminal region; Region: AsmA_2; cl15864 340054000099 2'-deoxycytidine 5'-triphosphate deaminase (DCD); Region: DCD; pfam06559 340054000100 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 340054000101 trimer interface [polypeptide binding]; other site 340054000102 active site 340054000103 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 340054000104 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 340054000105 putative active site [active] 340054000106 catalytic triad [active] 340054000107 putative dimer interface [polypeptide binding]; other site 340054000108 magnesium/cobalt efflux protein CorC; Provisional; Region: PRK15094 340054000109 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 340054000110 Transporter associated domain; Region: CorC_HlyC; cl08393 340054000111 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 340054000112 ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional; Region: rfaD; PRK11150 340054000113 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 340054000114 NADP binding site [chemical binding]; other site 340054000115 homopentamer interface [polypeptide binding]; other site 340054000116 substrate binding site [chemical binding]; other site 340054000117 active site 340054000118 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 340054000119 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 340054000120 active site 340054000121 dimer interface [polypeptide binding]; other site 340054000122 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 340054000123 dimer interface [polypeptide binding]; other site 340054000124 active site 340054000125 multidrug efflux system translocase MdfA; Provisional; Region: PRK15402 340054000126 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 340054000127 putative substrate translocation pore; other site 340054000128 multidrug efflux system translocase MdfA; Provisional; Region: PRK15402 340054000129 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 340054000130 putative substrate translocation pore; other site 340054000131 superoxide dismutase; Provisional; Region: PRK10925 340054000132 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 340054000133 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 340054000134 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 340054000135 substrate binding site [chemical binding]; other site 340054000136 dimer interface [polypeptide binding]; other site 340054000137 catalytic triad [active] 340054000138 ferredoxin-NADP reductase; Provisional; Region: PRK10926 340054000139 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 340054000140 FAD binding pocket [chemical binding]; other site 340054000141 FAD binding motif [chemical binding]; other site 340054000142 phosphate binding motif [ion binding]; other site 340054000143 beta-alpha-beta structure motif; other site 340054000144 NAD binding pocket [chemical binding]; other site 340054000145 SlyX; Region: SlyX; cl01090 340054000146 GTP-binding protein; Provisional; Region: PRK10218 340054000147 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 340054000148 G1 box; other site 340054000149 putative GEF interaction site [polypeptide binding]; other site 340054000150 GTP/Mg2+ binding site [chemical binding]; other site 340054000151 Switch I region; other site 340054000152 G2 box; other site 340054000153 G3 box; other site 340054000154 Switch II region; other site 340054000155 G4 box; other site 340054000156 G5 box; other site 340054000157 BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a...; Region: BipA_TypA_II; cd03691 340054000158 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly...; Region: BipA_TypA_C; cd03710 340054000159 BolA-like protein; Region: BolA; cl00386 340054000160 Putative exonuclease, RdgC; Region: RdgC; cl01122 340054000161 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 340054000162 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 340054000163 putative ABC transporter; Region: ycf24; CHL00085 340054000164 cysteine desulfurase ATPase component; Reviewed; Region: sufC; PRK09580 340054000165 ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under...; Region: ABC_FeS_Assembly; cd03217 340054000166 Walker A/P-loop; other site 340054000167 ATP binding site [chemical binding]; other site 340054000168 Q-loop/lid; other site 340054000169 ABC transporter signature motif; other site 340054000170 Walker B; other site 340054000171 D-loop; other site 340054000172 H-loop/switch region; other site 340054000173 cysteine desulfurase activator complex subunit SufD; Provisional; Region: PRK10948 340054000174 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 340054000175 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 340054000176 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 340054000177 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340054000178 catalytic residue [active] 340054000179 Fe-S metabolism associated domain; Region: SufE; cl00951 340054000180 UbiA prenyltransferase family; Region: UbiA; cl00337 340054000181 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 340054000182 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 340054000183 Subunit I/III interface [polypeptide binding]; other site 340054000184 Subunit III/IV interface [polypeptide binding]; other site 340054000185 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 340054000186 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 340054000187 D-pathway; other site 340054000188 Putative ubiquinol binding site [chemical binding]; other site 340054000189 Low-spin heme (heme b) binding site [chemical binding]; other site 340054000190 Putative water exit pathway; other site 340054000191 Binuclear center (heme o3/CuB) [ion binding]; other site 340054000192 K-pathway; other site 340054000193 Putative proton exit pathway; other site 340054000194 cytochrome o ubiquinol oxidase subunit II; Provisional; Region: PRK10525 340054000195 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 340054000196 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 340054000197 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Reviewed; Region: ubiF; PRK08020 340054000198 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054000199 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 340054000200 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340054000201 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340054000202 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 340054000203 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 340054000204 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 340054000205 carboxyltransferase (CT) interaction site; other site 340054000206 biotinylation site [posttranslational modification]; other site 340054000207 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 340054000208 active site 340054000209 trimer interface [polypeptide binding]; other site 340054000210 dimer interface [polypeptide binding]; other site 340054000211 NeuB family; Region: NeuB; cl00496 340054000212 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 340054000213 DsrE/DsrF-like family; Region: DrsE; cl00672 340054000214 DsrE/DsrF-like family; Region: DrsE; cl00672 340054000215 DsrE/DsrF-like family; Region: DrsE; cl00672 340054000216 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 340054000217 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 340054000218 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 340054000219 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional; Region: PRK09959 340054000220 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 340054000221 substrate binding pocket [chemical binding]; other site 340054000222 membrane-bound complex binding site; other site 340054000223 hinge residues; other site 340054000224 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 340054000225 substrate binding pocket [chemical binding]; other site 340054000226 membrane-bound complex binding site; other site 340054000227 hinge residues; other site 340054000228 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 340054000229 dimer interface [polypeptide binding]; other site 340054000230 phosphorylation site [posttranslational modification] 340054000231 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 340054000232 ATP binding site [chemical binding]; other site 340054000233 Mg2+ binding site [ion binding]; other site 340054000234 G-X-G motif; other site 340054000235 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340054000236 active site 340054000237 phosphorylation site [posttranslational modification] 340054000238 intermolecular recognition site; other site 340054000239 dimerization interface [polypeptide binding]; other site 340054000240 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 340054000241 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 340054000242 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 340054000243 active site residue [active] 340054000244 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 340054000245 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 340054000246 Protein export membrane protein; Region: SecD_SecF; cl14618 340054000247 SecD export protein N-terminal TM region; Region: SecD-TM1; cl08136 340054000248 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 340054000249 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 340054000250 Protein export membrane protein; Region: SecD_SecF; cl14618 340054000251 Preprotein translocase subunit; Region: YajC; cl00806 340054000252 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 340054000253 tRNA-guanine transglycosylases, various specificities; Region: tgt_general; TIGR00449 340054000254 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 340054000255 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 340054000256 peroxidase; Provisional; Region: PRK15000 340054000257 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 340054000258 dimer interface [polypeptide binding]; other site 340054000259 decamer (pentamer of dimers) interface [polypeptide binding]; other site 340054000260 catalytic triad [active] 340054000261 peroxidatic and resolving cysteines [active] 340054000262 VacJ like lipoprotein; Region: VacJ; cl01073 340054000263 Glycerol-3-phosphate O-acyltransferase [Lipid metabolism]; Region: PlsB; COG2937 340054000264 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 340054000265 putative acyl-acceptor binding pocket; other site 340054000266 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 340054000267 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 340054000268 ATP binding site [chemical binding]; other site 340054000269 Mg++ binding site [ion binding]; other site 340054000270 motif III; other site 340054000271 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 340054000272 nucleotide binding region [chemical binding]; other site 340054000273 ATP-binding site [chemical binding]; other site 340054000274 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 340054000275 catalytic residues [active] 340054000276 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 340054000277 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 340054000278 dimer interface [polypeptide binding]; other site 340054000279 active site 340054000280 Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide...; Region: GRX_family; cd02066 340054000281 GSH binding site [chemical binding]; other site 340054000282 catalytic residues [active] 340054000283 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 340054000284 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 340054000285 metal binding site [ion binding]; metal-binding site 340054000286 dimer interface [polypeptide binding]; other site 340054000287 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 340054000288 ArsC family; Region: ArsC; pfam03960 340054000289 putative catalytic residues [active] 340054000290 Chorismate mutase type II; Region: CM_2; cl00693 340054000291 Predicted GTPase [General function prediction only]; Region: COG0218 340054000292 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 340054000293 G1 box; other site 340054000294 GTP/Mg2+ binding site [chemical binding]; other site 340054000295 Switch I region; other site 340054000296 G2 box; other site 340054000297 G3 box; other site 340054000298 Switch II region; other site 340054000299 G4 box; other site 340054000300 G5 box; other site 340054000301 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 340054000302 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 340054000303 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340054000304 homodimer interface [polypeptide binding]; other site 340054000305 catalytic residue [active] 340054000306 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 340054000307 nucleotide binding site/active site [active] 340054000308 HIT family signature motif; other site 340054000309 catalytic residue [active] 340054000310 TolB amino-terminal domain; Region: TolB_N; cl00639 340054000311 ATP-dependent RNA helicase HrpA; Provisional; Region: PRK11131 340054000312 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 340054000313 ATP binding site [chemical binding]; other site 340054000314 putative Mg++ binding site [ion binding]; other site 340054000315 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 340054000316 nucleotide binding region [chemical binding]; other site 340054000317 ATP-binding site [chemical binding]; other site 340054000318 Helicase associated domain (HA2); Region: HA2; cl04503 340054000319 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 340054000320 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 340054000321 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 340054000322 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 340054000323 Conserved oligomeric complex COG6; Region: COG6; pfam06419 340054000324 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 340054000325 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 340054000326 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 340054000327 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054000328 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 340054000329 catalytic site [active] 340054000330 subunit interface [polypeptide binding]; other site 340054000331 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 340054000332 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340054000333 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340054000334 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 340054000335 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 340054000336 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340054000337 Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways...; Region: MGS_CPS_II; cd01424 340054000338 IMP binding site; other site 340054000339 dimer interface [polypeptide binding]; other site 340054000340 interdomain contacts; other site 340054000341 partial ornithine binding site; other site 340054000342 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 340054000343 translation initiation factor Sui1; Validated; Region: PRK06824 340054000344 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two...; Region: SUI1_eIF1; cd00474 340054000345 Predicted RNA interaction site [nucleotide binding]; other site 340054000346 putative binding site; other site 340054000347 Mutations affecting start-site selection; other site 340054000348 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 340054000349 active site 340054000350 dimer interface [polypeptide binding]; other site 340054000351 tetratricopeptide repeat protein; Provisional; Region: PRK11788 340054000352 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 340054000353 TPR motif; other site 340054000354 binding surface 340054000355 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 340054000356 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 340054000357 active site 340054000358 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 340054000359 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 340054000360 dimerization interface [polypeptide binding]; other site 340054000361 active site 340054000362 Integral membrane protein TerC family; Region: TerC; cl10468 340054000363 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 340054000364 dimer interface [polypeptide binding]; other site 340054000365 catalytic triad [active] 340054000366 peroxidatic and resolving cysteines [active] 340054000367 transcription-repair coupling factor; Provisional; Region: PRK10689 340054000368 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 340054000369 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 340054000370 ATP binding site [chemical binding]; other site 340054000371 putative Mg++ binding site [ion binding]; other site 340054000372 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 340054000373 nucleotide binding region [chemical binding]; other site 340054000374 ATP-binding site [chemical binding]; other site 340054000375 TRCF domain; Region: TRCF; cl04088 340054000376 outer membrane-specific lipoprotein transporter subunit LolC; Provisional; Region: PRK10814 340054000377 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 340054000378 FtsX-like permease family; Region: FtsX; cl15850 340054000379 lipoprotein transporter ATP-binding subunit; Provisional; Region: lolD; PRK11629 340054000380 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 340054000381 Walker A/P-loop; other site 340054000382 ATP binding site [chemical binding]; other site 340054000383 Q-loop/lid; other site 340054000384 ABC transporter signature motif; other site 340054000385 Walker B; other site 340054000386 D-loop; other site 340054000387 H-loop/switch region; other site 340054000388 outer membrane-specific lipoprotein transporter subunit LolE; Provisional; Region: PRK11146 340054000389 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 340054000390 FtsX-like permease family; Region: FtsX; cl15850 340054000391 type III secretion system protein SsaQ; Validated; Region: PRK08035 340054000392 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 340054000393 type III secretion system ATPase; Validated; Region: PRK06820 340054000394 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 340054000395 Walker A motif/ATP binding site; other site 340054000396 Walker B motif; other site 340054000397 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 340054000398 Type III secretory pathway, component EscV [Intracellular trafficking and secretion]; Region: EscV; COG4789 340054000399 type III secretion system protein SsaM; Provisional; Region: PRK15353 340054000400 type III secretion system protein SsaL; Provisional; Region: PRK15345 340054000401 TyeA; Region: TyeA; cl07611 340054000402 type III secretion system protein SsaK; Provisional; Region: PRK15354 340054000403 type III secretion apparatus protein, HrpE/YscL family; Region: HrpE_YscL_not; TIGR02499 340054000404 Type III secretion system subunit; Region: T3SS_LEE_assoc; pfam13327 340054000405 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 340054000406 Type III secretion needle MxiH like; Region: MxiH; cl09641 340054000407 Protein of unknown function (DUF1039); Region: DUF1039; cl05668 340054000408 Type III secretion needle MxiH like; Region: MxiH; cl09641 340054000409 Helix-turn-helix domain; Region: HTH_18; pfam12833 340054000410 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340054000411 pathogenicity island 2 effector protein SseD; Provisional; Region: PRK15361 340054000412 pathogenicity island 2 effector protein SseC; Provisional; Region: PRK15362 340054000413 EspA-like secreted protein; Region: EspA; cl04069 340054000414 Protein of unknown function (DUF1895); Region: DUF1895; cl07553 340054000415 type III secretion system protein SsaD; Provisional; Region: PRK15367 340054000416 type III secretion apparatus protein, YscD/HrpQ family; Region: type_III_yscD; TIGR02500 340054000417 outer membrane secretin SsaC; Provisional; Region: PRK15346 340054000418 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 340054000419 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340054000420 pathogenicity island chaperone protein SpiC; Provisional; Region: PRK15368 340054000421 two component system sensor kinase SsrA; Provisional; Region: PRK15347 340054000422 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 340054000423 dimer interface [polypeptide binding]; other site 340054000424 phosphorylation site [posttranslational modification] 340054000425 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 340054000426 ATP binding site [chemical binding]; other site 340054000427 Mg2+ binding site [ion binding]; other site 340054000428 G-X-G motif; other site 340054000429 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340054000430 active site 340054000431 phosphorylation site [posttranslational modification] 340054000432 intermolecular recognition site; other site 340054000433 dimerization interface [polypeptide binding]; other site 340054000434 two component system sensor kinase SsrB; Provisional; Region: PRK15369 340054000435 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340054000436 active site 340054000437 phosphorylation site [posttranslational modification] 340054000438 intermolecular recognition site; other site 340054000439 dimerization interface [polypeptide binding]; other site 340054000440 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054000441 DNA binding residues [nucleotide binding] 340054000442 dimerization interface [polypeptide binding]; other site 340054000443 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 340054000444 active site 340054000445 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 340054000446 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 340054000447 trimer interface [polypeptide binding]; other site 340054000448 active site 340054000449 substrate binding site [chemical binding]; other site 340054000450 CoA binding site [chemical binding]; other site 340054000451 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 340054000452 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 340054000453 Fe-S metabolism associated domain; Region: SufE; cl00951 340054000454 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 340054000455 DHH family; Region: DHH; pfam01368 340054000456 DHHA1 domain; Region: DHHA1; pfam02272 340054000457 Protein of unknown function (DUF986); Region: DUF986; cl01983 340054000458 PTS system mannose/fructose/sorbose family IID component; Region: EIID-AGA; cl01507 340054000459 PTS system sorbose-specific iic component; Region: EII-Sor; cl01506 340054000460 PTS system mannose-specific transporter subunits IIAB; Provisional; Region: PRK15088 340054000461 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cd00006 340054000462 active pocket/dimerization site; other site 340054000463 active site 340054000464 phosphorylation site [posttranslational modification] 340054000465 PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_man; cd00001 340054000466 active site 340054000467 phosphorylation site [posttranslational modification] 340054000468 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 340054000469 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 340054000470 dimer interface [polypeptide binding]; other site 340054000471 active site 340054000472 glycine-pyridoxal phosphate binding site [chemical binding]; other site 340054000473 folate binding site [chemical binding]; other site 340054000474 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 340054000475 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 340054000476 TolA protein; Region: tolA_full; TIGR02794 340054000477 Gram-negative bacterial tonB protein; Region: TonB; cl10048 340054000478 translocation protein TolB; Provisional; Region: tolB; PRK03629 340054000479 TolB amino-terminal domain; Region: TolB_N; cl00639 340054000480 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 340054000481 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 340054000482 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 340054000483 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340054000484 ligand binding site [chemical binding]; other site 340054000485 tol-pal system protein YbgF; Provisional; Region: PRK10803 340054000486 Tetratricopeptide repeat; Region: TPR_6; pfam13174 340054000487 Uncharacterized conserved protein [Function unknown]; Region: COG2850 340054000488 Sodium:solute symporter family; Region: SSF; cl00456 340054000489 Uncharacterized conserved protein [Function unknown]; Region: COG3535 340054000490 Protein of unknown function (DUF917); Region: DUF917; pfam06032 340054000491 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 340054000492 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; cl00668 340054000493 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 340054000494 PAS fold; Region: PAS_4; pfam08448 340054000495 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054000496 DNA binding residues [nucleotide binding] 340054000497 dimerization interface [polypeptide binding]; other site 340054000498 AntA/AntB antirepressor; Region: AntA; cl01430 340054000499 phosphomannomutase CpsG; Provisional; Region: PRK15414 340054000500 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 340054000501 active site 340054000502 substrate binding site [chemical binding]; other site 340054000503 metal binding site [ion binding]; metal-binding site 340054000504 Domain of unknown function DUF29; Region: DUF29; pfam01724 340054000505 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 340054000506 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054000507 NAD(P) binding site [chemical binding]; other site 340054000508 active site 340054000509 Glucosyl transferase GtrII; Region: Glucos_trans_II; cl10304 340054000510 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 340054000511 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 340054000512 dimer interface [polypeptide binding]; other site 340054000513 active site 340054000514 NTP_transferases catalyze the transfer of nucleotides onto phosphosugars; Region: NTP_transferase; cd04181 340054000515 active site 340054000516 Substrate binding site; other site 340054000517 Mg++ binding site; other site 340054000518 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 340054000519 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 340054000520 active site 340054000521 motif I; other site 340054000522 motif II; other site 340054000523 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054000524 active site 340054000525 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 340054000526 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 340054000527 active site 340054000528 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 340054000529 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054000530 NAD(P) binding site [chemical binding]; other site 340054000531 active site 340054000532 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 340054000533 UDP-glucose 4-epimerase; Region: PLN02240 340054000534 NAD binding site [chemical binding]; other site 340054000535 homodimer interface [polypeptide binding]; other site 340054000536 active site 340054000537 substrate binding site [chemical binding]; other site 340054000538 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340054000539 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340054000540 active site 340054000541 nucleotide binding site [chemical binding]; other site 340054000542 HIGH motif; other site 340054000543 KMSKS motif; other site 340054000544 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 340054000545 CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase; Region: Glyphos_transf; pfam04464 340054000546 LicD family; Region: LicD; cl01378 340054000547 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 340054000548 S-adenosylmethionine binding site [chemical binding]; other site 340054000549 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 340054000550 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 340054000551 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340054000552 catalytic residue [active] 340054000553 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 340054000554 phosphonopyruvate decarboxylase; Region: Ppyr-DeCO2ase; TIGR03297 340054000555 PYR/PP interface [polypeptide binding]; other site 340054000556 dimer interface [polypeptide binding]; other site 340054000557 TPP binding site [chemical binding]; other site 340054000558 Thiamine pyrophosphate (TPP) family, PpyrDC subfamily, TPP-binding module; composed of proteins similar to phosphonopyruvate decarboxylase (PpyrDC) proteins. PpyrDC is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as...; Region: TPP_PpyrDC; cd03371 340054000559 TPP-binding site; other site 340054000560 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 340054000561 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 340054000562 tetramer interface [polypeptide binding]; other site 340054000563 active site 340054000564 Mg2+/Mn2+ binding site [ion binding]; other site 340054000565 Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline; Region: PC_cytidylyltransferase; cd02523 340054000566 active site 340054000567 metal-binding site 340054000568 Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline; Region: PC_cytidylyltransferase; cd02523 340054000569 active site 340054000570 metal-binding site 340054000571 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 340054000572 ferrochelatase; Reviewed; Region: hemH; PRK00035 340054000573 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 340054000574 C-terminal domain interface [polypeptide binding]; other site 340054000575 active site 340054000576 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 340054000577 active site 340054000578 N-terminal domain interface [polypeptide binding]; other site 340054000579 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 340054000580 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 340054000581 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 340054000582 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 340054000583 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 340054000584 generic binding surface II; other site 340054000585 generic binding surface I; other site 340054000586 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 340054000587 Transcriptional regulator Crl; Region: Crl; cl11653 340054000588 NAD synthetase; Provisional; Region: PRK13981 340054000589 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 340054000590 multimer interface [polypeptide binding]; other site 340054000591 active site 340054000592 catalytic triad [active] 340054000593 protein interface 1 [polypeptide binding]; other site 340054000594 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 340054000595 homodimer interface [polypeptide binding]; other site 340054000596 NAD binding pocket [chemical binding]; other site 340054000597 ATP binding pocket [chemical binding]; other site 340054000598 Mg binding site [ion binding]; other site 340054000599 active-site loop [active] 340054000600 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 340054000601 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 340054000602 Ligand Binding Site [chemical binding]; other site 340054000603 TilS substrate binding domain; Region: TilS; pfam09179 340054000604 B3/4 domain; Region: B3_4; cl11458 340054000605 Protein of unknown function, DUF481; Region: DUF481; cl01213 340054000606 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 340054000607 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 340054000608 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 340054000609 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 340054000610 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 340054000611 HIGH motif; other site 340054000612 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 340054000613 active site 340054000614 KMSKS motif; other site 340054000615 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 340054000616 tRNA binding surface [nucleotide binding]; other site 340054000617 anticodon binding site; other site 340054000618 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 340054000619 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 340054000620 multifunctional aminopeptidase A; Provisional; Region: PRK00913 340054000621 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 340054000622 interface (dimer of trimers) [polypeptide binding]; other site 340054000623 Substrate-binding/catalytic site; other site 340054000624 Zn-binding sites [ion binding]; other site 340054000625 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 340054000626 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 340054000627 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 340054000628 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 340054000629 outer membrane protein A; Reviewed; Region: PRK10808 340054000630 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340054000631 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 340054000632 ligand binding site [chemical binding]; other site 340054000633 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 340054000634 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 340054000635 glutaminase active site [active] 340054000636 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 340054000637 dimer interface [polypeptide binding]; other site 340054000638 active site 340054000639 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 340054000640 dimer interface [polypeptide binding]; other site 340054000641 active site 340054000642 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 340054000643 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 340054000644 Substrate binding site; other site 340054000645 Mg++ binding site; other site 340054000646 N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two...; Region: LbH_GlmU_C; cd03353 340054000647 active site 340054000648 substrate binding site [chemical binding]; other site 340054000649 CoA binding site [chemical binding]; other site 340054000650 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 340054000651 Sulfatase; Region: Sulfatase; cl10460 340054000652 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 340054000653 Domain of unknown function DUF21; Region: DUF21; pfam01595 340054000654 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 340054000655 Transporter associated domain; Region: CorC_HlyC; cl08393 340054000656 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 340054000657 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 340054000658 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 340054000659 DNA-binding site [nucleotide binding]; DNA binding site 340054000660 RNA-binding motif; other site 340054000661 Trm112p-like protein; Region: Trm112p; cl01066 340054000662 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 340054000663 Ligand binding site; other site 340054000664 oligomer interface; other site 340054000665 putative ATP-dependent protease; Provisional; Region: PRK09862 340054000666 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 340054000667 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054000668 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 340054000669 Integrase core domain; Region: rve; cl01316 340054000670 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054000671 Type II/IV secretion system protein; Region: T2SE; pfam00437 340054000672 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 340054000673 Walker A motif; other site 340054000674 ATP binding site [chemical binding]; other site 340054000675 Walker B motif; other site 340054000676 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 340054000677 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 340054000678 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 340054000679 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 340054000680 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340054000681 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 340054000682 potential protein location (hypothetical protein) that overlaps protein (hypothetical protein) 340054000683 potential protein location (hypothetical protein) that overlaps protein (hypothetical protein) 340054000684 Transposase domain (DUF772); Region: DUF772; cl15789 340054000685 Transposase domain (DUF772); Region: DUF772; cl15789 340054000686 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 340054000687 Protein of unknown function (DUF3018); Region: DUF3018; pfam11455 340054000688 PemK-like protein; Region: PemK; cl00995 340054000689 Bacterial shufflon protein, N-terminal constant region; Region: Shufflon_N; pfam04917 340054000690 Plasmid stability protein [General function prediction only]; Region: StbC; COG4691 340054000691 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 340054000692 oligomeric interface; other site 340054000693 putative active site [active] 340054000694 homodimer interface [polypeptide binding]; other site 340054000695 PilS N terminal; Region: PilS; pfam08805 340054000696 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 340054000697 conjugal transfer relaxase TraI; Provisional; Region: PRK13878 340054000698 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 340054000699 IHF dimer interface [polypeptide binding]; other site 340054000700 IHF - DNA interface [nucleotide binding]; other site 340054000701 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 340054000702 catalytic core [active] 340054000703 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 340054000704 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 340054000705 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054000706 Walker A/P-loop; other site 340054000707 ATP binding site [chemical binding]; other site 340054000708 Q-loop/lid; other site 340054000709 ABC transporter signature motif; other site 340054000710 Walker B; other site 340054000711 D-loop; other site 340054000712 H-loop/switch region; other site 340054000713 acyl-CoA esterase; Provisional; Region: PRK10673 340054000714 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340054000715 SeqA protein; Region: SeqA; cl11470 340054000716 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 340054000717 NADH dehydrogenase subunit B; Validated; Region: PRK06411 340054000718 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 340054000719 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl15771 340054000720 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional; Region: PRK11742 340054000721 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 340054000722 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 340054000723 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 340054000724 putative dimer interface [polypeptide binding]; other site 340054000725 [2Fe-2S] cluster binding site [ion binding]; other site 340054000726 NADH dehydrogenase I subunit F; Provisional; Region: PRK11278 340054000727 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 340054000728 SLBB domain; Region: SLBB; pfam10531 340054000729 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 340054000730 A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine'...; Region: Peptidase_C39_likeA; cd02417 340054000731 type I secretion system ABC transporter, HlyB family; Region: type_I_sec_HlyB; TIGR01846 340054000732 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 340054000733 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054000734 Walker A/P-loop; other site 340054000735 ATP binding site [chemical binding]; other site 340054000736 Q-loop/lid; other site 340054000737 ABC transporter signature motif; other site 340054000738 Walker B; other site 340054000739 D-loop; other site 340054000740 H-loop/switch region; other site 340054000741 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 340054000742 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 340054000743 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 340054000744 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage...; Region: Peptidase_C39_like; cd02259 340054000745 type I secretion system ABC transporter, HlyB family; Region: type_I_sec_HlyB; TIGR01846 340054000746 putative active site [active] 340054000747 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 340054000748 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054000749 Walker A/P-loop; other site 340054000750 ATP binding site [chemical binding]; other site 340054000751 Q-loop/lid; other site 340054000752 ABC transporter signature motif; other site 340054000753 Walker B; other site 340054000754 D-loop; other site 340054000755 H-loop/switch region; other site 340054000756 adenosylmethionine--8-amino-7-oxononanoate transaminase; Validated; Region: PRK07986 340054000757 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 340054000758 inhibitor-cofactor binding pocket; inhibition site 340054000759 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340054000760 catalytic residue [active] 340054000761 autotransport protein MisL; Provisional; Region: PRK15313 340054000762 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 2, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of the nonprotease autotransporters, Ag43; Region: PL2_Passenger_AT; cd01344 340054000763 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 340054000764 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340054000765 Integrase core domain; Region: rve; cl01316 340054000766 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054000767 putative fimbrial protein TcfA; Provisional; Region: PRK15308 340054000768 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 340054000769 EamA-like transporter family; Region: EamA; cl01037 340054000770 EamA-like transporter family; Region: EamA; cl01037 340054000771 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 340054000772 homodimer interface [polypeptide binding]; other site 340054000773 substrate-cofactor binding pocket; other site 340054000774 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340054000775 catalytic residue [active] 340054000776 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 340054000777 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 340054000778 ATP binding site [chemical binding]; other site 340054000779 Mg++ binding site [ion binding]; other site 340054000780 motif III; other site 340054000781 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 340054000782 nucleotide binding region [chemical binding]; other site 340054000783 ATP-binding site [chemical binding]; other site 340054000784 AIR carboxylase; Region: AIRC; cl00310 340054000785 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 340054000786 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340054000787 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 340054000788 Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis; Region: DPCK; cd02022 340054000789 CoA-binding site [chemical binding]; other site 340054000790 ATP-binding [chemical binding]; other site 340054000791 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054000792 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054000793 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054000794 putative active site [active] 340054000795 putative NTP binding site [chemical binding]; other site 340054000796 putative nucleic acid binding site [nucleotide binding]; other site 340054000797 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054000798 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054000799 active site 340054000800 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 340054000801 Peptidase M15; Region: Peptidase_M15_3; cl01194 340054000802 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 340054000803 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 340054000804 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 340054000805 exoribonuclease R; Provisional; Region: PRK11642 340054000806 Ribonuclease R winged-helix domain; Region: HTH_12; pfam08461 340054000807 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 340054000808 RNB domain; Region: RNB; pfam00773 340054000809 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important...; Region: S1_RNase_R; cd04471 340054000810 RNA binding site [nucleotide binding]; other site 340054000811 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 340054000812 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 340054000813 GDP-binding site [chemical binding]; other site 340054000814 ACT binding site; other site 340054000815 IMP binding site; other site 340054000816 SH3 domain-containing protein; Provisional; Region: PRK10884 340054000817 Bacterial SH3 domain; Region: SH3_3; cl02551 340054000818 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 340054000819 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 340054000820 aromatic amino acid transport protein; Region: araaP; TIGR00837 340054000821 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 340054000822 dimer interface [polypeptide binding]; other site 340054000823 putative radical transfer pathway; other site 340054000824 diiron center [ion binding]; other site 340054000825 tyrosyl radical; other site 340054000826 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 340054000827 ATP cone domain; Region: ATP-cone; pfam03477 340054000828 Class I ribonucleotide reductase; Region: RNR_I; cd01679 340054000829 active site 340054000830 dimer interface [polypeptide binding]; other site 340054000831 catalytic residues [active] 340054000832 effector binding site; other site 340054000833 R2 peptide binding site; other site 340054000834 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 340054000835 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 340054000836 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340054000837 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340054000838 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 340054000839 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 340054000840 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 340054000841 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340054000842 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 340054000843 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 340054000844 PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_glc; cd00210 340054000845 HPr interaction site; other site 340054000846 glycerol kinase (GK) interaction site [polypeptide binding]; other site 340054000847 active site 340054000848 phosphorylation site [posttranslational modification] 340054000849 phosphoenolpyruvate-protein phosphotransferase; Provisional; Region: PRK11177 340054000850 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 340054000851 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 340054000852 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 340054000853 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 340054000854 dimerization domain swap beta strand [polypeptide binding]; other site 340054000855 regulatory protein interface [polypeptide binding]; other site 340054000856 active site 340054000857 regulatory phosphorylation site [posttranslational modification]; other site 340054000858 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 340054000859 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 340054000860 ATP binding site [chemical binding]; other site 340054000861 Mg++ binding site [ion binding]; other site 340054000862 motif III; other site 340054000863 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 340054000864 nucleotide binding region [chemical binding]; other site 340054000865 ATP-binding site [chemical binding]; other site 340054000866 DbpA RNA binding domain; Region: DbpA; pfam03880 340054000867 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 340054000868 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 340054000869 RNase E interface [polypeptide binding]; other site 340054000870 trimer interface [polypeptide binding]; other site 340054000871 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 340054000872 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 340054000873 RNase E interface [polypeptide binding]; other site 340054000874 trimer interface [polypeptide binding]; other site 340054000875 active site 340054000876 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 340054000877 putative nucleic acid binding region [nucleotide binding]; other site 340054000878 G-X-X-G motif; other site 340054000879 S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA; Region: S1_PNPase; cd04472 340054000880 RNA binding site [nucleotide binding]; other site 340054000881 domain interface; other site 340054000882 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome; Region: Ribosomal_S15p_S13e; cd00353 340054000883 16S/18S rRNA binding site [nucleotide binding]; other site 340054000884 S13e-L30e interaction site [polypeptide binding]; other site 340054000885 25S rRNA binding site [nucleotide binding]; other site 340054000886 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 340054000887 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 specific...; Region: PseudoU_synth_EcTruB; cd02573 340054000888 RNA binding site [nucleotide binding]; other site 340054000889 active site 340054000890 Ribosome-binding factor A; Region: RBFA; cl00542 340054000891 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 340054000892 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 340054000893 translation initiation factor IF-2; Region: IF-2; TIGR00487 340054000894 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 340054000895 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 340054000896 G1 box; other site 340054000897 putative GEF interaction site [polypeptide binding]; other site 340054000898 GTP/Mg2+ binding site [chemical binding]; other site 340054000899 Switch I region; other site 340054000900 G2 box; other site 340054000901 G3 box; other site 340054000902 Switch II region; other site 340054000903 G4 box; other site 340054000904 G5 box; other site 340054000905 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell; Region: IF2_mtIF2_II; cd03702 340054000906 Translation-initiation factor 2; Region: IF-2; pfam11987 340054000907 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor...; Region: mtIF2_IVc; cd03692 340054000908 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 340054000909 NusA N-terminal domain; Region: NusA_N; pfam08529 340054000910 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 340054000911 RNA binding site [nucleotide binding]; other site 340054000912 homodimer interface [polypeptide binding]; other site 340054000913 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 340054000914 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 340054000915 G-X-X-G motif; other site 340054000916 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 340054000917 ribosome maturation protein RimP; Reviewed; Region: PRK00092 340054000918 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 340054000919 YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix...; Region: YlxS_C; cd01734 340054000920 Sm1 motif; other site 340054000921 predicted subunit interaction site [polypeptide binding]; other site 340054000922 RNA binding pocket [nucleotide binding]; other site 340054000923 Sm2 motif; other site 340054000924 Preprotein translocase SecG subunit; Region: SecG; cl09123 340054000925 GTP-binding protein YchF; Reviewed; Region: PRK09601 340054000926 YchF GTPase; Region: YchF; cd01900 340054000927 G1 box; other site 340054000928 GTP/Mg2+ binding site [chemical binding]; other site 340054000929 Switch I region; other site 340054000930 G2 box; other site 340054000931 Switch II region; other site 340054000932 G3 box; other site 340054000933 G4 box; other site 340054000934 G5 box; other site 340054000935 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 340054000936 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 340054000937 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 340054000938 chorismate binding enzyme; Region: Chorismate_bind; cl10555 340054000939 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 340054000940 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 340054000941 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 340054000942 general secretion pathway protein L; Region: typeII_sec_gspL; TIGR01709 340054000943 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 340054000944 GspL periplasmic domain; Region: GspL_C; cl14909 340054000945 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 340054000946 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 340054000947 general secretion pathway protein J; Region: gspJ; TIGR01711 340054000948 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 340054000949 general secretion pathway protein I; Region: gspI; TIGR01707 340054000950 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 340054000951 general secretion pathway protein H; Region: typeII_sec_gspH; TIGR01708 340054000952 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 340054000953 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 340054000954 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 340054000955 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054000956 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054000957 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054000958 putative active site [active] 340054000959 putative NTP binding site [chemical binding]; other site 340054000960 putative nucleic acid binding site [nucleotide binding]; other site 340054000961 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054000962 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054000963 active site 340054000964 ribonuclease E; Reviewed; Region: rne; PRK10811 340054000965 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 340054000966 homodimer interface [polypeptide binding]; other site 340054000967 oligonucleotide binding site [chemical binding]; other site 340054000968 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 340054000969 active site 340054000970 substrate binding pocket [chemical binding]; other site 340054000971 dimer interface [polypeptide binding]; other site 340054000972 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 340054000973 GTPase CgtA; Reviewed; Region: obgE; PRK12298 340054000974 GTP1/OBG; Region: GTP1_OBG; pfam01018 340054000975 Obg GTPase; Region: Obg; cd01898 340054000976 G1 box; other site 340054000977 GTP/Mg2+ binding site [chemical binding]; other site 340054000978 Switch I region; other site 340054000979 G2 box; other site 340054000980 G3 box; other site 340054000981 Switch II region; other site 340054000982 G4 box; other site 340054000983 G5 box; other site 340054000984 murein transglycosylase C; Provisional; Region: mltC; PRK11671 340054000985 Domain of unknown function (DUF3393); Region: DUF3393; pfam11873 340054000986 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340054000987 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340054000988 catalytic residue [active] 340054000989 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 340054000990 adenine DNA glycosylase; Provisional; Region: PRK10880 340054000991 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 340054000992 minor groove reading motif; other site 340054000993 helix-hairpin-helix signature motif; other site 340054000994 substrate binding pocket [chemical binding]; other site 340054000995 active site 340054000996 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 340054000997 DNA binding and oxoG recognition site [nucleotide binding] 340054000998 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 340054000999 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional; Region: PRK14994 340054001000 AmiB activator; Provisional; Region: PRK11637 340054001001 Protein of unknown function (DUF441); Region: DUF441; cl01041 340054001002 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 340054001003 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 340054001004 active site 340054001005 HIGH motif; other site 340054001006 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 340054001007 active site 340054001008 KMSKS motif; other site 340054001009 Helix-turn-helix domains; Region: HTH; cl00088 340054001010 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 340054001011 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 340054001012 chaperone protein DnaJ; Provisional; Region: PRK10767 340054001013 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 340054001014 HSP70 interaction site [polypeptide binding]; other site 340054001015 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 340054001016 substrate binding site [polypeptide binding]; other site 340054001017 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 340054001018 Zn binding sites [ion binding]; other site 340054001019 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 340054001020 dimer interface [polypeptide binding]; other site 340054001021 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 340054001022 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 340054001023 dimer interface [polypeptide binding]; other site 340054001024 substrate binding site [chemical binding]; other site 340054001025 metal binding sites [ion binding]; metal-binding site 340054001026 soluble pyridine nucleotide transhydrogenase; Provisional; Region: PRK05249 340054001027 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340054001028 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340054001029 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 340054001030 Helix-turn-helix domains; Region: HTH; cl00088 340054001031 glutamine ABC transporter periplasmic protein; Reviewed; Region: glnH; PRK09495 340054001032 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 340054001033 substrate binding pocket [chemical binding]; other site 340054001034 membrane-bound complex binding site; other site 340054001035 hinge residues; other site 340054001036 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340054001037 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 340054001038 dimer interface [polypeptide binding]; other site 340054001039 conserved gate region; other site 340054001040 putative PBP binding loops; other site 340054001041 ABC-ATPase subunit interface; other site 340054001042 glutamine ABC transporter ATP-binding protein; Reviewed; Region: glnQ; PRK09493 340054001043 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340054001044 Walker A/P-loop; other site 340054001045 ATP binding site [chemical binding]; other site 340054001046 Q-loop/lid; other site 340054001047 ABC transporter signature motif; other site 340054001048 Walker B; other site 340054001049 D-loop; other site 340054001050 H-loop/switch region; other site 340054001051 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 340054001052 active site 340054001053 substrate-binding site [chemical binding]; other site 340054001054 metal-binding site [ion binding] 340054001055 ATP binding site [chemical binding]; other site 340054001056 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 340054001057 hypothetical protein; Provisional; Region: PRK10941 340054001058 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 340054001059 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 340054001060 NeuB family; Region: NeuB; cl00496 340054001061 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 340054001062 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC...; Region: ABC_MetN_methionine_transporter; cd03258 340054001063 Walker A/P-loop; other site 340054001064 ATP binding site [chemical binding]; other site 340054001065 Q-loop/lid; other site 340054001066 ABC transporter signature motif; other site 340054001067 Walker B; other site 340054001068 D-loop; other site 340054001069 H-loop/switch region; other site 340054001070 NIL domain; Region: NIL; cl09633 340054001071 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 340054001072 dimer interface [polypeptide binding]; other site 340054001073 conserved gate region; other site 340054001074 ABC-ATPase subunit interface; other site 340054001075 NMT1-like family; Region: NMT1_2; cl15260 340054001076 prolyl-tRNA synthetase; Provisional; Region: PRK09194 340054001077 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: ProRS_core_prok; cd00779 340054001078 dimer interface [polypeptide binding]; other site 340054001079 motif 1; other site 340054001080 active site 340054001081 motif 2; other site 340054001082 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 340054001083 putative deacylase active site [active] 340054001084 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches...; Region: class_II_aaRS-like_core; cl00268 340054001085 active site 340054001086 motif 3; other site 340054001087 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 340054001088 anticodon binding site; other site 340054001089 putative glycosyl transferase; Provisional; Region: PRK10073 340054001090 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 340054001091 active site 340054001092 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 340054001093 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 340054001094 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 340054001095 synthetase active site [active] 340054001096 NTP binding site [chemical binding]; other site 340054001097 metal binding site [ion binding]; metal-binding site 340054001098 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 after...; Region: TGS_RelA_SpoT; cd01668 340054001099 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 340054001100 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 340054001101 nucleoside/Zn binding site; other site 340054001102 dimer interface [polypeptide binding]; other site 340054001103 catalytic motif [active] 340054001104 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4884 340054001105 Protein-tyrosine phosphatase; Region: Y_phosphatase; pfam00102 340054001106 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 340054001107 active site 340054001108 Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not...; Region: ZnMc_serralysin_like; cd04277 340054001109 active site 340054001110 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 340054001111 putative proline-specific permease; Provisional; Region: proY; PRK10580 340054001112 Spore germination protein; Region: Spore_permease; cl15802 340054001113 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 340054001114 active site 340054001115 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 340054001116 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054001117 Walker A/P-loop; other site 340054001118 ATP binding site [chemical binding]; other site 340054001119 Q-loop/lid; other site 340054001120 ABC transporter signature motif; other site 340054001121 Walker B; other site 340054001122 D-loop; other site 340054001123 H-loop/switch region; other site 340054001124 ABC transporter; Region: ABC_tran_2; pfam12848 340054001125 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340054001126 Uncharacterized phage-encoded protein [Function unknown]; Region: COG3646 340054001127 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 340054001128 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 340054001129 Phage holin family (Lysis protein S); Region: Phage_holin_3; cl04938 340054001130 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 340054001131 active site 340054001132 metal binding site [ion binding]; metal-binding site 340054001133 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054001134 Integrase core domain; Region: rve; cl01316 340054001135 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054001136 Walker A motif; other site 340054001137 ATP binding site [chemical binding]; other site 340054001138 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 340054001139 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 340054001140 Walker A motif; other site 340054001141 hexamer interface [polypeptide binding]; other site 340054001142 ATP binding site [chemical binding]; other site 340054001143 Walker B motif; other site 340054001144 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 340054001145 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 340054001146 VirB7 interaction site; other site 340054001147 conjugal transfer relaxase TraI; Provisional; Region: PRK13878 340054001148 VirB8 protein; Region: VirB8; cl01500 340054001149 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 340054001150 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 340054001151 oligomeric interface; other site 340054001152 putative active site [active] 340054001153 homodimer interface [polypeptide binding]; other site 340054001154 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 340054001155 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 340054001156 oligomeric interface; other site 340054001157 putative active site [active] 340054001158 homodimer interface [polypeptide binding]; other site 340054001159 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 340054001160 P-type DNA transfer protein VirB5; Region: VirB5; TIGR02791 340054001161 Type IV secretion system proteins; Region: T4SS; pfam07996 340054001162 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 340054001163 Integrase core domain; Region: rve; cl01316 340054001164 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054001165 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 340054001166 Peptidase C80 family; Region: Peptidase_C80; pfam11713 340054001167 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054001168 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054001169 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054001170 putative active site [active] 340054001171 putative NTP binding site [chemical binding]; other site 340054001172 putative nucleic acid binding site [nucleotide binding]; other site 340054001173 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054001174 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054001175 active site 340054001176 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 340054001177 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 340054001178 active site 340054001179 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 340054001180 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 340054001181 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 340054001182 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 340054001183 dimer interface [polypeptide binding]; other site 340054001184 active site 340054001185 CoA binding pocket [chemical binding]; other site 340054001186 Acyl transferase domain; Region: Acyl_transf_1; cl08282 340054001187 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 340054001188 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 340054001189 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 340054001190 NAD(P) binding site [chemical binding]; other site 340054001191 homotetramer interface [polypeptide binding]; other site 340054001192 homodimer interface [polypeptide binding]; other site 340054001193 active site 340054001194 Phosphopantetheine attachment site; Region: PP-binding; cl09936 340054001195 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 340054001196 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 340054001197 dimer interface [polypeptide binding]; other site 340054001198 active site 340054001199 YceG-like family; Region: YceG; pfam02618 340054001200 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 340054001201 dimerization interface [polypeptide binding]; other site 340054001202 thymidylate kinase; Validated; Region: tmk; PRK00698 340054001203 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 340054001204 TMP-binding site; other site 340054001205 ATP-binding site [chemical binding]; other site 340054001206 DNA polymerase III subunit delta'; Validated; Region: PRK07993 340054001207 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054001208 DNA polymerase III, delta subunit, C terminal; Region: DNApol3-delta_C; pfam09115 340054001209 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 340054001210 active site 340054001211 PTS system glucose-specific transporter subunits IIBC; Provisional; Region: PRK11089 340054001212 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 340054001213 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 340054001214 active site turn [active] 340054001215 phosphorylation site [posttranslational modification] 340054001216 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 340054001217 ligand binding site [chemical binding]; other site 340054001218 active site 340054001219 UGI interface [polypeptide binding]; other site 340054001220 catalytic site [active] 340054001221 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 340054001222 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 340054001223 ATP binding site [chemical binding]; other site 340054001224 Mg++ binding site [ion binding]; other site 340054001225 motif III; other site 340054001226 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 340054001227 nucleotide binding region [chemical binding]; other site 340054001228 ATP-binding site [chemical binding]; other site 340054001229 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 340054001230 UGMP family protein; Validated; Region: PRK09604 340054001231 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 340054001232 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 340054001233 Tetramer interface [polypeptide binding]; other site 340054001234 active site 340054001235 FMN-binding site [chemical binding]; other site 340054001236 malate dehydrogenase; Provisional; Region: PRK05086 340054001237 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 340054001238 NAD binding site [chemical binding]; other site 340054001239 dimerization interface [polypeptide binding]; other site 340054001240 Substrate binding site [chemical binding]; other site 340054001241 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 340054001242 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 340054001243 Clp amino terminal domain; Region: Clp_N; pfam02861 340054001244 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 340054001245 Walker A motif; other site 340054001246 ATP binding site [chemical binding]; other site 340054001247 Walker B motif; other site 340054001248 arginine finger; other site 340054001249 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 340054001250 Walker A motif; other site 340054001251 ATP binding site [chemical binding]; other site 340054001252 Walker B motif; other site 340054001253 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 340054001254 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 340054001255 rRNA binding site [nucleotide binding]; other site 340054001256 predicted 30S ribosome binding site; other site 340054001257 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 340054001258 putative coenzyme Q binding site [chemical binding]; other site 340054001259 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 340054001260 5S rRNA interface [nucleotide binding]; other site 340054001261 CTC domain interface [polypeptide binding]; other site 340054001262 L16 interface [polypeptide binding]; other site 340054001263 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 340054001264 homooctamer interface [polypeptide binding]; other site 340054001265 active site 340054001266 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 340054001267 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 340054001268 putative substrate translocation pore; other site 340054001269 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 340054001270 Ligand Binding Site [chemical binding]; other site 340054001271 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 340054001272 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 340054001273 catalytic site [active] 340054001274 putative active site [active] 340054001275 putative substrate binding site [chemical binding]; other site 340054001276 dimer interface [polypeptide binding]; other site 340054001277 GTPase RsgA; Reviewed; Region: PRK12288 340054001278 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 340054001279 RNA binding site [nucleotide binding]; other site 340054001280 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 340054001281 GTPase/Zn-binding domain interface [polypeptide binding]; other site 340054001282 GTP/Mg2+ binding site [chemical binding]; other site 340054001283 G4 box; other site 340054001284 G5 box; other site 340054001285 G1 box; other site 340054001286 Switch I region; other site 340054001287 G2 box; other site 340054001288 G3 box; other site 340054001289 Switch II region; other site 340054001290 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 340054001291 putative mechanosensitive channel protein; Provisional; Region: PRK10929 340054001292 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 340054001293 Mechanosensitive ion channel; Region: MS_channel; pfam00924 340054001294 poxB regulator PoxA; Provisional; Region: PRK09350 340054001295 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches...; Region: class_II_aaRS-like_core; cl00268 340054001296 motif 1; other site 340054001297 dimer interface [polypeptide binding]; other site 340054001298 active site 340054001299 motif 2; other site 340054001300 motif 3; other site 340054001301 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 340054001302 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054001303 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054001304 Walker A motif; other site 340054001305 Walker A motif; other site 340054001306 ATP binding site [chemical binding]; other site 340054001307 ATP binding site [chemical binding]; other site 340054001308 Walker B motif; other site 340054001309 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 340054001310 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340054001311 catalytic residue [active] 340054001312 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 340054001313 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054001314 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 340054001315 Ferritin-like domain; Region: Ferritin; pfam00210 340054001316 ferroxidase diiron center [ion binding]; other site 340054001317 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 340054001318 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339; cl15420 340054001319 mannose-6-phosphate isomerase; Provisional; Region: PRK15131 340054001320 Phosphomannose isomerase type I; Region: PMI_typeI; cl15429 340054001321 protein disaggregation chaperone; Provisional; Region: PRK10865 340054001322 Clp amino terminal domain; Region: Clp_N; pfam02861 340054001323 Clp amino terminal domain; Region: Clp_N; pfam02861 340054001324 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 340054001325 Walker A motif; other site 340054001326 ATP binding site [chemical binding]; other site 340054001327 Walker B motif; other site 340054001328 arginine finger; other site 340054001329 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 340054001330 Walker A motif; other site 340054001331 ATP binding site [chemical binding]; other site 340054001332 Walker B motif; other site 340054001333 arginine finger; other site 340054001334 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 340054001335 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 340054001336 N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino...; Region: MurNAc-LAA; cd02696 340054001337 active site 340054001338 metal binding site [ion binding]; metal-binding site 340054001339 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 340054001340 putative peptidoglycan binding site; other site 340054001341 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 340054001342 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 340054001343 ATP binding site [chemical binding]; other site 340054001344 Mg2+ binding site [ion binding]; other site 340054001345 G-X-G motif; other site 340054001346 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 340054001347 ATP binding site [chemical binding]; other site 340054001348 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 340054001349 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054001350 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 340054001351 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 340054001352 Sm1 motif; other site 340054001353 intra - hexamer interaction site; other site 340054001354 inter - hexamer interaction site [polypeptide binding]; other site 340054001355 nucleotide binding pocket [chemical binding]; other site 340054001356 Sm2 motif; other site 340054001357 FtsH protease regulator HflK; Provisional; Region: PRK10930 340054001358 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 340054001359 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 340054001360 FtsH protease regulator HflC; Provisional; Region: PRK11029 340054001361 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 340054001362 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 340054001363 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340054001364 Coenzyme A binding pocket [chemical binding]; other site 340054001365 DNA polymerase III psi subunit; Region: DNA_III_psi; cl11436 340054001366 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 340054001367 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 340054001368 primosome assembly protein PriA; Validated; Region: PRK05580 340054001369 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 340054001370 ATP binding site [chemical binding]; other site 340054001371 putative Mg++ binding site [ion binding]; other site 340054001372 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 340054001373 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 340054001374 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 340054001375 S-adenosylmethionine synthetase; Validated; Region: PRK05250 340054001376 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 340054001377 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 340054001378 orotate phosphoribosyltransferase; Validated; Region: pyrE; PRK00455 340054001379 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340054001380 active site 340054001381 ribonuclease PH; Reviewed; Region: rph; PRK00173 340054001382 Ribonuclease PH; Region: RNase_PH_bact; cd11362 340054001383 hexamer interface [polypeptide binding]; other site 340054001384 active site 340054001385 hypothetical protein; Provisional; Region: PRK11820 340054001386 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 340054001387 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 340054001388 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 340054001389 spermidine synthase; Provisional; Region: PRK00811 340054001390 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 340054001391 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 340054001392 Uncharacterized BCR, COG1649; Region: DUF187; cl15398 340054001393 ribonuclease D; Provisional; Region: PRK10829 340054001394 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 340054001395 catalytic site [active] 340054001396 putative active site [active] 340054001397 putative substrate binding site [chemical binding]; other site 340054001398 HRDC domain; Region: HRDC; cl02578 340054001399 lipopolysaccharide core biosynthesis protein; Provisional; Region: PRK10422 340054001400 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 340054001401 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 340054001402 putative active site [active] 340054001403 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cl00436 340054001404 CPxP motif; other site 340054001405 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 340054001406 Major Facilitator Superfamily; Region: MFS_1; pfam07690 340054001407 putative substrate translocation pore; other site 340054001408 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 340054001409 Peptidase family M48; Region: Peptidase_M48; cl12018 340054001410 L-aspartate oxidase; Provisional; Region: PRK09077 340054001411 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054001412 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 340054001413 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 340054001414 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340054001415 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 340054001416 DNA binding residues [nucleotide binding] 340054001417 anti-RNA polymerase sigma factor SigE; Provisional; Region: PRK10863 340054001418 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 340054001419 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 340054001420 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 340054001421 GTP-binding protein LepA; Provisional; Region: PRK05433 340054001422 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 340054001423 G1 box; other site 340054001424 putative GEF interaction site [polypeptide binding]; other site 340054001425 GTP/Mg2+ binding site [chemical binding]; other site 340054001426 Switch I region; other site 340054001427 G2 box; other site 340054001428 G3 box; other site 340054001429 Switch II region; other site 340054001430 G4 box; other site 340054001431 G5 box; other site 340054001432 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 340054001433 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 340054001434 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 340054001435 signal peptidase I; Provisional; Region: PRK10861 340054001436 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 340054001437 Catalytic site [active] 340054001438 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 340054001439 ribonuclease III; Reviewed; Region: rnc; PRK00102 340054001440 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 340054001441 dimerization interface [polypeptide binding]; other site 340054001442 active site 340054001443 metal binding site [ion binding]; metal-binding site 340054001444 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III; Region: DSRM; cd00048 340054001445 dsRNA binding site [nucleotide binding]; other site 340054001446 GTPase Era; Reviewed; Region: era; PRK00089 340054001447 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 340054001448 G1 box; other site 340054001449 GTP/Mg2+ binding site [chemical binding]; other site 340054001450 Switch I region; other site 340054001451 G2 box; other site 340054001452 Switch II region; other site 340054001453 G3 box; other site 340054001454 G4 box; other site 340054001455 G5 box; other site 340054001456 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 340054001457 Recombination protein O N terminal; Region: RecO_N; cl15812 340054001458 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 340054001459 Recombination protein O C terminal; Region: RecO_C; pfam02565 340054001460 mechanosensitive channel MscS; Provisional; Region: PRK10334 340054001461 Conserved TM helix; Region: TM_helix; pfam05552 340054001462 Mechanosensitive ion channel; Region: MS_channel; pfam00924 340054001463 LPS O-antigen length regulator; Provisional; Region: PRK10381 340054001464 Chain length determinant protein; Region: Wzz; cl15801 340054001465 Chain length determinant protein; Region: Wzz; cl15801 340054001466 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 340054001467 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054001468 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 340054001469 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054001470 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 340054001471 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 340054001472 Walker A/P-loop; other site 340054001473 ATP binding site [chemical binding]; other site 340054001474 Q-loop/lid; other site 340054001475 ABC transporter signature motif; other site 340054001476 Walker B; other site 340054001477 D-loop; other site 340054001478 H-loop/switch region; other site 340054001479 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 340054001480 FtsX-like permease family; Region: FtsX; cl15850 340054001481 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054001482 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054001483 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054001484 putative active site [active] 340054001485 putative NTP binding site [chemical binding]; other site 340054001486 putative nucleic acid binding site [nucleotide binding]; other site 340054001487 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054001488 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054001489 active site 340054001490 macrolide transporter subunit MacA; Provisional; Region: PRK11578 340054001491 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 340054001492 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 340054001493 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 340054001494 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 340054001495 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340054001496 catalytic residue [active] 340054001497 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 340054001498 active site 340054001499 8-oxo-dGMP binding site [chemical binding]; other site 340054001500 nudix motif; other site 340054001501 metal binding site [ion binding]; metal-binding site 340054001502 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 340054001503 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 340054001504 NifU-like domain; Region: NifU; cl00484 340054001505 DNA utilization protein GntX; Provisional; Region: PRK11595 340054001506 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340054001507 active site 340054001508 carboxylesterase BioH; Provisional; Region: PRK10349 340054001509 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340054001510 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 340054001511 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 340054001512 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 340054001513 RNA binding surface [nucleotide binding]; other site 340054001514 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 340054001515 active site 340054001516 outer membrane biogenesis protein BamD; Provisional; Region: PRK10866 340054001517 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site; Region: RaiA; cd00552 340054001518 30S subunit binding site; other site 340054001519 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 340054001520 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 340054001521 adenylosuccinate lyase; Provisional; Region: PRK09285 340054001522 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 340054001523 tetramer interface [polypeptide binding]; other site 340054001524 active site 340054001525 Protein of unknown function (DUF1434); Region: DUF1434; pfam07254 340054001526 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 340054001527 Protein of unknown function (DUF904); Region: DUF904; cl11531 340054001528 putative fimbrial protein TcfA; Provisional; Region: PRK15308 340054001529 putative fimbrial protein TcfA; Provisional; Region: PRK15308 340054001530 P22-like integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial and phage integrases, including those similar to phage P22-like integrases, DLP12 and APSE-1; Region: INT_P22_C; cd01192 340054001531 Int/Topo IB signature motif; other site 340054001532 Protein of unknown function (DUF1640); Region: DUF1640; pfam07798 340054001533 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 340054001534 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 340054001535 dimer interface [polypeptide binding]; other site 340054001536 ssDNA binding site [nucleotide binding]; other site 340054001537 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340054001538 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340054001539 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]; Region: RPT1; COG1222 340054001540 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 340054001541 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054001542 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054001543 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054001544 putative active site [active] 340054001545 putative NTP binding site [chemical binding]; other site 340054001546 putative nucleic acid binding site [nucleotide binding]; other site 340054001547 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054001548 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054001549 active site 340054001550 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 340054001551 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 340054001552 dimer interface [polypeptide binding]; other site 340054001553 ssDNA binding site [nucleotide binding]; other site 340054001554 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340054001555 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 340054001556 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 340054001557 RNA/DNA hybrid binding site [nucleotide binding]; other site 340054001558 active site 340054001559 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 340054001560 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 340054001561 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 340054001562 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 340054001563 active site 340054001564 FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid...; Region: FabZ; cd01288 340054001565 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 340054001566 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 340054001567 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 340054001568 trimer interface [polypeptide binding]; other site 340054001569 active site 340054001570 UDP-GlcNAc binding site [chemical binding]; other site 340054001571 lipid binding site [chemical binding]; lipid-binding site 340054001572 periplasmic chaperone; Provisional; Region: PRK10780 340054001573 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 340054001574 outer membrane protein assembly factor YaeT; Provisional; Region: PRK11067 340054001575 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 340054001576 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 340054001577 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 340054001578 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 340054001579 Surface antigen; Region: Bac_surface_Ag; cl03097 340054001580 zinc metallopeptidase RseP; Provisional; Region: PRK10779 340054001581 RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog...; Region: S2P-M50_PDZ_RseP-like; cd06163 340054001582 active site 340054001583 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 340054001584 protein binding site [polypeptide binding]; other site 340054001585 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 340054001586 protein binding site [polypeptide binding]; other site 340054001587 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 340054001588 putative substrate binding region [chemical binding]; other site 340054001589 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 340054001590 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 340054001591 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 340054001592 catalytic residue [active] 340054001593 putative FPP diphosphate binding site; other site 340054001594 putative FPP binding hydrophobic cleft; other site 340054001595 dimer interface [polypeptide binding]; other site 340054001596 putative IPP diphosphate binding site; other site 340054001597 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; cl01113 340054001598 agmatine deiminase; Region: agmatine_aguA; TIGR03380 340054001599 N-carbamolyputrescine amidase; Region: PLN02747 340054001600 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 340054001601 putative active site; other site 340054001602 catalytic triad [active] 340054001603 putative dimer interface [polypeptide binding]; other site 340054001604 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 340054001605 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 340054001606 glutathione synthetase; Provisional; Region: PRK05246 340054001607 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 340054001608 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340054001609 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 340054001610 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 340054001611 thiamine transporter ATP-binding subunit; Provisional; Region: thiQ; PRK10771 340054001612 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054001613 Walker A/P-loop; other site 340054001614 ATP binding site [chemical binding]; other site 340054001615 Q-loop/lid; other site 340054001616 ABC transporter signature motif; other site 340054001617 Walker B; other site 340054001618 D-loop; other site 340054001619 H-loop/switch region; other site 340054001620 thiamine transporter membrane protein; Reviewed; Region: thiP; PRK09433 340054001621 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 340054001622 dimer interface [polypeptide binding]; other site 340054001623 conserved gate region; other site 340054001624 putative PBP binding loops; other site 340054001625 ABC-ATPase subunit interface; other site 340054001626 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 340054001627 dimer interface [polypeptide binding]; other site 340054001628 conserved gate region; other site 340054001629 putative PBP binding loops; other site 340054001630 ABC-ATPase subunit interface; other site 340054001631 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 340054001632 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 340054001633 type IV pilin biogenesis protein; Provisional; Region: PRK10573 340054001634 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340054001635 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340054001636 hypothetical protein; Provisional; Region: PRK10436 340054001637 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 340054001638 Walker A motif; other site 340054001639 ATP binding site [chemical binding]; other site 340054001640 Walker B motif; other site 340054001641 putative major pilin subunit; Provisional; Region: PRK10574 340054001642 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 340054001643 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 340054001644 dimer interface [polypeptide binding]; other site 340054001645 motif 1; other site 340054001646 active site 340054001647 motif 2; other site 340054001648 motif 3; other site 340054001649 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 340054001650 autotransport protein MisL; Provisional; Region: PRK15313 340054001651 Pertactin-like passenger domains (virulence factors) of autotransporter proteins of the type V secretion system. Autotransporters are proteins used by Gram-negative bacteria to transport proteins across their outer membranes. The C-terminal (beta) domain...; Region: PL_Passenger_AT; cl00185 340054001652 Integrase core domain; Region: rve; cl01316 340054001653 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054001654 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases; Region: PL1_Passenger_AT; cd01343 340054001655 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases; Region: PL1_Passenger_AT; cd01343 340054001656 autotransport protein MisL; Provisional; Region: PRK15313 340054001657 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054001658 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054001659 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054001660 putative active site [active] 340054001661 putative NTP binding site [chemical binding]; other site 340054001662 putative nucleic acid binding site [nucleotide binding]; other site 340054001663 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054001664 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054001665 active site 340054001666 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 340054001667 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 340054001668 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 340054001669 Lumazine binding domain; Region: Lum_binding; pfam00677 340054001670 Lumazine binding domain; Region: Lum_binding; pfam00677 340054001671 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 340054001672 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 340054001673 catalytic site [active] 340054001674 G-X2-G-X-G-K; other site 340054001675 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 340054001676 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 340054001677 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 340054001678 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 340054001679 synthetase active site [active] 340054001680 NTP binding site [chemical binding]; other site 340054001681 metal binding site [ion binding]; metal-binding site 340054001682 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 after...; Region: TGS_RelA_SpoT; cd01668 340054001683 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 340054001684 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 340054001685 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 340054001686 ssDNA binding site; other site 340054001687 generic binding surface II; other site 340054001688 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 340054001689 ATP binding site [chemical binding]; other site 340054001690 putative Mg++ binding site [ion binding]; other site 340054001691 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 340054001692 nucleotide binding region [chemical binding]; other site 340054001693 ATP-binding site [chemical binding]; other site 340054001694 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 340054001695 oligomerisation interface [polypeptide binding]; other site 340054001696 mobile loop; other site 340054001697 roof hairpin; other site 340054001698 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 340054001699 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 340054001700 ring oligomerisation interface [polypeptide binding]; other site 340054001701 ATP/Mg binding site [chemical binding]; other site 340054001702 stacking interactions; other site 340054001703 hinge regions; other site 340054001704 Peptidase C80 family; Region: Peptidase_C80; pfam11713 340054001705 dihydrodipicolinate reductase; Provisional; Region: PRK00048 340054001706 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054001707 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 340054001708 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 340054001709 arginyl-tRNA synthetase; Region: argS; TIGR00456 340054001710 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 340054001711 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 340054001712 active site 340054001713 HIGH motif; other site 340054001714 KMSK motif region; other site 340054001715 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 340054001716 tRNA binding surface [nucleotide binding]; other site 340054001717 anticodon binding site; other site 340054001718 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 340054001719 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 340054001720 putative catalytic site [active] 340054001721 putative phosphate binding site [ion binding]; other site 340054001722 active site 340054001723 metal binding site A [ion binding]; metal-binding site 340054001724 DNA binding site [nucleotide binding] 340054001725 putative AP binding site [nucleotide binding]; other site 340054001726 putative metal binding site B [ion binding]; other site 340054001727 protease 4; Provisional; Region: PRK10949 340054001728 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 340054001729 tandem repeat interface [polypeptide binding]; other site 340054001730 oligomer interface [polypeptide binding]; other site 340054001731 active site residues [active] 340054001732 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 340054001733 tandem repeat interface [polypeptide binding]; other site 340054001734 oligomer interface [polypeptide binding]; other site 340054001735 active site residues [active] 340054001736 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 340054001737 DNA primase; Validated; Region: dnaG; PRK05667 340054001738 CHC2 zinc finger; Region: zf-CHC2; cl15369 340054001739 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 340054001740 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 340054001741 active site 340054001742 metal binding site [ion binding]; metal-binding site 340054001743 interdomain interaction site; other site 340054001744 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 340054001745 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 340054001746 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 340054001747 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 340054001748 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 340054001749 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 340054001750 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340054001751 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 340054001752 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 340054001753 DNA binding residues [nucleotide binding] 340054001754 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 340054001755 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 340054001756 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 340054001757 Helix-turn-helix domains; Region: HTH; cl00088 340054001758 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 340054001759 ABC-ATPase subunit interface; other site 340054001760 dimer interface [polypeptide binding]; other site 340054001761 putative PBP binding regions; other site 340054001762 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 340054001763 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 340054001764 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 340054001765 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 340054001766 metal binding site [ion binding]; metal-binding site 340054001767 putative peptidase; Provisional; Region: PRK11649 340054001768 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 340054001769 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 340054001770 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 340054001771 putative acyl-acceptor binding pocket; other site 340054001772 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 340054001773 putative active site [active] 340054001774 Ap4A binding site [chemical binding]; other site 340054001775 nudix motif; other site 340054001776 putative metal binding site [ion binding]; other site 340054001777 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 340054001778 quinone interaction residues [chemical binding]; other site 340054001779 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 340054001780 active site 340054001781 catalytic residues [active] 340054001782 FMN binding site [chemical binding]; other site 340054001783 substrate binding site [chemical binding]; other site 340054001784 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 340054001785 THUMP domain; Region: THUMP; cl12076 340054001786 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054001787 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 340054001788 S-adenosylmethionine binding site [chemical binding]; other site 340054001789 ABC transporter ATPase component; Reviewed; Region: PRK11147 340054001790 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340054001791 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340054001792 ABC transporter; Region: ABC_tran_2; pfam12848 340054001793 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 340054001794 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 340054001795 transcriptional regulator SlyA; Provisional; Region: PRK03573 340054001796 Helix-turn-helix domains; Region: HTH; cl00088 340054001797 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 340054001798 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 340054001799 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 340054001800 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 340054001801 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 340054001802 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 340054001803 active site 340054001804 HIGH motif; other site 340054001805 dimer interface [polypeptide binding]; other site 340054001806 KMSKS motif; other site 340054001807 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 340054001808 RNA binding surface [nucleotide binding]; other site 340054001809 penicillin-binding protein 2; Provisional; Region: PRK10795 340054001810 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 340054001811 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340054001812 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 340054001813 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional; Region: PRK10793 340054001814 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340054001815 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 340054001816 Protein of unknown function (DUF493); Region: DUF493; cl01102 340054001817 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 340054001818 lipoyl synthase; Provisional; Region: PRK05481 340054001819 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cl15377 340054001820 FeS/SAM binding site; other site 340054001821 replicative DNA helicase; Provisional; Region: PRK08006 340054001822 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 340054001823 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 340054001824 Walker A motif; other site 340054001825 ATP binding site [chemical binding]; other site 340054001826 Walker B motif; other site 340054001827 DNA binding loops [nucleotide binding] 340054001828 alanine racemase; Reviewed; Region: alr; PRK00053 340054001829 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 340054001830 active site 340054001831 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340054001832 substrate binding site [chemical binding]; other site 340054001833 catalytic residues [active] 340054001834 dimer interface [polypeptide binding]; other site 340054001835 lysine transporter; Provisional; Region: PRK10836 340054001836 amino acid transporter; Region: 2A0306; TIGR00909 340054001837 Spore germination protein; Region: Spore_permease; cl15802 340054001838 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 340054001839 RNA/DNA hybrid binding site [nucleotide binding]; other site 340054001840 active site 340054001841 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 340054001842 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 340054001843 active site 340054001844 catalytic site [active] 340054001845 substrate binding site [chemical binding]; other site 340054001846 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 340054001847 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 340054001848 dimerization interface [polypeptide binding]; other site 340054001849 putative ATP binding site [chemical binding]; other site 340054001850 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 340054001851 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 340054001852 active site 340054001853 substrate binding site [chemical binding]; other site 340054001854 cosubstrate binding site; other site 340054001855 catalytic site [active] 340054001856 spermidine N1-acetyltransferase; Provisional; Region: PRK15130 340054001857 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340054001858 3-phosphoshikimate 1-carboxyvinyltransferase; Region: PLN02338 340054001859 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 340054001860 hinge; other site 340054001861 active site 340054001862 cytidylate kinase; Provisional; Region: cmk; PRK00023 340054001863 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 340054001864 CMP-binding site; other site 340054001865 The sites determining sugar specificity; other site 340054001866 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 340054001867 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 340054001868 RNA binding site [nucleotide binding]; other site 340054001869 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 340054001870 RNA binding site [nucleotide binding]; other site 340054001871 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 340054001872 RNA binding site [nucleotide binding]; other site 340054001873 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 340054001874 RNA binding site [nucleotide binding]; other site 340054001875 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec5; cd05690 340054001876 RNA binding site [nucleotide binding]; other site 340054001877 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 340054001878 RNA binding site [nucleotide binding]; other site 340054001879 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 340054001880 IHF dimer interface [polypeptide binding]; other site 340054001881 IHF - DNA interface [nucleotide binding]; other site 340054001882 Prokaryotic lipoprotein-attachment site; Region: LPAM_2; cl02361 340054001883 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 340054001884 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 340054001885 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 340054001886 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 340054001887 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054001888 Family description; Region: UvrD_C_2; cl15862 340054001889 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 340054001890 SmpB-tmRNA interface; other site 340054001891 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 340054001892 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 340054001893 domain interfaces; other site 340054001894 active site 340054001895 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 340054001896 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 340054001897 active site 340054001898 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 340054001899 putative protoheme IX biogenesis protein; Provisional; Region: PRK10747 340054001900 HemY protein N-terminus; Region: HemY_N; pfam07219 340054001901 autotransport protein MisL; Provisional; Region: PRK15313 340054001902 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 2, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of the nonprotease autotransporters, Ag43; Region: PL2_Passenger_AT; cd01344 340054001903 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340054001904 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 340054001905 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 340054001906 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 340054001907 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 340054001908 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 340054001909 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 340054001910 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 340054001911 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 340054001912 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 340054001913 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 340054001914 DNA binding site [nucleotide binding] 340054001915 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 340054001916 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 340054001917 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 340054001918 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 340054001919 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 340054001920 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 340054001921 RPB11 interaction site [polypeptide binding]; other site 340054001922 RPB12 interaction site [polypeptide binding]; other site 340054001923 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 340054001924 RPB3 interaction site [polypeptide binding]; other site 340054001925 RPB1 interaction site [polypeptide binding]; other site 340054001926 RPB11 interaction site [polypeptide binding]; other site 340054001927 RPB10 interaction site [polypeptide binding]; other site 340054001928 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 340054001929 core dimer interface [polypeptide binding]; other site 340054001930 peripheral dimer interface [polypeptide binding]; other site 340054001931 L10 interface [polypeptide binding]; other site 340054001932 L11 interface [polypeptide binding]; other site 340054001933 putative EF-Tu interaction site [polypeptide binding]; other site 340054001934 putative EF-G interaction site [polypeptide binding]; other site 340054001935 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 340054001936 23S rRNA interface [nucleotide binding]; other site 340054001937 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 340054001938 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds...; Region: Ribosomal_L1; cd00403 340054001939 mRNA/rRNA interface [nucleotide binding]; other site 340054001940 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 340054001941 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 340054001942 23S rRNA interface [nucleotide binding]; other site 340054001943 L7/L12 interface [polypeptide binding]; other site 340054001944 putative thiostrepton binding site; other site 340054001945 L25 interface [polypeptide binding]; other site 340054001946 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 340054001947 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 340054001948 putative homodimer interface [polypeptide binding]; other site 340054001949 KOW motif; Region: KOW; cl00354 340054001950 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 340054001951 elongation factor Tu; Reviewed; Region: PRK00049 340054001952 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 340054001953 G1 box; other site 340054001954 GEF interaction site [polypeptide binding]; other site 340054001955 GTP/Mg2+ binding site [chemical binding]; other site 340054001956 Switch I region; other site 340054001957 G2 box; other site 340054001958 G3 box; other site 340054001959 Switch II region; other site 340054001960 G4 box; other site 340054001961 G5 box; other site 340054001962 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 340054001963 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 340054001964 Antibiotic Binding Site [chemical binding]; other site 340054001965 elongation factor G; Reviewed; Region: PRK00007 340054001966 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 340054001967 G1 box; other site 340054001968 putative GEF interaction site [polypeptide binding]; other site 340054001969 GTP/Mg2+ binding site [chemical binding]; other site 340054001970 Switch I region; other site 340054001971 G2 box; other site 340054001972 G3 box; other site 340054001973 Switch II region; other site 340054001974 G4 box; other site 340054001975 G5 box; other site 340054001976 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 340054001977 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 340054001978 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 340054001979 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 340054001980 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 340054001981 S17 interaction site [polypeptide binding]; other site 340054001982 S8 interaction site; other site 340054001983 16S rRNA interaction site [nucleotide binding]; other site 340054001984 streptomycin interaction site [chemical binding]; other site 340054001985 23S rRNA interaction site [nucleotide binding]; other site 340054001986 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 340054001987 transaldolase-like protein; Provisional; Region: PTZ00411 340054001988 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 340054001989 active site 340054001990 dimer interface [polypeptide binding]; other site 340054001991 catalytic residue [active] 340054001992 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054001993 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 340054001994 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054001995 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054001996 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054001997 putative active site [active] 340054001998 putative NTP binding site [chemical binding]; other site 340054001999 putative nucleic acid binding site [nucleotide binding]; other site 340054002000 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054002001 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054002002 active site 340054002003 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl15270 340054002004 putative RNA binding sites [nucleotide binding]; other site 340054002005 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 340054002006 hypothetical protein; Provisional; Region: PRK09956 340054002007 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 340054002008 IHF dimer interface [polypeptide binding]; other site 340054002009 IHF - DNA interface [nucleotide binding]; other site 340054002010 conjugal transfer relaxosome component TraJ; Provisional; Region: PRK13877 340054002011 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 340054002012 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 340054002013 P-loop; other site 340054002014 Magnesium ion binding site [ion binding]; other site 340054002015 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 340054002016 HicB family; Region: HicB; pfam05534 340054002017 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 340054002018 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 340054002019 catalytic residues [active] 340054002020 catalytic nucleophile [active] 340054002021 Presynaptic Site I dimer interface [polypeptide binding]; other site 340054002022 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 340054002023 Synaptic Flat tetramer interface [polypeptide binding]; other site 340054002024 Synaptic Site I dimer interface [polypeptide binding]; other site 340054002025 DNA binding site [nucleotide binding] 340054002026 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 340054002027 DNA-binding interface [nucleotide binding]; DNA binding site 340054002028 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 340054002029 active site 340054002030 DNA binding site [nucleotide binding] 340054002031 Int/Topo IB signature motif; other site 340054002032 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 340054002033 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 340054002034 Catalytic site [active] 340054002035 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 340054002036 Restriction endonuclease; Region: Mrr_cat; cl00516 340054002037 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 340054002038 active site 340054002039 multimer interface [polypeptide binding]; other site 340054002040 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 340054002041 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 340054002042 FeS/SAM binding site; other site 340054002043 Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilF; COG3063 340054002044 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 340054002045 binding surface 340054002046 TPR motif; other site 340054002047 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 340054002048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 340054002049 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 340054002050 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 340054002051 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 340054002052 dimer interface [polypeptide binding]; other site 340054002053 motif 1; other site 340054002054 active site 340054002055 motif 2; other site 340054002056 motif 3; other site 340054002057 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 340054002058 anticodon binding site; other site 340054002059 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 340054002060 outer membrane biogenesis protein BamB; Provisional; Region: PRK11138 340054002061 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 340054002062 Trp docking motif [polypeptide binding]; other site 340054002063 GTP-binding protein Der; Reviewed; Region: PRK00093 340054002064 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 340054002065 G1 box; other site 340054002066 GTP/Mg2+ binding site [chemical binding]; other site 340054002067 Switch I region; other site 340054002068 G2 box; other site 340054002069 Switch II region; other site 340054002070 G3 box; other site 340054002071 G4 box; other site 340054002072 G5 box; other site 340054002073 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 340054002074 G1 box; other site 340054002075 GTP/Mg2+ binding site [chemical binding]; other site 340054002076 Switch I region; other site 340054002077 G2 box; other site 340054002078 G3 box; other site 340054002079 Switch II region; other site 340054002080 G4 box; other site 340054002081 G5 box; other site 340054002082 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 340054002083 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340054002084 active site 340054002085 HIGH motif; other site 340054002086 nucleotide binding site [chemical binding]; other site 340054002087 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 340054002088 KMSKS motif; other site 340054002089 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 340054002090 CTP synthetase; Validated; Region: pyrG; PRK05380 340054002091 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 340054002092 Catalytic site [active] 340054002093 active site 340054002094 UTP binding site [chemical binding]; other site 340054002095 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 340054002096 active site 340054002097 putative oxyanion hole; other site 340054002098 catalytic triad [active] 340054002099 enolase; Provisional; Region: eno; PRK00077 340054002100 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 340054002101 dimer interface [polypeptide binding]; other site 340054002102 metal binding site [ion binding]; metal-binding site 340054002103 substrate binding pocket [chemical binding]; other site 340054002104 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 340054002105 Ligand Binding Site [chemical binding]; other site 340054002106 cell division protein ZipA; Provisional; Region: PRK03427 340054002107 ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic...; Region: ZipA; cl12038 340054002108 FtsZ protein binding site [polypeptide binding]; other site 340054002109 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 340054002110 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 340054002111 nucleotide binding pocket [chemical binding]; other site 340054002112 K-X-D-G motif; other site 340054002113 catalytic site [active] 340054002114 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 340054002115 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 340054002116 Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo...; Region: BRCT; cd00027 340054002117 Dimer interface [polypeptide binding]; other site 340054002118 BRCT sequence motif; other site 340054002119 OpgC protein; Region: OpgC_C; cl00792 340054002120 Acyltransferase family; Region: Acyl_transf_3; pfam01757 340054002121 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 340054002122 Mitochondrial protein from FMP27; Region: Fmp27; pfam10344 340054002123 Family of unknown function (DUF490); Region: DUF490; pfam04357 340054002124 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 340054002125 Surface antigen; Region: Bac_surface_Ag; cl03097 340054002126 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 340054002127 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 340054002128 active site 340054002129 metal binding site [ion binding]; metal-binding site 340054002130 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054002131 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 340054002132 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 340054002133 SurA N-terminal domain; Region: SurA_N_3; cl07813 340054002134 PPIC-type PPIASE domain; Region: Rotamase; cl08278 340054002135 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 340054002136 OstA-like protein; Region: OstA; cl00844 340054002137 Organic solvent tolerance protein; Region: OstA_C; pfam04453 340054002138 erythronate-4-phosphate dehydrogenase PdxB; Provisional; Region: PRK15438 340054002139 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054002140 Domain of unknown function (DUF3410); Region: DUF3410; pfam11890 340054002141 putative semialdehyde dehydrogenase; Provisional; Region: PRK08040 340054002142 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054002143 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 340054002144 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 340054002145 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 340054002146 dimerization interface 3.5A [polypeptide binding]; other site 340054002147 active site 340054002148 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 340054002149 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 340054002150 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 340054002151 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 340054002152 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340054002153 cell division protein DedD; Provisional; Region: PRK11633 340054002154 Sporulation related domain; Region: SPOR; cl10051 340054002155 Colicin V production protein; Region: Colicin_V; cl00567 340054002156 amidophosphoribosyltransferase; Provisional; Region: PRK09246 340054002157 Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the...; Region: GPATase_N; cd00715 340054002158 active site 340054002159 tetramer interface [polypeptide binding]; other site 340054002160 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340054002161 active site 340054002162 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 340054002163 Flavoprotein; Region: Flavoprotein; cl08021 340054002164 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 340054002165 active site residue [active] 340054002166 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 340054002167 SecA binding site; other site 340054002168 Preprotein binding site; other site 340054002169 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 340054002170 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054002171 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 340054002172 serine acetyltransferase; Provisional; Region: cysE; PRK11132 340054002173 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 340054002174 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 340054002175 trimer interface [polypeptide binding]; other site 340054002176 active site 340054002177 substrate binding site [chemical binding]; other site 340054002178 CoA binding site [chemical binding]; other site 340054002179 Membrane fusogenic activity; Region: BMFP; cl01115 340054002180 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 340054002181 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 340054002182 putative ribose interaction site [chemical binding]; other site 340054002183 putative ADP binding site [chemical binding]; other site 340054002184 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340054002185 active site 340054002186 HIGH motif; other site 340054002187 nucleotide binding site [chemical binding]; other site 340054002188 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 340054002189 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 340054002190 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 340054002191 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054002192 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054002193 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054002194 putative active site [active] 340054002195 putative NTP binding site [chemical binding]; other site 340054002196 putative nucleic acid binding site [nucleotide binding]; other site 340054002197 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054002198 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054002199 active site 340054002200 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 340054002201 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 340054002202 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 340054002203 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 340054002204 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 340054002205 anchoring element; other site 340054002206 dimer interface [polypeptide binding]; other site 340054002207 ATP binding site [chemical binding]; other site 340054002208 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 340054002209 active site 340054002210 metal binding site [ion binding]; metal-binding site 340054002211 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 340054002212 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 340054002213 dimer interface [polypeptide binding]; other site 340054002214 catalytic triad [active] 340054002215 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 340054002216 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 340054002217 CAP-like domain; other site 340054002218 active site 340054002219 primary dimer interface [polypeptide binding]; other site 340054002220 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional; Region: PRK15018 340054002221 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 340054002222 putative acyl-acceptor binding pocket; other site 340054002223 pyruvate kinase; Provisional; Region: PRK09206 340054002224 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; cd00288 340054002225 domain interfaces; other site 340054002226 active site 340054002227 competence protein ComEA helix-hairpin-helix repeat region; Region: TIGR00426 340054002228 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 340054002229 periplasmic folding chaperone; Provisional; Region: PRK10788 340054002230 SurA N-terminal domain; Region: SurA_N_3; cl07813 340054002231 PPIC-type PPIASE domain; Region: Rotamase; cl08278 340054002232 DNA-binding ATP-dependent protease La; Provisional; Region: PRK10787 340054002233 Found in ATP-dependent protease La (LON); Region: LON; smart00464 340054002234 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 340054002235 Walker A motif; other site 340054002236 ATP binding site [chemical binding]; other site 340054002237 Walker B motif; other site 340054002238 arginine finger; other site 340054002239 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 340054002240 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 340054002241 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 340054002242 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 340054002243 Walker A motif; other site 340054002244 ATP binding site [chemical binding]; other site 340054002245 Walker B motif; other site 340054002246 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 340054002247 Clp protease; Region: CLP_protease; pfam00574 340054002248 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 340054002249 oligomer interface [polypeptide binding]; other site 340054002250 active site residues [active] 340054002251 trigger factor; Provisional; Region: tig; PRK01490 340054002252 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 340054002253 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 340054002254 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 340054002255 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054002256 Sodium:solute symporter family; Region: SSF; cl00456 340054002257 Protein of unknown function (DUF997); Region: DUF997; cl01614 340054002258 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 340054002259 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 340054002260 glutamine binding [chemical binding]; other site 340054002261 catalytic triad [active] 340054002262 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 340054002263 putative acyl-acceptor binding pocket; other site 340054002264 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 340054002265 DNA-binding site [nucleotide binding]; DNA binding site 340054002266 RNA-binding motif; other site 340054002267 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 340054002268 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 340054002269 ligand binding site [chemical binding]; other site 340054002270 flexible hinge region; other site 340054002271 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 340054002272 putative switch regulator; other site 340054002273 non-specific DNA interactions [nucleotide binding]; other site 340054002274 DNA binding site [nucleotide binding] 340054002275 sequence specific DNA binding site [nucleotide binding]; other site 340054002276 putative cAMP binding site [chemical binding]; other site 340054002277 recombination and repair protein; Provisional; Region: PRK10869 340054002278 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 340054002279 Walker A/P-loop; other site 340054002280 ATP binding site [chemical binding]; other site 340054002281 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 340054002282 ABC transporter signature motif; other site 340054002283 Walker B; other site 340054002284 D-loop; other site 340054002285 H-loop/switch region; other site 340054002286 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 340054002287 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 340054002288 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 340054002289 active site 340054002290 Riboflavin kinase; Region: Flavokinase; cl03312 340054002291 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 340054002292 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340054002293 active site 340054002294 HIGH motif; other site 340054002295 nucleotide binding site [chemical binding]; other site 340054002296 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 340054002297 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 340054002298 active site 340054002299 KMSKS motif; other site 340054002300 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 340054002301 tRNA binding surface [nucleotide binding]; other site 340054002302 anticodon binding site; other site 340054002303 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 340054002304 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 340054002305 lipoprotein signal peptidase; Provisional; Region: PRK14787 340054002306 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 340054002307 LytB protein; Region: LYTB; cl00507 340054002308 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 340054002309 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 340054002310 Integrase core domain; Region: rve; cl01316 340054002311 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054002312 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 340054002313 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 340054002314 putative active site [active] 340054002315 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 340054002316 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 340054002317 putative active site [active] 340054002318 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 340054002319 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 340054002320 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 340054002321 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 340054002322 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 340054002323 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054002324 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054002325 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054002326 putative active site [active] 340054002327 putative NTP binding site [chemical binding]; other site 340054002328 putative nucleic acid binding site [nucleotide binding]; other site 340054002329 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054002330 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054002331 active site 340054002332 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 340054002333 Peptidase C80 family; Region: Peptidase_C80; pfam11713 340054002334 YqjK-like protein; Region: YqjK; pfam13997 340054002335 Protein of unknown function (DUF1469); Region: DUF1469; cl12095 340054002336 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 340054002337 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 340054002338 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 340054002339 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 340054002340 Ligand binding site; other site 340054002341 Putative Catalytic site; other site 340054002342 DXD motif; other site 340054002343 bifunctional UDP-glucuronic acid decarboxylase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase; Validated; Region: PRK08125 340054002344 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 340054002345 active site 340054002346 substrate binding site [chemical binding]; other site 340054002347 cosubstrate binding site; other site 340054002348 catalytic site [active] 340054002349 C-terminal subdomain of the formyltransferase domain on ArnA, which modifies lipid A with 4-amino-4-deoxy-l-arabinose; Region: Arna_FMT_C; cd08702 340054002350 active site 340054002351 hexamer interface [polypeptide binding]; other site 340054002352 Arna decarboxylase_like, extended (e) SDRs; Region: Arna_like_SDR_e; cd05257 340054002353 NAD binding site [chemical binding]; other site 340054002354 substrate binding site [chemical binding]; other site 340054002355 active site 340054002356 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional; Region: PRK15394 340054002357 Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD and other bacterial homologs; Region: CE4_ArnD; cd10939 340054002358 putative active site [active] 340054002359 putative catalytic site [active] 340054002360 putative Zn binding site [ion binding]; other site 340054002361 4-amino-4-deoxy-L-arabinose transferase; Provisional; Region: arnT; PRK13279 340054002362 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 340054002363 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 340054002364 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 340054002365 bifunctional glycosyl transferase/transpeptidase; Reviewed; Region: mrcB; PRK09506 340054002366 Transglycosylase; Region: Transgly; cl07896 340054002367 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340054002368 DNA polymerase I; Provisional; Region: PRK05755 340054002369 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 340054002370 active site 340054002371 metal binding site 1 [ion binding]; metal-binding site 340054002372 putative 5' ssDNA interaction site; other site 340054002373 metal binding site 3; metal-binding site 340054002374 metal binding site 2 [ion binding]; metal-binding site 340054002375 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 340054002376 putative DNA binding site [nucleotide binding]; other site 340054002377 putative metal binding site [ion binding]; other site 340054002378 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 340054002379 active site 340054002380 catalytic site [active] 340054002381 substrate binding site [chemical binding]; other site 340054002382 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 340054002383 active site 340054002384 DNA binding site [nucleotide binding] 340054002385 catalytic site [active] 340054002386 Salmonella outer protein D; Region: SopD; cl14701 340054002387 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 340054002388 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 340054002389 domain interface [polypeptide binding]; other site 340054002390 putative active site [active] 340054002391 catalytic site [active] 340054002392 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 340054002393 domain interface [polypeptide binding]; other site 340054002394 putative active site [active] 340054002395 catalytic site [active] 340054002396 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 340054002397 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 340054002398 dimer interface [polypeptide binding]; other site 340054002399 anticodon binding site; other site 340054002400 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 340054002401 homodimer interface [polypeptide binding]; other site 340054002402 motif 1; other site 340054002403 active site 340054002404 motif 2; other site 340054002405 GAD domain; Region: GAD; pfam02938 340054002406 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches...; Region: class_II_aaRS-like_core; cl00268 340054002407 active site 340054002408 motif 3; other site 340054002409 Transcriptional regulator; Region: Transcrip_reg; cl00361 340054002410 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 340054002411 active site 340054002412 putative DNA-binding cleft [nucleotide binding]; other site 340054002413 dimer interface [polypeptide binding]; other site 340054002414 Autoinducer synthetase; Region: Autoind_synth; pfam00765 340054002415 Autoinducer binding domain; Region: Autoind_bind; pfam03472 340054002416 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054002417 DNA binding residues [nucleotide binding] 340054002418 dimerization interface [polypeptide binding]; other site 340054002419 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 340054002420 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat1; cd02203 340054002421 dimerization interface [polypeptide binding]; other site 340054002422 ATP binding site [chemical binding]; other site 340054002423 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 340054002424 dimerization interface [polypeptide binding]; other site 340054002425 ATP binding site [chemical binding]; other site 340054002426 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 340054002427 putative active site [active] 340054002428 catalytic triad [active] 340054002429 aminopeptidase N; Provisional; Region: pepN; PRK14015 340054002430 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 340054002431 active site 340054002432 Zn binding site [ion binding]; other site 340054002433 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 340054002434 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 (OB...; Region: EcAsnRS_like_N; cd04318 340054002435 putative dimer interface [polypeptide binding]; other site 340054002436 putative anticodon binding site; other site 340054002437 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 as...; Region: AsxRS_core; cd00776 340054002438 homodimer interface [polypeptide binding]; other site 340054002439 motif 1; other site 340054002440 motif 2; other site 340054002441 active site 340054002442 motif 3; other site 340054002443 Endodeoxyribonuclease RusA; Region: RusA; cl01885 340054002444 Phage antitermination protein Q; Region: Phage_antitermQ; pfam06530 340054002445 Phage holin family (Lysis protein S); Region: Phage_holin_3; cl04938 340054002446 Bacteriophage lysis protein; Region: Phage_lysis; pfam03245 340054002447 Phage tail tube protein; Region: Tail_tube; pfam10618 340054002448 virion protein; Provisional; Region: V; PHA02564 340054002449 Mu-like prophage DNA circulation protein [General function prediction only]; Region: COG4228 340054002450 DNA circulation protein N-terminus; Region: DNA_circ_N; pfam07157 340054002451 Phage protein GP46; Region: GP46; cl01814 340054002452 Baseplate J-like protein; Region: Baseplate_J; cl01294 340054002453 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; cl05448 340054002454 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 340054002455 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 340054002456 cofactor binding site; other site 340054002457 DNA binding site [nucleotide binding] 340054002458 substrate interaction site [chemical binding]; other site 340054002459 autotransport protein MisL; Provisional; Region: PRK15313 340054002460 hypothetical protein; Provisional; Region: PRK09956 340054002461 NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]; Region: Lig; COG0272 340054002462 HIRAN domain; Region: HIRAN; cl07418 340054002463 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 340054002464 non-specific DNA binding site [nucleotide binding]; other site 340054002465 salt bridge; other site 340054002466 sequence-specific DNA binding site [nucleotide binding]; other site 340054002467 Regulatory phage protein cox; Region: Phage_Cox; pfam10743 340054002468 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 340054002469 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 340054002470 dimer interface [polypeptide binding]; other site 340054002471 ssDNA binding site [nucleotide binding]; other site 340054002472 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340054002473 Protein of unknown function (DUF1640); Region: DUF1640; pfam07798 340054002474 ORF6N domain; Region: ORF6N; pfam10543 340054002475 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 340054002476 Phage antirepressor protein KilAC domain; Region: ANT; cl01462 340054002477 Integrase core domain; Region: rve; cl01316 340054002478 Integrase core domain; Region: rve_3; cl15866 340054002479 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340054002480 VIP2; A family of actin-ADP-ribosylating toxin. A member of the Bacillus-prodiced vegetative insecticidal proteins (VIPs) possesses high specificity against the major insect pest, corn rootworms, and belongs to a classs of binary toxins and regulators of...; Region: VIP2; cl00173 340054002481 active site 340054002482 conformational flexibility of ligand binding pocket; other site 340054002483 ADP-ribosylating toxin turn-turn motif; other site 340054002484 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 340054002485 catalytic nucleophile [active] 340054002486 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 340054002487 Integrase core domain; Region: rve; cl01316 340054002488 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054002489 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 340054002490 Transposase domain (DUF772); Region: DUF772; cl15789 340054002491 Transposase domain (DUF772); Region: DUF772; cl15789 340054002492 Domain of unknown function (DUF4415); Region: DUF4415; cl01401 340054002493 Protein of unknown function (DUF497); Region: DUF497; cl01108 340054002494 Pilin accessory protein (PilO); Region: PAP_PilO; pfam06864 340054002495 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 340054002496 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 340054002497 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054002498 Walker A motif; other site 340054002499 ATP binding site [chemical binding]; other site 340054002500 Walker B motif; other site 340054002501 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340054002502 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340054002503 PilS N terminal; Region: PilS; pfam08805 340054002504 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 340054002505 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 340054002506 Bacterial shufflon protein, N-terminal constant region; Region: Shufflon_N; pfam04917 340054002507 PilM; Region: PilM; pfam07419 340054002508 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 340054002509 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340054002510 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340054002511 catalytic residue [active] 340054002512 plasmid transfer ATPase TraJ; Region: plasmid_TraJ; TIGR02525 340054002513 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054002514 Walker A motif; other site 340054002515 ATP binding site [chemical binding]; other site 340054002516 Walker B motif; other site 340054002517 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 340054002518 oligomeric interface; other site 340054002519 putative active site [active] 340054002520 homodimer interface [polypeptide binding]; other site 340054002521 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 340054002522 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 340054002523 conjugal transfer relaxase TraI; Provisional; Region: PRK13878 340054002524 Macrophage killing protein with similarity to conjugation protein; Region: IcmL; pfam11393 340054002525 Protein of unknown function (DUF3625); Region: DUF3625; pfam12293 340054002526 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]; Region: VirB4; COG3451 340054002527 AAA-like domain; Region: AAA_10; pfam12846 340054002528 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 340054002529 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 340054002530 oligomeric interface; other site 340054002531 putative active site [active] 340054002532 homodimer interface [polypeptide binding]; other site 340054002533 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 340054002534 catalytic residues [active] 340054002535 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054002536 Walker A motif; other site 340054002537 ATP binding site [chemical binding]; other site 340054002538 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054002539 active site 340054002540 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054002541 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054002542 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054002543 putative active site [active] 340054002544 putative NTP binding site [chemical binding]; other site 340054002545 putative nucleic acid binding site [nucleotide binding]; other site 340054002546 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054002547 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054002548 active site 340054002549 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054002550 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054002551 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054002552 putative active site [active] 340054002553 putative NTP binding site [chemical binding]; other site 340054002554 putative nucleic acid binding site [nucleotide binding]; other site 340054002555 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054002556 hypothetical protein; Validated; Region: PRK08116 340054002557 Bacteriophage replication protein O; Region: Phage_rep_O; cl04545 340054002558 Ash protein family; Region: Phage_ASH; pfam10554 340054002559 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340054002560 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 340054002561 non-specific DNA binding site [nucleotide binding]; other site 340054002562 Predicted transcriptional regulator [Transcription]; Region: COG2932 340054002563 salt bridge; other site 340054002564 sequence-specific DNA binding site [nucleotide binding]; other site 340054002565 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 340054002566 Catalytic site [active] 340054002567 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054002568 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054002569 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054002570 putative active site [active] 340054002571 putative NTP binding site [chemical binding]; other site 340054002572 putative nucleic acid binding site [nucleotide binding]; other site 340054002573 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054002574 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054002575 active site 340054002576 Yersinia/Haemophilus virulence surface antigen; Region: Peptidase_C58; cl04145 340054002577 Integrase core domain; Region: rve; cl01316 340054002578 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054002579 Phage holin family (Lysis protein S); Region: Phage_holin_3; cl04938 340054002580 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054002581 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054002582 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 340054002583 catalytic residues [active] 340054002584 Sif protein; Region: Sif; cl11505 340054002585 Bacteriophage lysis protein; Region: Phage_lysis; pfam03245 340054002586 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054002587 active site 340054002588 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340054002589 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 340054002590 Phage terminase, small subunit; Region: Terminase_4; cl01525 340054002591 Integrase core domain; Region: rve; cl01316 340054002592 Transposase domain (DUF772); Region: DUF772; cl15789 340054002593 Transposase domain (DUF772); Region: DUF772; cl15789 340054002594 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054002595 beta-lactamase TEM; Provisional; Region: PRK15442 340054002596 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340054002597 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 340054002598 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 340054002599 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340054002600 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340054002601 IncFII RepA protein family; Region: IncFII_repA; cl11495 340054002602 conjugal transfer relaxosome component TraJ; Provisional; Region: PRK13877 340054002603 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 340054002604 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340054002605 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; cl01912 340054002606 ParA-like protein; Provisional; Region: PHA02518 340054002607 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 340054002608 P-loop; other site 340054002609 Magnesium ion binding site [ion binding]; other site 340054002610 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 340054002611 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 340054002612 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 340054002613 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 340054002614 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 340054002615 catalytic residues [active] 340054002616 catalytic nucleophile [active] 340054002617 Presynaptic Site I dimer interface [polypeptide binding]; other site 340054002618 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 340054002619 Synaptic Flat tetramer interface [polypeptide binding]; other site 340054002620 Synaptic Site I dimer interface [polypeptide binding]; other site 340054002621 DNA binding site [nucleotide binding] 340054002622 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 340054002623 DNA-binding interface [nucleotide binding]; DNA binding site 340054002624 Uncharacterized conserved protein [Function unknown]; Region: COG1656; cl09136 340054002625 Protein of unknown function (DUF433); Region: DUF433; cl01030 340054002626 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340054002627 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 340054002628 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340054002629 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 340054002630 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 340054002631 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340054002632 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340054002633 Initiator Replication protein; Region: Rep_3; cl03080 340054002634 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 340054002635 Domain of unknown function DUF29; Region: DUF29; pfam01724 340054002636 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 340054002637 PAS fold; Region: PAS_4; pfam08448 340054002638 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054002639 DNA binding residues [nucleotide binding] 340054002640 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 340054002641 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 340054002642 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 340054002643 Integrase core domain; Region: rve; cl01316 340054002644 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054002645 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 340054002646 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 340054002647 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 340054002648 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 340054002649 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 340054002650 PAS fold; Region: PAS_4; pfam08448 340054002651 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 340054002652 ParG; Region: ParG; pfam09274 340054002653 ParA-like protein; Provisional; Region: PHA02518 340054002654 autotransport protein MisL; Provisional; Region: PRK15313 340054002655 Integrase core domain; Region: rve; cl01316 340054002656 Integrase core domain; Region: rve_3; cl15866 340054002657 putative transposase OrfB; Reviewed; Region: PHA02517 340054002658 Phage terminase, small subunit; Region: Terminase_4; cl01525 340054002659 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054002660 active site 340054002661 potential frameshift: common BLAST hit: gi|146294922|ref|YP_001185346.1| integrase catalytic subunit 340054002662 putative transposase OrfB; Reviewed; Region: PHA02517 340054002663 Integrase core domain; Region: rve; cl01316 340054002664 Integrase core domain; Region: rve_3; cl15866 340054002665 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 340054002666 active site 340054002667 metal binding site [ion binding]; metal-binding site 340054002668 MAEBL; Provisional; Region: PTZ00121 340054002669 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 340054002670 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 340054002671 active site 340054002672 DNA binding site [nucleotide binding] 340054002673 Uncharacterized conserved protein [Function unknown]; Region: COG2850 340054002674 PAS fold; Region: PAS_4; pfam08448 340054002675 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054002676 DNA binding residues [nucleotide binding] 340054002677 dimerization interface [polypeptide binding]; other site 340054002678 RelB antitoxin; Region: RelB; cl01171 340054002679 LuxR family transcriptional regulatory, chaperone HchA-associated; Region: reg_near_HchA; TIGR03541 340054002680 Helix-turn-helix domains; Region: HTH; cl00088 340054002681 DNA binding residues [nucleotide binding] 340054002682 hypothetical protein; Provisional; Region: PRK09956 340054002683 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 340054002684 non-specific DNA binding site [nucleotide binding]; other site 340054002685 salt bridge; other site 340054002686 sequence-specific DNA binding site [nucleotide binding]; other site 340054002687 Protein of unknown function (DUF1044); Region: DUF1044; cl01955 340054002688 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 340054002689 Uncharacterized conserved protein [Function unknown]; Region: COG2850 340054002690 Replication initiator protein A; Region: RPA; cl02339 340054002691 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 340054002692 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 340054002693 catalytic residues [active] 340054002694 catalytic nucleophile [active] 340054002695 Presynaptic Site I dimer interface [polypeptide binding]; other site 340054002696 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 340054002697 Synaptic Flat tetramer interface [polypeptide binding]; other site 340054002698 Synaptic Site I dimer interface [polypeptide binding]; other site 340054002699 Anthrax toxin LF subunit; Region: Anthrax_toxA; pfam03497 340054002700 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054002701 ParA-like protein; Provisional; Region: PHA02518 340054002702 flagellar biosynthesis regulator FlhF; Provisional; Region: flhF; PRK14723 340054002703 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340054002704 Integrase core domain; Region: rve; cl01316 340054002705 Bacteriophage Mu Gp45 protein; Region: Phage_Mu_Gp45; cl15410 340054002706 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 340054002707 Yersinia/Haemophilus virulence surface antigen; Region: Peptidase_C58; cl04145 340054002708 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054002709 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054002710 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054002711 putative active site [active] 340054002712 putative NTP binding site [chemical binding]; other site 340054002713 putative nucleic acid binding site [nucleotide binding]; other site 340054002714 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054002715 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054002716 active site 340054002717 Yersinia/Haemophilus virulence surface antigen; Region: Peptidase_C58; cl04145 340054002718 Peptidase C80 family; Region: Peptidase_C80; pfam11713 340054002719 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 340054002720 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 340054002721 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 340054002722 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 340054002723 dimer interface [polypeptide binding]; other site 340054002724 FMN binding site [chemical binding]; other site 340054002725 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 340054002726 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 340054002727 IHF - DNA interface [nucleotide binding]; other site 340054002728 IHF dimer interface [polypeptide binding]; other site 340054002729 Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches; Region: Vsr; cd00221 340054002730 additional DNA contacts [nucleotide binding]; other site 340054002731 mismatch recognition site; other site 340054002732 active site 340054002733 zinc binding site [ion binding]; other site 340054002734 DNA intercalation site [nucleotide binding]; other site 340054002735 EcoRII C terminal; Region: EcoRII-C; pfam09019 340054002736 Transposase domain (DUF772); Region: DUF772; cl15789 340054002737 PIN domain of the VapC-like Sll0205 protein and homologs; Region: PIN_Sll0205; cd09872 340054002738 putative active site [active] 340054002739 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 340054002740 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340054002741 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 340054002742 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 340054002743 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054002744 dimerization interface [polypeptide binding]; other site 340054002745 DNA binding residues [nucleotide binding] 340054002746 Transposase domain (DUF772); Region: DUF772; cl15789 340054002747 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 340054002748 Protein of unknown function, DUF412; Region: DUF412; cl01183 340054002749 AAA domain; Region: AAA_26; pfam13500 340054002750 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054002751 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054002752 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 340054002753 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 340054002754 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 340054002755 S-adenosylmethionine binding site [chemical binding]; other site 340054002756 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 340054002757 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 340054002758 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340054002759 catalytic residue [active] 340054002760 biotin synthase; Provisional; Region: PRK15108 340054002761 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 340054002762 FeS/SAM binding site; other site 340054002763 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 340054002764 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 340054002765 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 340054002766 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 340054002767 Walker A/P-loop; other site 340054002768 ATP binding site [chemical binding]; other site 340054002769 Q-loop/lid; other site 340054002770 ABC transporter signature motif; other site 340054002771 Walker B; other site 340054002772 D-loop; other site 340054002773 H-loop/switch region; other site 340054002774 ComEC family competence protein; Provisional; Region: PRK11539 340054002775 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 340054002776 Competence protein; Region: Competence; cl00471 340054002777 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 340054002778 trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: putA; PRK11809 340054002779 Proline dehydrogenase; Region: Pro_dh; cl03282 340054002780 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 340054002781 Glutamate binding site [chemical binding]; other site 340054002782 NAD binding site [chemical binding]; other site 340054002783 catalytic residues [active] 340054002784 Sodium:solute symporter family; Region: SSF; cl00456 340054002785 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 340054002786 Phosphopantetheine attachment site; Region: PP-binding; cl09936 340054002787 invasion protein OrgB; Provisional; Region: PRK15322 340054002788 Plant ATP synthase F0; Region: YMF19; cl07975 340054002789 Bacterial type III secretion apparatus protein (OrgA_MxiK); Region: OrgA_MxiK; cl09716 340054002790 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 340054002791 type III secretion system needle complex protein PrgJ; Provisional; Region: PRK15325 340054002792 Type III secretion needle MxiH like; Region: MxiH; cl09641 340054002793 type III secretion system needle complex protein PrgH; Provisional; Region: PRK15327; cl12363 340054002794 Type III secretion system protein PrgH-EprH (PrgH); Region: PrgH; pfam09480 340054002795 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054002796 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054002797 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054002798 putative active site [active] 340054002799 putative NTP binding site [chemical binding]; other site 340054002800 putative nucleic acid binding site [nucleotide binding]; other site 340054002801 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054002802 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054002803 active site 340054002804 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 340054002805 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 340054002806 putative dimer interface [polypeptide binding]; other site 340054002807 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340054002808 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340054002809 PilS N terminal; Region: PilS; pfam08805 340054002810 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340054002811 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340054002812 catalytic residue [active] 340054002813 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 340054002814 RelB antitoxin; Region: RelB; cl01171 340054002815 Integrase core domain; Region: rve; cl01316 340054002816 Integrase core domain; Region: rve_3; cl15866 340054002817 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 340054002818 Transposase domain (DUF772); Region: DUF772; cl15789 340054002819 Transposase domain (DUF772); Region: DUF772; cl15789 340054002820 K+ potassium transporter; Region: K_trans; cl15781 340054002821 potassium uptake protein; Region: kup; TIGR00794 340054002822 Transposase domain (DUF772); Region: DUF772; cl15789 340054002823 Shigella flexneri OspC protein; Region: Shigella_OspC; pfam06128 340054002824 Peptidase C80 family; Region: Peptidase_C80; pfam11713 340054002825 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 340054002826 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 340054002827 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054002828 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054002829 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054002830 putative active site [active] 340054002831 putative NTP binding site [chemical binding]; other site 340054002832 putative nucleic acid binding site [nucleotide binding]; other site 340054002833 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054002834 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054002835 active site 340054002836 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 340054002837 Domain of unknown function (DUF4354); Region: DUF4354; pfam14263 340054002838 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 340054002839 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 340054002840 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 340054002841 shikimate binding site; other site 340054002842 NAD(P) binding site [chemical binding]; other site 340054002843 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 340054002844 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 340054002845 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 340054002846 active site 340054002847 uracil binding [chemical binding]; other site 340054002848 6-phosphogluconolactonase; Provisional; Region: PRK11028 340054002849 Protein of unknown function (DUF2592); Region: DUF2592; pfam10766 340054002850 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 340054002851 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 340054002852 23S rRNA interface [nucleotide binding]; other site 340054002853 L3 interface [polypeptide binding]; other site 340054002854 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 340054002855 stringent starvation protein A; Provisional; Region: sspA; PRK09481 340054002856 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 340054002857 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 340054002858 dimer interface [polypeptide binding]; other site 340054002859 N-terminal domain interface [polypeptide binding]; other site 340054002860 Stringent starvation protein B; Region: SspB; cl01120 340054002861 Protein of unknown function (DUF3792); Region: DUF3792; cl14821 340054002862 phosphodiesterase; Provisional; Region: PRK12704 340054002863 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 340054002864 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 340054002865 Walker A motif; other site 340054002866 ATP binding site [chemical binding]; other site 340054002867 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054002868 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 340054002869 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 340054002870 active site 340054002871 HslU subunit interaction site [polypeptide binding]; other site 340054002872 Sporulation related domain; Region: SPOR; cl10051 340054002873 cell division protein FtsN; Provisional; Region: PRK12757 340054002874 Sporulation related domain; Region: SPOR; cl10051 340054002875 aromatic amino acid transporter; Provisional; Region: PRK10238 340054002876 quinolinate phosphoribosyltransferase; Validated; Region: PRK09016 340054002877 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 340054002878 dimerization interface [polypeptide binding]; other site 340054002879 active site 340054002880 Protein of unknown function (DUF328); Region: DUF328; cl01143 340054002881 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 340054002882 DNA photolyase; Region: DNA_photolyase; pfam00875 340054002883 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 340054002884 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 340054002885 Uncharacterized conserved protein [Function unknown]; Region: COG0327 340054002886 seryl-tRNA synthetase; Provisional; Region: PRK05431 340054002887 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 340054002888 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound...; Region: SerRS_core; cd00770 340054002889 dimer interface [polypeptide binding]; other site 340054002890 active site 340054002891 motif 1; other site 340054002892 motif 2; other site 340054002893 motif 3; other site 340054002894 Protein of unknown function (DUF421); Region: DUF421; cl00990 340054002895 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 340054002896 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 340054002897 generic binding surface II; other site 340054002898 generic binding surface I; other site 340054002899 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 340054002900 magnesium-transporting ATPase; Provisional; Region: PRK15122 340054002901 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 340054002902 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 340054002903 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 340054002904 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 340054002905 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 340054002906 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 340054002907 DNA-binding site [nucleotide binding]; DNA binding site 340054002908 RNA-binding motif; other site 340054002909 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3009 340054002910 Protein of unknown function (DUF330); Region: DUF330; cl01135 340054002911 paraquat-inducible protein B; Provisional; Region: PRK10807 340054002912 mce related protein; Region: MCE; pfam02470 340054002913 mce related protein; Region: MCE; pfam02470 340054002914 mce related protein; Region: MCE; pfam02470 340054002915 paraquat-inducible membrane protein A; Provisional; Region: PRK15103 340054002916 Paraquat-inducible protein A; Region: PqiA; pfam04403 340054002917 Paraquat-inducible protein A; Region: PqiA; pfam04403 340054002918 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340054002919 Integrase core domain; Region: rve; cl01316 340054002920 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054002921 AIDA autotransporter-like protein ShdA; Provisional; Region: PRK15319 340054002922 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases; Region: PL1_Passenger_AT; cd01343 340054002923 AIDA autotransporter-like protein ShdA; Provisional; Region: PRK15319 340054002924 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases; Region: PL1_Passenger_AT; cd01343 340054002925 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases; Region: PL1_Passenger_AT; cd01343 340054002926 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340054002927 DNA repair protein RadA; Provisional; Region: PRK11823 340054002928 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 340054002929 Walker A motif/ATP binding site; other site 340054002930 ATP binding site [chemical binding]; other site 340054002931 Walker B motif; other site 340054002932 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 340054002933 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 340054002934 S-adenosylmethionine binding site [chemical binding]; other site 340054002935 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054002936 aconitate hydratase; Validated; Region: PRK09277 340054002937 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 340054002938 substrate binding site [chemical binding]; other site 340054002939 ligand binding site [chemical binding]; other site 340054002940 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 340054002941 substrate binding site [chemical binding]; other site 340054002942 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 340054002943 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 340054002944 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 340054002945 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 340054002946 ribosome recycling factor; Reviewed; Region: frr; PRK00083 340054002947 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 340054002948 hinge region; other site 340054002949 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 340054002950 putative nucleotide binding site [chemical binding]; other site 340054002951 uridine monophosphate binding site [chemical binding]; other site 340054002952 homohexameric interface [polypeptide binding]; other site 340054002953 elongation factor Ts; Provisional; Region: tsf; PRK09377 340054002954 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 340054002955 Elongation factor TS; Region: EF_TS; pfam00889 340054002956 Elongation factor TS; Region: EF_TS; pfam00889 340054002957 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 340054002958 rRNA interaction site [nucleotide binding]; other site 340054002959 S8 interaction site; other site 340054002960 putative laminin-1 binding site; other site 340054002961 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 340054002962 dimerization interface [polypeptide binding]; other site 340054002963 substrate binding site [chemical binding]; other site 340054002964 active site 340054002965 calcium binding site [ion binding]; other site 340054002966 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 340054002967 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 340054002968 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 340054002969 active site 340054002970 DNA binding site [nucleotide binding] 340054002971 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054002972 DNA binding residues [nucleotide binding] 340054002973 dimerization interface [polypeptide binding]; other site 340054002974 TrbC/VIRB2 family; Region: TrbC; cl01583 340054002975 P-type DNA transfer protein VirB5; Region: VirB5; TIGR02791 340054002976 Type IV secretion system proteins; Region: T4SS; pfam07996 340054002977 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 340054002978 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 340054002979 catalytic residues [active] 340054002980 catalytic nucleophile [active] 340054002981 Presynaptic Site I dimer interface [polypeptide binding]; other site 340054002982 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 340054002983 Synaptic Flat tetramer interface [polypeptide binding]; other site 340054002984 Synaptic Site I dimer interface [polypeptide binding]; other site 340054002985 DNA binding site [nucleotide binding] 340054002986 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 340054002987 DNA-binding interface [nucleotide binding]; DNA binding site 340054002988 VirB8 protein; Region: VirB8; cl01500 340054002989 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 340054002990 VirB7 interaction site; other site 340054002991 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 340054002992 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 340054002993 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 340054002994 ATP binding site [chemical binding]; other site 340054002995 Walker A motif; other site 340054002996 hexamer interface [polypeptide binding]; other site 340054002997 Walker B motif; other site 340054002998 Type IV secretory system Conjugative DNA transfer; Region: T4SS-DNA_transf; pfam02534 340054002999 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054003000 Walker A motif; other site 340054003001 ATP binding site [chemical binding]; other site 340054003002 Walker B motif; other site 340054003003 Cag pathogenicity island protein Cag12; Region: Cag12; pfam13117 340054003004 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 340054003005 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054003006 Integrase core domain; Region: rve; cl01316 340054003007 PilM; Region: PilM; pfam07419 340054003008 type IVB pilus formation outer membrane protein, R64 PilN family; Region: pilus_B_mal_scr; TIGR02520 340054003009 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 340054003010 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340054003011 Pilin accessory protein (PilO); Region: PAP_PilO; pfam06864 340054003012 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 340054003013 Type II/IV secretion system protein; Region: T2SE; pfam00437 340054003014 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054003015 Walker A motif; other site 340054003016 ATP binding site [chemical binding]; other site 340054003017 Walker B motif; other site 340054003018 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 340054003019 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 340054003020 putative dimer interface [polypeptide binding]; other site 340054003021 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 340054003022 Bacterial shufflon protein, N-terminal constant region; Region: Shufflon_N; pfam04917 340054003023 Bacterial shufflon protein, N-terminal constant region; Region: Shufflon_N; pfam04917 340054003024 Replication initiator protein A; Region: RPA; cl02339 340054003025 Replication initiator protein A; Region: RPA; cl02339 340054003026 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 340054003027 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 340054003028 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 340054003029 Salmonella outer protein D; Region: SopD; cl14701 340054003030 Integrase core domain; Region: rve; cl01316 340054003031 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054003032 hypothetical protein; Provisional; Region: PRK09956 340054003033 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 340054003034 active site 340054003035 NAD binding site [chemical binding]; other site 340054003036 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054003037 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054003038 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054003039 putative active site [active] 340054003040 putative NTP binding site [chemical binding]; other site 340054003041 putative nucleic acid binding site [nucleotide binding]; other site 340054003042 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054003043 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054003044 active site 340054003045 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 340054003046 non-specific DNA binding site [nucleotide binding]; other site 340054003047 salt bridge; other site 340054003048 sequence-specific DNA binding site [nucleotide binding]; other site 340054003049 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 340054003050 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 340054003051 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 340054003052 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 340054003053 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 340054003054 ATP binding site [chemical binding]; other site 340054003055 Mg2+ binding site [ion binding]; other site 340054003056 G-X-G motif; other site 340054003057 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 340054003058 ATP binding site [chemical binding]; other site 340054003059 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 340054003060 Transposase domain (DUF772); Region: DUF772; cl15789 340054003061 PemK-like protein; Region: PemK; cl00995 340054003062 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 340054003063 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 340054003064 Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient...; Region: SR_Res_par; cd03767 340054003065 catalytic residues [active] 340054003066 catalytic nucleophile [active] 340054003067 ParA-like protein; Provisional; Region: PHA02518 340054003068 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 340054003069 P-loop; other site 340054003070 Magnesium ion binding site [ion binding]; other site 340054003071 ParG; Region: ParG; pfam09274 340054003072 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 340054003073 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 340054003074 potential frameshift: common BLAST hit: gi|51597529|ref|YP_071720.1| pore forming RTX toxin family protein 340054003075 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 340054003076 Peptidase C80 family; Region: Peptidase_C80; pfam11713 340054003077 conjugal transfer relaxosome component TraJ; Provisional; Region: PRK13877 340054003078 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 340054003079 conjugal transfer relaxase TraI; Provisional; Region: PRK13878 340054003080 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 340054003081 IHF dimer interface [polypeptide binding]; other site 340054003082 IHF - DNA interface [nucleotide binding]; other site 340054003083 putative transposase; Provisional; Region: PRK09857 340054003084 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 340054003085 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl15270 340054003086 putative RNA binding sites [nucleotide binding]; other site 340054003087 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054003088 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054003089 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054003090 putative active site [active] 340054003091 putative NTP binding site [chemical binding]; other site 340054003092 putative nucleic acid binding site [nucleotide binding]; other site 340054003093 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054003094 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054003095 active site 340054003096 plasmid transfer ATPase TraJ; Region: plasmid_TraJ; TIGR02525 340054003097 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054003098 Walker A motif; other site 340054003099 ATP binding site [chemical binding]; other site 340054003100 Walker B motif; other site 340054003101 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340054003102 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340054003103 catalytic residue [active] 340054003104 PilM; Region: PilM; pfam07419 340054003105 Bacterial shufflon protein, N-terminal constant region; Region: Shufflon_N; pfam04917 340054003106 PilS N terminal; Region: PilS; pfam08805 340054003107 Type II/IV secretion system protein; Region: T2SE; pfam00437 340054003108 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054003109 Walker A motif; other site 340054003110 ATP binding site [chemical binding]; other site 340054003111 Walker B motif; other site 340054003112 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 340054003113 Pilin accessory protein (PilO); Region: PAP_PilO; pfam06864 340054003114 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340054003115 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 340054003116 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; Region: NGN_SP_AnfA1; cd09894 340054003117 transcriptional activator RfaH; Region: RfaH; TIGR01955 340054003118 Integrase core domain; Region: rve; cl01316 340054003119 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054003120 Phage capsid family; Region: Phage_capsid; pfam05065 340054003121 Caudovirus prohead protease; Region: Peptidase_U35; cl01521 340054003122 Phage-related protein [Function unknown]; Region: COG4695; cl01923 340054003123 Phage portal protein; Region: Phage_portal; pfam04860 340054003124 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054003125 Integrase core domain; Region: rve; cl01316 340054003126 Phage terminase-like protein, large subunit [General function prediction only]; Region: COG4626 340054003127 Phage Terminase; Region: Terminase_1; pfam03354 340054003128 Phage terminase, small subunit; Region: Terminase_4; cl01525 340054003129 RelB antitoxin; Region: RelB; cl01171 340054003130 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 340054003131 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054003132 active site 340054003133 Protein of unknown function (DUF551); Region: DUF551; pfam04448 340054003134 Trypanosomal VSG domain; Region: VSG_B; cl11958 340054003135 Bacteriophage lysis protein; Region: Phage_lysis; pfam03245 340054003136 KilA-N domain; Region: KilA-N; pfam04383 340054003137 P22_AR N-terminal domain; Region: P22_AR_N; pfam10547 340054003138 ORF11CD3 domain; Region: ORF11CD3; pfam10549 340054003139 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 340054003140 catalytic residues [active] 340054003141 Integrase core domain; Region: rve; cl01316 340054003142 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054003143 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 340054003144 Sodium:solute symporter family; Region: SSF; cl00456 340054003145 Salmonella outer protein D; Region: SopD; cl14701 340054003146 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 340054003147 active site 340054003148 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases; Region: PL1_Passenger_AT; cd01343 340054003149 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340054003150 putative transposase; Provisional; Region: PRK09857 340054003151 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 340054003152 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 340054003153 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 340054003154 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 340054003155 serine endoprotease; Provisional; Region: PRK10942 340054003156 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 340054003157 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 340054003158 protein binding site [polypeptide binding]; other site 340054003159 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 340054003160 protein binding site [polypeptide binding]; other site 340054003161 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl15270 340054003162 putative RNA binding sites [nucleotide binding]; other site 340054003163 carboxy-terminal protease; Provisional; Region: PRK11186 340054003164 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 340054003165 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 340054003166 protein binding site [polypeptide binding]; other site 340054003167 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 340054003168 Catalytic dyad [active] 340054003169 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 340054003170 Peptidase family M48; Region: Peptidase_M48; cl12018 340054003171 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 340054003172 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 340054003173 amidase catalytic site [active] 340054003174 Zn binding residues [ion binding]; other site 340054003175 substrate binding site [chemical binding]; other site 340054003176 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 340054003177 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 340054003178 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 340054003179 amidase catalytic site [active] 340054003180 Zn binding residues [ion binding]; other site 340054003181 substrate binding site [chemical binding]; other site 340054003182 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 340054003183 Peptidase family M48; Region: Peptidase_M48; cl12018 340054003184 carboxy-terminal protease; Provisional; Region: PRK11186 340054003185 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 340054003186 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 340054003187 protein binding site [polypeptide binding]; other site 340054003188 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 340054003189 Catalytic dyad [active] 340054003190 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 340054003191 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl15270 340054003192 putative RNA binding sites [nucleotide binding]; other site 340054003193 serine endoprotease; Provisional; Region: PRK10942 340054003194 Herpesvirus transcription activation factor (transactivator); Region: Herpes_TAF50; pfam03326 340054003195 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 340054003196 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 340054003197 protein binding site [polypeptide binding]; other site 340054003198 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 340054003199 protein binding site [polypeptide binding]; other site 340054003200 deoxyguanosinetriphosphate triphosphohydrolase; Provisional; Region: dgt; PRK04926 340054003201 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 340054003202 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 340054003203 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 340054003204 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 340054003205 putative GSH binding site [chemical binding]; other site 340054003206 catalytic residues [active] 340054003207 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 340054003208 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 340054003209 active site 340054003210 catalytic site [active] 340054003211 substrate binding site [chemical binding]; other site 340054003212 invasion protein regulator; Provisional; Region: PRK12370 340054003213 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 340054003214 DNA binding site [nucleotide binding] 340054003215 transcriptional regulator InvF; Provisional; Region: PRK15340 340054003216 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 340054003217 type III secretion system outer membrane pore InvG; Provisional; Region: PRK15339 340054003218 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 340054003219 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340054003220 type III secretion system regulator InvE; Provisional; Region: PRK15338 340054003221 HrpJ-like domain; Region: HrpJ; cl15454 340054003222 type III secretion system protein InvA; Provisional; Region: PRK15337 340054003223 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 340054003224 Invasion protein B family; Region: Invas_SpaK; cl04129 340054003225 ATP synthase SpaL; Validated; Region: PRK08149 340054003226 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 340054003227 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054003228 Walker A motif; other site 340054003229 ATP binding site [chemical binding]; other site 340054003230 Walker B motif; other site 340054003231 Salmonella surface presentation of antigen gene type M protein; Region: SPAM; cl03442 340054003232 Surface presentation of antigens protein; Region: SPAN; cl03629 340054003233 type III secretion system protein SpaO; Validated; Region: PRK08158 340054003234 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 340054003235 FliP family; Region: FliP; cl00593 340054003236 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 340054003237 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 340054003238 type III secretion system protein SpaS; Validated; Region: PRK08156 340054003239 eIF3 subunit 6 N terminal domain; Region: eIF3_N; pfam09440 340054003240 chaperone protein SicA; Provisional; Region: PRK15331 340054003241 Tetratricopeptide repeat; Region: TPR_3; pfam07720 340054003242 pathogenicity island 1 effector protein SipB; Provisional; Region: PRK15374 340054003243 DNA gyrase subunit A; Validated; Region: PRK05560 340054003244 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 340054003245 CAP-like domain; other site 340054003246 active site 340054003247 primary dimer interface [polypeptide binding]; other site 340054003248 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340054003249 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340054003250 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340054003251 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340054003252 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 340054003253 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 340054003254 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 340054003255 S-adenosylmethionine binding site [chemical binding]; other site 340054003256 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 340054003257 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 340054003258 inhibitor-cofactor binding pocket; inhibition site 340054003259 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340054003260 catalytic residue [active] 340054003261 aerobic respiration control sensor protein ArcB; Provisional; Region: PRK11091 340054003262 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 340054003263 dimer interface [polypeptide binding]; other site 340054003264 phosphorylation site [posttranslational modification] 340054003265 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 340054003266 ATP binding site [chemical binding]; other site 340054003267 Mg2+ binding site [ion binding]; other site 340054003268 G-X-G motif; other site 340054003269 Response regulator receiver domain; Region: Response_reg; pfam00072 340054003270 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340054003271 active site 340054003272 phosphorylation site [posttranslational modification] 340054003273 intermolecular recognition site; other site 340054003274 dimerization interface [polypeptide binding]; other site 340054003275 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 340054003276 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 340054003277 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 340054003278 IHF dimer interface [polypeptide binding]; other site 340054003279 IHF - DNA interface [nucleotide binding]; other site 340054003280 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 340054003281 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 340054003282 arginine decarboxylase; Provisional; Region: PRK05354 340054003283 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 340054003284 active site 340054003285 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340054003286 catalytic residues [active] 340054003287 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 340054003288 transketolase; Reviewed; Region: PRK12753 340054003289 Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the...; Region: TPP_TK; cd02012 340054003290 TPP-binding site [chemical binding]; other site 340054003291 dimer interface [polypeptide binding]; other site 340054003292 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 340054003293 PYR/PP interface [polypeptide binding]; other site 340054003294 dimer interface [polypeptide binding]; other site 340054003295 TPP binding site [chemical binding]; other site 340054003296 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 340054003297 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 340054003298 response regulator; Provisional; Region: PRK09483 340054003299 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340054003300 active site 340054003301 phosphorylation site [posttranslational modification] 340054003302 intermolecular recognition site; other site 340054003303 dimerization interface [polypeptide binding]; other site 340054003304 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054003305 DNA binding residues [nucleotide binding] 340054003306 dimerization interface [polypeptide binding]; other site 340054003307 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 340054003308 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 340054003309 GIY-YIG motif/motif A; other site 340054003310 active site 340054003311 catalytic site [active] 340054003312 putative DNA binding site [nucleotide binding]; other site 340054003313 metal binding site [ion binding]; metal-binding site 340054003314 UvrB/uvrC motif; Region: UVR; pfam02151 340054003315 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 340054003316 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 340054003317 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 340054003318 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 340054003319 dimer interface [polypeptide binding]; other site 340054003320 ssDNA binding site [nucleotide binding]; other site 340054003321 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340054003322 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 340054003323 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 340054003324 active site 340054003325 NTP binding site [chemical binding]; other site 340054003326 metal binding triad [ion binding]; metal-binding site 340054003327 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 340054003328 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 340054003329 Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is...; Region: FBP_aldolase_IIA; cd00946 340054003330 active site 340054003331 intersubunit interface [polypeptide binding]; other site 340054003332 zinc binding site [ion binding]; other site 340054003333 Na+ binding site [ion binding]; other site 340054003334 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 340054003335 Phosphoglycerate kinase; Region: PGK; pfam00162 340054003336 substrate binding site [chemical binding]; other site 340054003337 hinge regions; other site 340054003338 ADP binding site [chemical binding]; other site 340054003339 catalytic site [active] 340054003340 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 340054003341 catalytic core [active] 340054003342 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 340054003343 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 340054003344 active site 340054003345 HIGH motif; other site 340054003346 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 340054003347 KMSKS motif; other site 340054003348 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 340054003349 tRNA binding surface [nucleotide binding]; other site 340054003350 anticodon binding site; other site 340054003351 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 340054003352 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 340054003353 putative active site [active] 340054003354 putative metal binding site [ion binding]; other site 340054003355 DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol...; Region: DsbA_DsbA; cd03019 340054003356 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 340054003357 catalytic residues [active] 340054003358 hinge region; other site 340054003359 alpha helical domain; other site 340054003360 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 340054003361 flagellar biosynthesis regulator FlhF; Provisional; Region: flhF; PRK14723 340054003362 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; cl05448 340054003363 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 340054003364 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 340054003365 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340054003366 secreted effector protein PipB2; Provisional; Region: PRK15196 340054003367 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340054003368 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 340054003369 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340054003370 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 340054003371 Mor transcription activator family; Region: Mor; cl02360 340054003372 putative replication protein; Provisional; Region: PRK12377 340054003373 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 340054003374 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 340054003375 non-specific DNA binding site [nucleotide binding]; other site 340054003376 salt bridge; other site 340054003377 sequence-specific DNA binding site [nucleotide binding]; other site 340054003378 BRO family, N-terminal domain; Region: Bro-N; cl10591 340054003379 Bacteriophage lambda integrase, N-terminal domain; Region: Phage_integ_N; pfam09003 340054003380 AntA/AntB antirepressor; Region: AntA; cl01430 340054003381 BRO family, N-terminal domain; Region: Bro-N; cl10591 340054003382 BRO family, N-terminal domain; Region: Bro-N; cl10591 340054003383 Staphylococcal nuclease homologues; Region: SNc; smart00318 340054003384 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 340054003385 Catalytic site; other site 340054003386 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 340054003387 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 340054003388 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 340054003389 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054003390 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 340054003391 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 340054003392 endonuclease III; Provisional; Region: PRK10702 340054003393 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 340054003394 minor groove reading motif; other site 340054003395 helix-hairpin-helix signature motif; other site 340054003396 substrate binding pocket [chemical binding]; other site 340054003397 active site 340054003398 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 340054003399 Helix-turn-helix domains; Region: HTH; cl00088 340054003400 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 340054003401 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 340054003402 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 340054003403 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 340054003404 FAD binding domain; Region: FAD_binding_4; pfam01565 340054003405 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 340054003406 HemK family putative methylases; Region: hemK_fam; TIGR00536 340054003407 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 340054003408 S-adenosylmethionine binding site [chemical binding]; other site 340054003409 PAS fold; Region: PAS_4; pfam08448 340054003410 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054003411 DNA binding residues [nucleotide binding] 340054003412 dimerization interface [polypeptide binding]; other site 340054003413 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 340054003414 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 340054003415 substrate binding pocket [chemical binding]; other site 340054003416 chain length determination region; other site 340054003417 substrate-Mg2+ binding site; other site 340054003418 catalytic residues [active] 340054003419 aspartate-rich region 1; other site 340054003420 active site lid residues [active] 340054003421 aspartate-rich region 2; other site 340054003422 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 340054003423 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 340054003424 TPP-binding site; other site 340054003425 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 340054003426 PYR/PP interface [polypeptide binding]; other site 340054003427 dimer interface [polypeptide binding]; other site 340054003428 TPP binding site [chemical binding]; other site 340054003429 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 340054003430 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 340054003431 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 340054003432 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 340054003433 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 340054003434 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 340054003435 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 340054003436 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 340054003437 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 340054003438 4Fe-4S binding domain; Region: Fer4; cl02805 340054003439 4Fe-4S binding domain; Region: Fer4; cl02805 340054003440 NADH dehydrogenase; Region: NADHdh; cl00469 340054003441 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 340054003442 NADH-quinone oxidoreductase, chain G; Region: NuoG; TIGR01973 340054003443 catalytic loop [active] 340054003444 iron binding site [ion binding]; other site 340054003445 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 340054003446 MopB_NDH-1_NuoG2-N7: The second domain of the NuoG subunit (with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory...; Region: MopB_NDH-1_NuoG2-N7; cd02771 340054003447 [4Fe-4S] binding site [ion binding]; other site 340054003448 NADH dehydrogenase subunit G; Validated; Region: PRK08166 340054003449 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex...; Region: MopB_CT_NDH-1_NuoG2-N7; cd02788 340054003450 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 340054003451 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340054003452 Walker A/P-loop; other site 340054003453 ATP binding site [chemical binding]; other site 340054003454 Q-loop/lid; other site 340054003455 ABC transporter signature motif; other site 340054003456 Walker B; other site 340054003457 D-loop; other site 340054003458 H-loop/switch region; other site 340054003459 excinuclease ABC subunit B; Provisional; Region: PRK05298 340054003460 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 340054003461 ATP binding site [chemical binding]; other site 340054003462 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 340054003463 nucleotide binding region [chemical binding]; other site 340054003464 ATP-binding site [chemical binding]; other site 340054003465 Ultra-violet resistance protein B; Region: UvrB; pfam12344 340054003466 UvrB/uvrC motif; Region: UVR; pfam02151 340054003467 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 340054003468 poly(A) polymerase; Region: pcnB; TIGR01942 340054003469 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 340054003470 active site 340054003471 NTP binding site [chemical binding]; other site 340054003472 metal binding triad [ion binding]; metal-binding site 340054003473 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 340054003474 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 340054003475 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 340054003476 catalytic center binding site [active] 340054003477 ATP binding site [chemical binding]; other site 340054003478 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 340054003479 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 340054003480 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 340054003481 multidrug efflux system protein AcrB; Provisional; Region: PRK15127 340054003482 Protein export membrane protein; Region: SecD_SecF; cl14618 340054003483 Protein export membrane protein; Region: SecD_SecF; cl14618 340054003484 Haemolysin expression modulating protein; Region: HHA; cl11501 340054003485 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 340054003486 folate binding site [chemical binding]; other site 340054003487 NADP+ binding site [chemical binding]; other site 340054003488 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 340054003489 MutS domain I; Region: MutS_I; pfam01624 340054003490 MutS domain II; Region: MutS_II; pfam05188 340054003491 MutS family domain IV; Region: MutS_IV; pfam05190 340054003492 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 340054003493 Walker A/P-loop; other site 340054003494 ATP binding site [chemical binding]; other site 340054003495 Q-loop/lid; other site 340054003496 ABC transporter signature motif; other site 340054003497 Walker B; other site 340054003498 D-loop; other site 340054003499 H-loop/switch region; other site 340054003500 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 340054003501 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 340054003502 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 340054003503 dimer interface [polypeptide binding]; other site 340054003504 phosphorylation site [posttranslational modification] 340054003505 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 340054003506 ATP binding site [chemical binding]; other site 340054003507 Mg2+ binding site [ion binding]; other site 340054003508 G-X-G motif; other site 340054003509 Uncharacterized domain of BarA-like signal transduction histidine kinases [Signal transduction mechanisms]; Region: COG4999 340054003510 Response regulator receiver domain; Region: Response_reg; pfam00072 340054003511 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340054003512 active site 340054003513 phosphorylation site [posttranslational modification] 340054003514 intermolecular recognition site; other site 340054003515 dimerization interface [polypeptide binding]; other site 340054003516 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 340054003517 Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ...; Region: Met_repressor_MetJ; cd00490 340054003518 dimerization interface [polypeptide binding]; other site 340054003519 DNA binding site [nucleotide binding] 340054003520 corepressor binding sites; other site 340054003521 UbiA prenyltransferase family; Region: UbiA; cl00337 340054003522 UTRA domain; Region: UTRA; cl01230 340054003523 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 340054003524 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 340054003525 active site 340054003526 HIGH motif; other site 340054003527 dimer interface [polypeptide binding]; other site 340054003528 KMSKS motif; other site 340054003529 Autoinducer binding domain; Region: Autoind_bind; pfam03472 340054003530 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054003531 DNA binding residues [nucleotide binding] 340054003532 dimerization interface [polypeptide binding]; other site 340054003533 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 340054003534 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 340054003535 substrate binding site [chemical binding]; other site 340054003536 hexamer interface [polypeptide binding]; other site 340054003537 metal binding site [ion binding]; metal-binding site 340054003538 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054003539 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 340054003540 active site 340054003541 dimer interface [polypeptide binding]; other site 340054003542 metal binding site [ion binding]; metal-binding site 340054003543 shikimate kinase; Reviewed; Region: aroK; PRK00131 340054003544 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 340054003545 ADP binding site [chemical binding]; other site 340054003546 magnesium binding site [ion binding]; other site 340054003547 putative shikimate binding site; other site 340054003548 RIO kinase family; RIO1, RIO3 and similar proteins, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein...; Region: RIO1_like; cd05145 340054003549 ATP binding site [chemical binding]; other site 340054003550 phosphate acetyltransferase; Reviewed; Region: PRK05632 340054003551 DRTGG domain; Region: DRTGG; cl12147 340054003552 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 340054003553 propionate/acetate kinase; Provisional; Region: PRK12379 340054003554 Acetokinase family; Region: Acetate_kinase; cl01029 340054003555 APSE-2 prophage: right integration boundary (attR) 340054003556 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 340054003557 P22-like integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial and phage integrases, including those similar to phage P22-like integrases, DLP12 and APSE-1; Region: INT_P22_C; cd01192 340054003558 Int/Topo IB signature motif; other site 340054003559 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 340054003560 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 340054003561 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 340054003562 ATP binding site [chemical binding]; other site 340054003563 putative Mg++ binding site [ion binding]; other site 340054003564 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054003565 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 340054003566 BRO family, N-terminal domain; Region: Bro-N; cl10591 340054003567 KilA-N domain; Region: KilA-N; pfam04383 340054003568 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 340054003569 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 340054003570 DNA binding site [nucleotide binding] 340054003571 active site 340054003572 catalytic site [active] 340054003573 DNA recombination protein RecA; Reviewed; Region: recA; PRK09519 340054003574 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 340054003575 Protein of unknown function (DUF1640); Region: DUF1640; pfam07798 340054003576 potential protein location (APSE-2 prophage; conserved hypothetical [Candidatus Hamiltonella defensa 5AT (Acyrthosiphon pisum)]) that overlaps RNA (tRNA-K) 340054003577 Protein of unknown function (DUF2815); Region: DUF2815; pfam10991 340054003578 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 340054003579 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 340054003580 non-specific DNA binding site [nucleotide binding]; other site 340054003581 salt bridge; other site 340054003582 sequence-specific DNA binding site [nucleotide binding]; other site 340054003583 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 340054003584 Catalytic site [active] 340054003585 putative Cro-like protein; Region: PHA00542 340054003586 Virulence-associated protein E; Region: VirE; pfam05272 340054003587 Phage antitermination protein Q; Region: Phage_antitermQ; pfam06530 340054003588 CdtB, the catalytic DNase I-like subunit of cytolethal distending toxin (CDT) protein; Region: CdtB; cd09081 340054003589 putative catalytic site [active] 340054003590 CdtC interface [polypeptide binding]; other site 340054003591 heterotrimer interface [polypeptide binding]; other site 340054003592 CdtA interface [polypeptide binding]; other site 340054003593 putative metal binding site [ion binding]; other site 340054003594 putative phosphate binding site [ion binding]; other site 340054003595 Phage holin family (Lysis protein S); Region: Phage_holin_3; cl04938 340054003596 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 340054003597 catalytic residues [active] 340054003598 Phage terminase large subunit; Region: Terminase_3; cl12054 340054003599 P22 coat protein - gene protein 5; Region: P22_CoatProtein; cl10302 340054003600 P22 tail accessory factor; Region: P22_Tail-4; pfam11650 340054003601 Phage stabilisation protein; Region: Phage_stabilise; pfam11134 340054003602 Protein of unknown function (DUF2824); Region: DUF2824; cl10279 340054003603 Head binding; Region: Head_binding; pfam09008 340054003604 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; cl05448 340054003605 APSE-2 prophage: left integration boundary (attL) 340054003606 integrase; Provisional; Region: int; PHA02601 340054003607 P22-like integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial and phage integrases, including those similar to phage P22-like integrases, DLP12 and APSE-1; Region: INT_P22_C; cd01192 340054003608 Int/Topo IB signature motif; other site 340054003609 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 340054003610 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054003611 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 340054003612 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 340054003613 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 340054003614 Integrase core domain; Region: rve; cl01316 340054003615 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054003616 Bacteriophage lambda integrase, N-terminal domain; Region: Phage_integ_N; pfam09003 340054003617 Peptidase C80 family; Region: Peptidase_C80; pfam11713 340054003618 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 340054003619 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 340054003620 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340054003621 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 340054003622 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 340054003623 DNA binding residues [nucleotide binding] 340054003624 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 340054003625 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 340054003626 putative peptidoglycan binding site; other site 340054003627 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 340054003628 homotrimer interaction site [polypeptide binding]; other site 340054003629 zinc binding site [ion binding]; other site 340054003630 CDP-binding sites; other site 340054003631 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 340054003632 substrate binding site; other site 340054003633 dimer interface; other site 340054003634 Septum formation initiator; Region: DivIC; cl11433 340054003635 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 340054003636 active site 340054003637 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 340054003638 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 340054003639 active site 340054003640 catalytic residues [active] 340054003641 metal binding site [ion binding]; metal-binding site 340054003642 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 340054003643 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 340054003644 putative active site [active] 340054003645 substrate binding site [chemical binding]; other site 340054003646 putative cosubstrate binding site; other site 340054003647 catalytic site [active] 340054003648 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 340054003649 substrate binding site [chemical binding]; other site 340054003650 16S rRNA methyltransferase B; Provisional; Region: PRK10901 340054003651 N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological...; Region: Methyltransferase_Sun; cd00620 340054003652 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 340054003653 S-adenosylmethionine binding site [chemical binding]; other site 340054003654 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 340054003655 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054003656 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 340054003657 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054003658 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 340054003659 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 340054003660 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 340054003661 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 340054003662 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 340054003663 RNA binding site [nucleotide binding]; other site 340054003664 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 340054003665 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 340054003666 inhibitor-cofactor binding pocket; inhibition site 340054003667 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340054003668 catalytic residue [active] 340054003669 rod shape-determining protein MreB; Provisional; Region: PRK13927 340054003670 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 340054003671 ATP binding site [chemical binding]; other site 340054003672 profilin binding site; other site 340054003673 rod shape-determining protein MreC; Provisional; Region: PRK13922 340054003674 rod shape-determining protein MreC; Region: MreC; pfam04085 340054003675 rod shape-determining protein MreD; Region: MreD; cl01087 340054003676 ribonuclease G; Provisional; Region: PRK11712 340054003677 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 340054003678 homodimer interface [polypeptide binding]; other site 340054003679 oligonucleotide binding site [chemical binding]; other site 340054003680 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 340054003681 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 340054003682 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 340054003683 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 340054003684 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 340054003685 S-adenosylmethionine binding site [chemical binding]; other site 340054003686 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 340054003687 SCP-2 sterol transfer family; Region: SCP2; cl01225 340054003688 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 340054003689 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 340054003690 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 340054003691 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 340054003692 pantothenate kinase; Provisional; Region: PRK05439 340054003693 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in...; Region: PanK; cd02025 340054003694 ATP-binding site [chemical binding]; other site 340054003695 CoA-binding site [chemical binding]; other site 340054003696 Mg2+-binding site [ion binding]; other site 340054003697 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 340054003698 DnaA N-terminal domain; Region: DnaA_N; pfam11638 340054003699 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 340054003700 Walker A motif; other site 340054003701 ATP binding site [chemical binding]; other site 340054003702 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054003703 Walker B motif; other site 340054003704 arginine finger; other site 340054003705 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 340054003706 DnaA box-binding interface [nucleotide binding]; other site 340054003707 DNA polymerase III subunit beta; Validated; Region: PRK05643 340054003708 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cd00140 340054003709 putative DNA binding surface [nucleotide binding]; other site 340054003710 dimer interface [polypeptide binding]; other site 340054003711 beta-clamp/clamp loader binding surface; other site 340054003712 beta-clamp/translesion DNA polymerase binding surface; other site 340054003713 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 340054003714 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 340054003715 Mg2+ binding site [ion binding]; other site 340054003716 G-X-G motif; other site 340054003717 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 340054003718 anchoring element; other site 340054003719 dimer interface [polypeptide binding]; other site 340054003720 ATP binding site [chemical binding]; other site 340054003721 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 340054003722 active site 340054003723 putative metal-binding site [ion binding]; other site 340054003724 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 340054003725 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional; Region: PRK15114 340054003726 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 340054003727 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 340054003728 active site 340054003729 dimerization interface [polypeptide binding]; other site 340054003730 fumarate hydratase; Reviewed; Region: fumC; PRK00485 340054003731 Class II fumarases; Region: Fumarase_classII; cd01362 340054003732 active site 340054003733 tetramer interface [polypeptide binding]; other site 340054003734 Quinolinate synthetase A protein; Region: NadA; cl00420 340054003735 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 340054003736 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 340054003737 dimer interface [polypeptide binding]; other site 340054003738 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 340054003739 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 340054003740 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03708 340054003741 outer membrane lipoprotein; Provisional; Region: PRK11023 340054003742 BON domain; Region: BON; cl02771 340054003743 BON domain; Region: BON; cl02771 340054003744 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 340054003745 dimer interface [polypeptide binding]; other site 340054003746 active site 340054003747 Restriction endonuclease; Region: Mrr_cat; cl00516 340054003748 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 340054003749 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 340054003750 substrate binding pocket [chemical binding]; other site 340054003751 chain length determination region; other site 340054003752 substrate-Mg2+ binding site; other site 340054003753 catalytic residues [active] 340054003754 aspartate-rich region 1; other site 340054003755 active site lid residues [active] 340054003756 aspartate-rich region 2; other site 340054003757 Putative transcription regulator (DUF1323); Region: DUF1323; pfam07037 340054003758 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340054003759 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340054003760 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 340054003761 Helix-turn-helix domains; Region: HTH; cl00088 340054003762 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 340054003763 substrate binding site [chemical binding]; other site 340054003764 dimerization interface [polypeptide binding]; other site 340054003765 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 340054003766 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 340054003767 active site 340054003768 interdomain interaction site; other site 340054003769 putative metal-binding site [ion binding]; other site 340054003770 nucleotide binding site [chemical binding]; other site 340054003771 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 340054003772 domain I; other site 340054003773 DNA binding groove [nucleotide binding] 340054003774 phosphate binding site [ion binding]; other site 340054003775 domain II; other site 340054003776 domain III; other site 340054003777 nucleotide binding site [chemical binding]; other site 340054003778 catalytic site [active] 340054003779 domain IV; other site 340054003780 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 340054003781 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 340054003782 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 340054003783 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 340054003784 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 340054003785 putative inner membrane peptidase; Provisional; Region: PRK11778 340054003786 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 340054003787 tandem repeat interface [polypeptide binding]; other site 340054003788 oligomer interface [polypeptide binding]; other site 340054003789 active site residues [active] 340054003790 Choline Kinase (ChoK). The ChoK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: ChoK; cd05151 340054003791 Phosphotransferase enzyme family; Region: APH; pfam01636 340054003792 active site 340054003793 ATP binding site [chemical binding]; other site 340054003794 substrate binding site [chemical binding]; other site 340054003795 dimer interface [polypeptide binding]; other site 340054003796 arginine transporter ATP-binding subunit; Provisional; Region: artP; PRK11124 340054003797 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 340054003798 Walker A/P-loop; other site 340054003799 ATP binding site [chemical binding]; other site 340054003800 Q-loop/lid; other site 340054003801 ABC transporter signature motif; other site 340054003802 Walker B; other site 340054003803 D-loop; other site 340054003804 H-loop/switch region; other site 340054003805 putative ABC transporter arginine-biding protein; Provisional; Region: PRK15007 340054003806 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 340054003807 substrate binding pocket [chemical binding]; other site 340054003808 membrane-bound complex binding site; other site 340054003809 hinge residues; other site 340054003810 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340054003811 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 340054003812 dimer interface [polypeptide binding]; other site 340054003813 conserved gate region; other site 340054003814 putative PBP binding loops; other site 340054003815 ABC-ATPase subunit interface; other site 340054003816 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 340054003817 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 340054003818 dimer interface [polypeptide binding]; other site 340054003819 conserved gate region; other site 340054003820 putative PBP binding loops; other site 340054003821 ABC-ATPase subunit interface; other site 340054003822 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 340054003823 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 340054003824 Protein of unknown function (DUF1471); Region: DUF1471; cl11507 340054003825 ABC-2 type transporter; Region: ABC2_membrane; cl11417 340054003826 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 340054003827 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054003828 Walker A/P-loop; other site 340054003829 ATP binding site [chemical binding]; other site 340054003830 Q-loop/lid; other site 340054003831 ABC transporter signature motif; other site 340054003832 Walker B; other site 340054003833 D-loop; other site 340054003834 H-loop/switch region; other site 340054003835 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 340054003836 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 340054003837 cell division protein FtsZ; Validated; Region: PRK09330 340054003838 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at...; Region: FtsZ_type1; cd02201 340054003839 nucleotide binding site [chemical binding]; other site 340054003840 SulA interaction site; other site 340054003841 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 340054003842 Cell division protein FtsA; Region: FtsA; cl11496 340054003843 Cell division protein FtsA; Region: FtsA; cl11496 340054003844 cell division protein FtsQ; Provisional; Region: PRK10775 340054003845 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 340054003846 Cell division protein FtsQ; Region: FtsQ; pfam03799 340054003847 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 340054003848 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 340054003849 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340054003850 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 340054003851 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 340054003852 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340054003853 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340054003854 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 340054003855 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 340054003856 active site 340054003857 homodimer interface [polypeptide binding]; other site 340054003858 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 340054003859 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03806 340054003860 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 340054003861 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340054003862 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340054003863 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 340054003864 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 340054003865 Mg++ binding site [ion binding]; other site 340054003866 putative catalytic motif [active] 340054003867 putative substrate binding site [chemical binding]; other site 340054003868 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed; Region: murF; PRK10773 340054003869 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 340054003870 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340054003871 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340054003872 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 340054003873 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 340054003874 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 340054003875 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 340054003876 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 340054003877 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 340054003878 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 340054003879 Septum formation initiator; Region: DivIC; cl11433 340054003880 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054003881 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 340054003882 cell division protein MraZ; Reviewed; Region: PRK00326 340054003883 MraZ protein; Region: MraZ; pfam02381 340054003884 MraZ protein; Region: MraZ; pfam02381 340054003885 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 340054003886 Helix-turn-helix domains; Region: HTH; cl00088 340054003887 The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; Region: PBP2_LeuO; cd08466 340054003888 putative substrate binding pocket [chemical binding]; other site 340054003889 putative dimerization interface [polypeptide binding]; other site 340054003890 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 340054003891 intimin-like protein SinH; Provisional; Region: PRK15318 340054003892 intimin-like protein SinH; Provisional; Region: PRK15318 340054003893 intimin-like protein SinH; Provisional; Region: PRK15318 340054003894 Protein of unknown function (DUF3442); Region: DUF3442; pfam11924 340054003895 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 340054003896 transcriptional regulator RcsB; Provisional; Region: PRK10840 340054003897 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340054003898 active site 340054003899 phosphorylation site [posttranslational modification] 340054003900 intermolecular recognition site; other site 340054003901 dimerization interface [polypeptide binding]; other site 340054003902 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054003903 DNA binding residues [nucleotide binding] 340054003904 dimerization interface [polypeptide binding]; other site 340054003905 DNA-binding transcriptional regulator CpxR; Provisional; Region: PRK10955 340054003906 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340054003907 active site 340054003908 phosphorylation site [posttranslational modification] 340054003909 intermolecular recognition site; other site 340054003910 dimerization interface [polypeptide binding]; other site 340054003911 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 340054003912 DNA binding site [nucleotide binding] 340054003913 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 340054003914 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 340054003915 putative active site [active] 340054003916 malate dehydrogenase; Provisional; Region: PRK13529 340054003917 Malic enzyme, N-terminal domain; Region: malic; pfam00390 340054003918 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 340054003919 NAD(P) binding site [chemical binding]; other site 340054003920 methionyl-tRNA synthetase; Reviewed; Region: PRK12268 340054003921 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 340054003922 active site 340054003923 HIGH motif; other site 340054003924 KMSKS motif; other site 340054003925 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 340054003926 tRNA binding surface [nucleotide binding]; other site 340054003927 anticodon binding site; other site 340054003928 antiporter inner membrane protein; Provisional; Region: PRK11670 340054003929 MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions...; Region: MRP-like; cd02037 340054003930 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340054003931 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 340054003932 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 340054003933 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 340054003934 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 340054003935 putative metal binding site; other site 340054003936 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 340054003937 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 340054003938 active site 340054003939 (T/H)XGH motif; other site 340054003940 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 340054003941 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 340054003942 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 340054003943 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 340054003944 Predicted ATPase [General function prediction only]; Region: COG1485 340054003945 Protein of unknown function (DUF1043); Region: DUF1043; cl11473 340054003946 serine endoprotease; Provisional; Region: PRK10898 340054003947 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 340054003948 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 340054003949 protein binding site [polypeptide binding]; other site 340054003950 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 340054003951 aromatic amino acid transport protein; Region: araaP; TIGR00837 340054003952 bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein; Provisional; Region: PRK11109 340054003953 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 340054003954 active site 340054003955 phosphorylation site [posttranslational modification] 340054003956 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 340054003957 dimerization domain swap beta strand [polypeptide binding]; other site 340054003958 regulatory protein interface [polypeptide binding]; other site 340054003959 active site 340054003960 regulatory phosphorylation site [posttranslational modification]; other site 340054003961 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 340054003962 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 340054003963 putative substrate binding site [chemical binding]; other site 340054003964 putative ATP binding site [chemical binding]; other site 340054003965 PTS system fructose-specific transporter subunits IIBC; Provisional; Region: PRK10712 340054003966 N-terminal domain of the phosphotransferase system fructose-specific component IIB [Carbohydrate transport and metabolism]; Region: COG3925 340054003967 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 340054003968 active site 340054003969 P-loop; other site 340054003970 phosphorylation site [posttranslational modification] 340054003971 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 340054003972 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 340054003973 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 340054003974 pyridoxal 5'-phosphate binding site [chemical binding]; other site 340054003975 homodimer interface [polypeptide binding]; other site 340054003976 catalytic residue [active] 340054003977 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 340054003978 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 340054003979 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 340054003980 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 340054003981 active site 340054003982 dimer interface [polypeptide binding]; other site 340054003983 motif 1; other site 340054003984 motif 2; other site 340054003985 motif 3; other site 340054003986 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 340054003987 anticodon binding site; other site 340054003988 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 340054003989 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 340054003990 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 340054003991 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 340054003992 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 340054003993 23S rRNA binding site [nucleotide binding]; other site 340054003994 L21 binding site [polypeptide binding]; other site 340054003995 L13 binding site [polypeptide binding]; other site 340054003996 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 340054003997 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 340054003998 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 340054003999 dimer interface [polypeptide binding]; other site 340054004000 motif 1; other site 340054004001 active site 340054004002 motif 2; other site 340054004003 motif 3; other site 340054004004 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 340054004005 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 340054004006 putative tRNA-binding site [nucleotide binding]; other site 340054004007 B3/4 domain; Region: B3_4; cl11458 340054004008 tRNA synthetase B5 domain; Region: B5; cl08394 340054004009 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 340054004010 dimer interface [polypeptide binding]; other site 340054004011 motif 1; other site 340054004012 motif 3; other site 340054004013 motif 2; other site 340054004014 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 340054004015 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 340054004016 IHF - DNA interface [nucleotide binding]; other site 340054004017 IHF dimer interface [polypeptide binding]; other site 340054004018 KicB killing factor; Region: KicB; cl11468 340054004019 MukE-like family; Region: MukE; cl11471 340054004020 cell division protein MukB; Provisional; Region: mukB; PRK04863 340054004021 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054004022 Putative exonuclease SbcCD, C subunit; Region: SbcCD_C; pfam13558 340054004023 murein L,D-transpeptidase; Provisional; Region: PRK10594 340054004024 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 340054004025 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 340054004026 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 340054004027 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 340054004028 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 340054004029 active site 340054004030 Zn binding site [ion binding]; other site 340054004031 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 340054004032 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 340054004033 ATP binding site [chemical binding]; other site 340054004034 active site 340054004035 substrate binding site [chemical binding]; other site 340054004036 lipoprotein; Provisional; Region: PRK11679 340054004037 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 340054004038 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 340054004039 dihydrodipicolinate synthase; Region: dapA; TIGR00674 340054004040 dimer interface [polypeptide binding]; other site 340054004041 active site 340054004042 catalytic residue [active] 340054004043 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 340054004044 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 340054004045 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 340054004046 alphaNTD homodimer interface [polypeptide binding]; other site 340054004047 alphaNTD - beta interaction site [polypeptide binding]; other site 340054004048 alphaNTD - beta' interaction site [polypeptide binding]; other site 340054004049 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 340054004050 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 340054004051 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 340054004052 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 340054004053 RNA binding surface [nucleotide binding]; other site 340054004054 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 340054004055 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 340054004056 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 340054004057 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 340054004058 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 340054004059 SecY translocase; Region: SecY; pfam00344 340054004060 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 340054004061 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 340054004062 23S rRNA binding site [nucleotide binding]; other site 340054004063 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 340054004064 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 340054004065 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 340054004066 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 340054004067 23S rRNA interface [nucleotide binding]; other site 340054004068 L21e interface [polypeptide binding]; other site 340054004069 5S rRNA interface [nucleotide binding]; other site 340054004070 L27 interface [polypeptide binding]; other site 340054004071 L5 interface [polypeptide binding]; other site 340054004072 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 340054004073 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 340054004074 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 340054004075 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 340054004076 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 340054004077 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 340054004078 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 340054004079 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 340054004080 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 340054004081 KOW motif; Region: KOW; cl00354 340054004082 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 340054004083 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 340054004084 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cl09943 340054004085 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 340054004086 23S rRNA interface [nucleotide binding]; other site 340054004087 5S rRNA interface [nucleotide binding]; other site 340054004088 putative antibiotic binding site [chemical binding]; other site 340054004089 L25 interface [polypeptide binding]; other site 340054004090 L27 interface [polypeptide binding]; other site 340054004091 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 340054004092 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 340054004093 G-X-X-G motif; other site 340054004094 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 340054004095 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 340054004096 protein-rRNA interface [nucleotide binding]; other site 340054004097 putative translocon binding site; other site 340054004098 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 340054004099 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 340054004100 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 340054004101 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 340054004102 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 340054004103 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 340054004104 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 340054004105 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 340054004106 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 340054004107 ABC-ATPase subunit interface; other site 340054004108 dimer interface [polypeptide binding]; other site 340054004109 putative PBP binding regions; other site 340054004110 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 340054004111 putative substrate translocation pore; other site 340054004112 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004113 NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain; Region: Octopine_DH; pfam02317 340054004114 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 340054004115 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340054004116 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 340054004117 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 340054004118 catalytic residue [active] 340054004119 FeoA domain; Region: FeoA; cl00838 340054004120 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 340054004121 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 340054004122 G1 box; other site 340054004123 GTP/Mg2+ binding site [chemical binding]; other site 340054004124 Switch I region; other site 340054004125 G2 box; other site 340054004126 G3 box; other site 340054004127 Switch II region; other site 340054004128 G4 box; other site 340054004129 G5 box; other site 340054004130 Nucleoside recognition; Region: Gate; cl00486 340054004131 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 340054004132 Nucleoside recognition; Region: Gate; cl00486 340054004133 Helix-turn-helix domains; Region: HTH; cl00088 340054004134 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 340054004135 dimer interface [polypeptide binding]; other site 340054004136 Citrate synthase; Region: Citrate_synt; pfam00285 340054004137 active site 340054004138 citrylCoA binding site [chemical binding]; other site 340054004139 NADH binding [chemical binding]; other site 340054004140 cationic pore residues; other site 340054004141 oxalacetate/citrate binding site [chemical binding]; other site 340054004142 coenzyme A binding site [chemical binding]; other site 340054004143 catalytic triad [active] 340054004144 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 340054004145 Iron-sulfur protein interface; other site 340054004146 proximal quinone binding site [chemical binding]; other site 340054004147 SdhD (CybS) interface [polypeptide binding]; other site 340054004148 proximal heme binding site [chemical binding]; other site 340054004149 Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, transmembrane subunits; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR; Region: SQR_QFR_TM; cl00881 340054004150 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08958 340054004151 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004152 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 340054004153 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 340054004154 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 340054004155 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 340054004156 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 340054004157 TPP-binding site [chemical binding]; other site 340054004158 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 340054004159 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 340054004160 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 340054004161 E3 interaction surface; other site 340054004162 lipoyl attachment site [posttranslational modification]; other site 340054004163 e3 binding domain; Region: E3_binding; pfam02817 340054004164 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 340054004165 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 340054004166 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340054004167 CoA-ligase; Region: Ligase_CoA; cl02894 340054004168 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 340054004169 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004170 CoA-ligase; Region: Ligase_CoA; cl02894 340054004171 Peptidase S8 family domain in Autotransporter serine proteases; Region: Peptidases_S8_Autotransporter_serine_protease_like; cd04848 340054004172 putative active site [active] 340054004173 AIDA autotransporter-like protein ShdA; Provisional; Region: PRK15319 340054004174 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; cl15373 340054004175 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340054004176 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include bacterial ATP-dependent...; Region: Bacterial_PFK; cd00763 340054004177 active site 340054004178 ADP/pyrophosphate binding site [chemical binding]; other site 340054004179 dimerization interface [polypeptide binding]; other site 340054004180 allosteric effector site; other site 340054004181 fructose-1,6-bisphosphate binding site; other site 340054004182 elongation factor P; Validated; Region: PRK00529 340054004183 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 340054004184 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 340054004185 RNA binding site [nucleotide binding]; other site 340054004186 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 340054004187 RNA binding site [nucleotide binding]; other site 340054004188 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 340054004189 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cl15377 340054004190 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 340054004191 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 340054004192 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 340054004193 homodimer interface [polypeptide binding]; other site 340054004194 NADP binding site [chemical binding]; other site 340054004195 substrate binding site [chemical binding]; other site 340054004196 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 340054004197 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 340054004198 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 340054004199 catalytic residue [active] 340054004200 homoserine kinase; Provisional; Region: PRK01212 340054004201 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 340054004202 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 340054004203 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 340054004204 AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli...; Region: AAK_AK-HSDH; cd04257 340054004205 putative catalytic residues [active] 340054004206 putative nucleotide binding site [chemical binding]; other site 340054004207 putative aspartate binding site [chemical binding]; other site 340054004208 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 340054004209 dimer interface [polypeptide binding]; other site 340054004210 putative threonine allosteric regulatory site; other site 340054004211 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 340054004212 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004213 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 340054004214 two-component response regulator; Provisional; Region: PRK11173 340054004215 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340054004216 active site 340054004217 phosphorylation site [posttranslational modification] 340054004218 intermolecular recognition site; other site 340054004219 dimerization interface [polypeptide binding]; other site 340054004220 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 340054004221 DNA binding site [nucleotide binding] 340054004222 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054004223 Integrase core domain; Region: rve; cl01316 340054004224 MutH is a 28kD endonuclease involved in methyl-directed DNA mismatch repair in gram negative bacteria. MutH is both sequence-specific and methylation-specific, introducing a nick in the unmethylated strand of a hemi-methylated d(GATC) DNA duplex. MutH...; Region: MutH_Sau3AI; cd00583 340054004225 putative DNA-binding cleft [nucleotide binding]; other site 340054004226 putative DNA clevage site; other site 340054004227 molecular lever; other site 340054004228 threonine and homoserine efflux system; Provisional; Region: PRK10532 340054004229 EamA-like transporter family; Region: EamA; cl01037 340054004230 glutathione reductase; Validated; Region: PRK06116 340054004231 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340054004232 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340054004233 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054004234 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 340054004235 hypothetical protein; Reviewed; Region: PRK00024 340054004236 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 340054004237 MPN+ (JAMM) motif; other site 340054004238 Zinc-binding site [ion binding]; other site 340054004239 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 340054004240 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 340054004241 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 340054004242 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 340054004243 dimerization interface [polypeptide binding]; other site 340054004244 active site 340054004245 DsrC like protein; Region: DsrC; cl01101 340054004246 exonuclease I; Provisional; Region: sbcB; PRK11779 340054004247 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 340054004248 active site 340054004249 catalytic site [active] 340054004250 substrate binding site [chemical binding]; other site 340054004251 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 340054004252 HemN family oxidoreductase; Provisional; Region: PRK05660 340054004253 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 340054004254 FeS/SAM binding site; other site 340054004255 HemN C-terminal domain; Region: HemN_C; pfam06969 340054004256 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 340054004257 active site 340054004258 dimerization interface [polypeptide binding]; other site 340054004259 YGGT family; Region: YGGT; cl00508 340054004260 YGGT family; Region: YGGT; cl00508 340054004261 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 340054004262 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 340054004263 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 340054004264 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine...; Region: IMPDH; cd00381 340054004265 active site 340054004266 GMP synthase; Reviewed; Region: guaA; PRK00074 340054004267 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 340054004268 AMP/PPi binding site [chemical binding]; other site 340054004269 candidate oxyanion hole; other site 340054004270 catalytic triad [active] 340054004271 potential glutamine specificity residues [chemical binding]; other site 340054004272 The C-terminal domain of GMP synthetase. It contains two subdomains; the ATP pyrophosphatase domain which closes to the N-termial and the dimerization domain at C-terminal end. The ATP-PPase is a twisted, five-stranded parallel beta-sheet sandwiched...; Region: GMP_synthase_C; cd01997 340054004273 ATP Binding subdomain [chemical binding]; other site 340054004274 Ligand Binding sites [chemical binding]; other site 340054004275 Dimerization subdomain; other site 340054004276 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 340054004277 tetramer interfaces [polypeptide binding]; other site 340054004278 binuclear metal-binding site [ion binding]; other site 340054004279 thiamine monophosphate kinase; Provisional; Region: PRK05731 340054004280 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 340054004281 ATP binding site [chemical binding]; other site 340054004282 dimerization interface [polypeptide binding]; other site 340054004283 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 340054004284 putative RNA binding site [nucleotide binding]; other site 340054004285 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 340054004286 homopentamer interface [polypeptide binding]; other site 340054004287 active site 340054004288 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054004289 Integrase core domain; Region: rve; cl01316 340054004290 Peptidase C80 family; Region: Peptidase_C80; pfam11713 340054004291 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054004292 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054004293 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054004294 putative active site [active] 340054004295 putative NTP binding site [chemical binding]; other site 340054004296 putative nucleic acid binding site [nucleotide binding]; other site 340054004297 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054004298 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054004299 active site 340054004300 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 340054004301 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 340054004302 Walker A motif; other site 340054004303 ATP binding site [chemical binding]; other site 340054004304 Walker B motif; other site 340054004305 arginine finger; other site 340054004306 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 340054004307 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 340054004308 RuvA N terminal domain; Region: RuvA_N; pfam01330 340054004309 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 340054004310 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 340054004311 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 340054004312 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004313 P-loop ATPase protein family; Region: ATP_bind_2; cl15794 340054004314 Predicted P-loop-containing kinase [General function prediction only]; Region: COG1660 340054004315 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 340054004316 active site 340054004317 phosphorylation site [posttranslational modification] 340054004318 lipopolysaccharide ABC transporter ATP-binding protein; Provisional; Region: PRK10895 340054004319 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 340054004320 Walker A/P-loop; other site 340054004321 ATP binding site [chemical binding]; other site 340054004322 Q-loop/lid; other site 340054004323 ABC transporter signature motif; other site 340054004324 Walker B; other site 340054004325 D-loop; other site 340054004326 H-loop/switch region; other site 340054004327 OstA-like protein; Region: OstA; cl00844 340054004328 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 340054004329 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 340054004330 Low specificity phosphatase (HAD superfamily) [General function prediction only]; Region: COG1778 340054004331 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 340054004332 active site 340054004333 motif I; other site 340054004334 motif II; other site 340054004335 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 340054004336 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 340054004337 putative active site [active] 340054004338 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 340054004339 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 340054004340 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 340054004341 Walker A/P-loop; other site 340054004342 ATP binding site [chemical binding]; other site 340054004343 Q-loop/lid; other site 340054004344 ABC transporter signature motif; other site 340054004345 Walker B; other site 340054004346 D-loop; other site 340054004347 H-loop/switch region; other site 340054004348 Permease; Region: Permease; cl00510 340054004349 mce related protein; Region: MCE; pfam02470 340054004350 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 340054004351 BolA-like protein; Region: BolA; cl00386 340054004352 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 340054004353 UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes enolpyruvyl transfer as part of the first step in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. The reaction is phosphoenolpyruvate + UDP-N-acetyl-D-glucosamine =...; Region: UdpNAET; cd01555 340054004354 hinge; other site 340054004355 active site 340054004356 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 340054004357 active site clefts [active] 340054004358 zinc binding site [ion binding]; other site 340054004359 dimer interface [polypeptide binding]; other site 340054004360 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 340054004361 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 340054004362 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 340054004363 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 340054004364 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 340054004365 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 340054004366 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 340054004367 active site 340054004368 substrate binding site [chemical binding]; other site 340054004369 metal binding site [ion binding]; metal-binding site 340054004370 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 340054004371 dihydropteroate synthase; Region: DHPS; TIGR01496 340054004372 substrate binding pocket [chemical binding]; other site 340054004373 dimer interface [polypeptide binding]; other site 340054004374 inhibitor binding site; inhibition site 340054004375 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 340054004376 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 340054004377 Walker A motif; other site 340054004378 ATP binding site [chemical binding]; other site 340054004379 Walker B motif; other site 340054004380 arginine finger; other site 340054004381 Peptidase family M41; Region: Peptidase_M41; pfam01434 340054004382 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 340054004383 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 340054004384 S-adenosylmethionine binding site [chemical binding]; other site 340054004385 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 340054004386 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 340054004387 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 340054004388 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 340054004389 DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]; Region: DjlA; COG1076 340054004390 putative metal binding site [ion binding]; other site 340054004391 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 340054004392 HSP70 interaction site [polypeptide binding]; other site 340054004393 Protein of unknown function (DUF520); Region: DUF520; cl00723 340054004394 Anthrax toxin LF subunit; Region: Anthrax_toxA; pfam03497 340054004395 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340054004396 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 340054004397 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340054004398 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 340054004399 Catalytic site [active] 340054004400 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 340054004401 Transposase domain (DUF772); Region: DUF772; cl15789 340054004402 Transposase domain (DUF772); Region: DUF772; cl15789 340054004403 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 340054004404 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 340054004405 PAS fold; Region: PAS_4; pfam08448 340054004406 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054004407 DNA binding residues [nucleotide binding] 340054004408 dimerization interface [polypeptide binding]; other site 340054004409 Domain of unknown function (DUF378); Region: DUF378; cl00943 340054004410 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004411 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004412 NAD(P) binding site [chemical binding]; other site 340054004413 active site 340054004414 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 340054004415 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 340054004416 D-pathway; other site 340054004417 Putative ubiquinol binding site [chemical binding]; other site 340054004418 Low-spin heme (heme b) binding site [chemical binding]; other site 340054004419 Putative water exit pathway; other site 340054004420 Binuclear center (heme o3/CuB) [ion binding]; other site 340054004421 K-pathway; other site 340054004422 Putative proton exit pathway; other site 340054004423 flagellar biosynthesis regulator FlhF; Provisional; Region: flhF; PRK14723 340054004424 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054004425 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054004426 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054004427 putative active site [active] 340054004428 putative NTP binding site [chemical binding]; other site 340054004429 putative nucleic acid binding site [nucleotide binding]; other site 340054004430 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054004431 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054004432 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054004433 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054004434 putative active site [active] 340054004435 putative NTP binding site [chemical binding]; other site 340054004436 putative nucleic acid binding site [nucleotide binding]; other site 340054004437 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054004438 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054004439 active site 340054004440 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054004441 active site 340054004442 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 340054004443 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 340054004444 active site 340054004445 DNA binding site [nucleotide binding] 340054004446 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 340054004447 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 340054004448 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 340054004449 trmE is a tRNA modification GTPase; Region: trmE; cd04164 340054004450 G1 box; other site 340054004451 GTP/Mg2+ binding site [chemical binding]; other site 340054004452 Switch I region; other site 340054004453 G2 box; other site 340054004454 Switch II region; other site 340054004455 G3 box; other site 340054004456 G4 box; other site 340054004457 G5 box; other site 340054004458 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 340054004459 membrane protein insertase; Provisional; Region: PRK01318 340054004460 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 340054004461 Haemolytic domain; Region: Haemolytic; cl00506 340054004462 Ribonuclease P; Region: Ribonuclease_P; cl00457 340054004463 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 340054004464 Peptidase C80 family; Region: Peptidase_C80; pfam11713 340054004465 potential frameshift: common BLAST hit: gi|170023074|ref|YP_001719579.1| virulence determinant 340054004466 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 340054004467 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 340054004468 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 340054004469 FMN binding site [chemical binding]; other site 340054004470 active site 340054004471 catalytic residues [active] 340054004472 substrate binding site [chemical binding]; other site 340054004473 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054004474 active site 340054004475 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054004476 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054004477 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054004478 putative active site [active] 340054004479 putative NTP binding site [chemical binding]; other site 340054004480 putative nucleic acid binding site [nucleotide binding]; other site 340054004481 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054004482 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054004483 active site 340054004484 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054004485 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054004486 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054004487 putative active site [active] 340054004488 putative NTP binding site [chemical binding]; other site 340054004489 putative nucleic acid binding site [nucleotide binding]; other site 340054004490 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054004491 undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphate transferase; Provisional; Region: PRK15119 340054004492 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 340054004493 Mg++ binding site [ion binding]; other site 340054004494 putative catalytic motif [active] 340054004495 substrate binding site [chemical binding]; other site 340054004496 transcription termination factor Rho; Provisional; Region: rho; PRK09376 340054004497 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 340054004498 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 340054004499 RNA binding site [nucleotide binding]; other site 340054004500 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 340054004501 multimer interface [polypeptide binding]; other site 340054004502 Walker A motif; other site 340054004503 ATP binding site [chemical binding]; other site 340054004504 Walker B motif; other site 340054004505 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 340054004506 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 340054004507 purine monophosphate binding site [chemical binding]; other site 340054004508 dimer interface [polypeptide binding]; other site 340054004509 putative catalytic residues [active] 340054004510 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 340054004511 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 340054004512 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 340054004513 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 340054004514 ATP-grasp domain; Region: ATP-grasp_4; cl03087 340054004515 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 340054004516 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 340054004517 Cation transport protein; Region: TrkH; cl10514 340054004518 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 340054004519 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 340054004520 HIGH motif; other site 340054004521 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 340054004522 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 340054004523 active site 340054004524 KMSKS motif; other site 340054004525 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 340054004526 tRNA binding surface [nucleotide binding]; other site 340054004527 Lipopolysaccharide-assembly; Region: LptE; cl01125 340054004528 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 340054004529 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 340054004530 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 340054004531 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 340054004532 active site 340054004533 (T/H)XGH motif; other site 340054004534 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 340054004535 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004536 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 340054004537 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 340054004538 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 340054004539 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 340054004540 E3 interaction surface; other site 340054004541 lipoyl attachment site [posttranslational modification]; other site 340054004542 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 340054004543 E3 interaction surface; other site 340054004544 lipoyl attachment site [posttranslational modification]; other site 340054004545 e3 binding domain; Region: E3_binding; pfam02817 340054004546 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 340054004547 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 340054004548 Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative...; Region: TPP_E1_EcPDC_like; cd02017 340054004549 dimer interface [polypeptide binding]; other site 340054004550 TPP-binding site [chemical binding]; other site 340054004551 Integrase core domain; Region: rve; cl01316 340054004552 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054004553 AntA/AntB antirepressor; Region: AntA; cl01430 340054004554 BRO family, N-terminal domain; Region: Bro-N; cl10591 340054004555 BRO family, N-terminal domain; Region: Bro-N; cl10591 340054004556 Staphylococcal nuclease homologues; Region: SNc; smart00318 340054004557 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 340054004558 Catalytic site; other site 340054004559 DNA-binding transcriptional activator EvgA; Provisional; Region: PRK09958 340054004560 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 340054004561 active site 340054004562 phosphorylation site [posttranslational modification] 340054004563 intermolecular recognition site; other site 340054004564 dimerization interface [polypeptide binding]; other site 340054004565 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054004566 DNA binding residues [nucleotide binding] 340054004567 dimerization interface [polypeptide binding]; other site 340054004568 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 340054004569 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 340054004570 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 340054004571 putative active site [active] 340054004572 putative substrate binding site [chemical binding]; other site 340054004573 putative cosubstrate binding site; other site 340054004574 catalytic site [active] 340054004575 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 340054004576 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 340054004577 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 340054004578 Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins; Region: PLDc_EcCLS_like_1; cd09152 340054004579 putative active site [active] 340054004580 catalytic site [active] 340054004581 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins; Region: PLDc_EcCLS_like_2; cd09158 340054004582 putative active site [active] 340054004583 catalytic site [active] 340054004584 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 340054004585 Gram-negative bacterial tonB protein; Region: TonB; cl10048 340054004586 Intracellular septation protein A; Region: IspA; cl01098 340054004587 Uncharacterized protein family (UPF0259); Region: UPF0259; cl11642 340054004588 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 340054004589 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004590 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 340054004591 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 340054004592 active site 340054004593 O-Antigen ligase; Region: Wzy_C; cl04850 340054004594 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 340054004595 tetramer (dimer of dimers) interface [polypeptide binding]; other site 340054004596 active site 340054004597 dimer interface [polypeptide binding]; other site 340054004598 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 340054004599 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004600 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 340054004601 L-serine binding site [chemical binding]; other site 340054004602 ACT domain interface; other site 340054004603 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 340054004604 Cell division protein ZapA; Region: ZapA; cl01146 340054004605 putative global regulator; Reviewed; Region: PRK09559 340054004606 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 340054004607 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004608 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 340054004609 hypothetical protein; Provisional; Region: PRK04946 340054004610 Smr domain; Region: Smr; cl02619 340054004611 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 340054004612 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 340054004613 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340054004614 active site 340054004615 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 340054004616 putative active site [active] 340054004617 catalytic residue [active] 340054004618 TfoX N-terminal domain; Region: TfoX_N; cl01167 340054004619 TfoX N-terminal domain; Region: TfoX_N; cl01167 340054004620 Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism]; Region: Apt; COG0503 340054004621 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 340054004622 active site 340054004623 DNA polymerase III subunits gamma and tau; Validated; Region: PRK07994 340054004624 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 340054004625 Walker A motif; other site 340054004626 ATP binding site [chemical binding]; other site 340054004627 Walker B motif; other site 340054004628 arginine finger; other site 340054004629 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 340054004630 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 340054004631 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 340054004632 recombination protein RecR; Reviewed; Region: recR; PRK00076 340054004633 RecR protein; Region: RecR; pfam02132 340054004634 TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a...; Region: TOPRIM_recR; cd01025 340054004635 putative active site [active] 340054004636 putative metal-binding site [ion binding]; other site 340054004637 tetramer interface [polypeptide binding]; other site 340054004638 heat shock protein 90; Provisional; Region: PRK05218 340054004639 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 340054004640 ATP binding site [chemical binding]; other site 340054004641 Mg2+ binding site [ion binding]; other site 340054004642 G-X-G motif; other site 340054004643 adenylate kinase; Reviewed; Region: adk; PRK00279 340054004644 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 340054004645 AMP-binding site [chemical binding]; other site 340054004646 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 340054004647 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 340054004648 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 340054004649 SEC-C motif; Region: SEC-C; pfam02810 340054004650 Protein of unknown function (DUF721); Region: DUF721; cl02324 340054004651 asparagine synthetase B; Provisional; Region: asnB; PRK09431 340054004652 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 340054004653 active site 340054004654 dimer interface [polypeptide binding]; other site 340054004655 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 340054004656 Ligand Binding Site [chemical binding]; other site 340054004657 Molecular Tunnel; other site 340054004658 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 340054004659 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 340054004660 Sulfatase; Region: Sulfatase; cl10460 340054004661 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 340054004662 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 340054004663 NAD binding site [chemical binding]; other site 340054004664 homotetramer interface [polypeptide binding]; other site 340054004665 homodimer interface [polypeptide binding]; other site 340054004666 substrate binding site [chemical binding]; other site 340054004667 active site 340054004668 antimicrobial peptide ABC system ATP-binding protein SapF; Provisional; Region: PRK15112 340054004669 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 340054004670 Walker A/P-loop; other site 340054004671 ATP binding site [chemical binding]; other site 340054004672 Q-loop/lid; other site 340054004673 ABC transporter signature motif; other site 340054004674 Walker B; other site 340054004675 D-loop; other site 340054004676 H-loop/switch region; other site 340054004677 antimicrobial peptide ABC transporter ATP-binding protein; Provisional; Region: PRK15093 340054004678 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 340054004679 Walker A/P-loop; other site 340054004680 ATP binding site [chemical binding]; other site 340054004681 Q-loop/lid; other site 340054004682 ABC transporter signature motif; other site 340054004683 Walker B; other site 340054004684 D-loop; other site 340054004685 H-loop/switch region; other site 340054004686 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 340054004687 antimicrobial peptide ABC transporter permease SapC; Provisional; Region: PRK15111 340054004688 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 340054004689 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 340054004690 antimicrobial peptide ABC transporter permease SapB; Provisional; Region: PRK15110 340054004691 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 340054004692 putative PBP binding loops; other site 340054004693 dimer interface [polypeptide binding]; other site 340054004694 ABC-ATPase subunit interface; other site 340054004695 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 340054004696 dimer interface [polypeptide binding]; other site 340054004697 active site 340054004698 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 340054004699 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 340054004700 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 340054004701 DNA binding residues [nucleotide binding] 340054004702 FMN reductase; Validated; Region: fre; PRK08051 340054004703 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN; Region: flavin_oxioreductase; cd06189 340054004704 FAD binding pocket [chemical binding]; other site 340054004705 FAD binding motif [chemical binding]; other site 340054004706 phosphate binding motif [ion binding]; other site 340054004707 beta-alpha-beta structure motif; other site 340054004708 NAD binding pocket [chemical binding]; other site 340054004709 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 340054004710 transcriptional activator RfaH; Provisional; Region: rfaH; PRK09014 340054004711 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 340054004712 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 340054004713 dimer interface [polypeptide binding]; other site 340054004714 active site 340054004715 aspartate-rich active site metal binding site; other site 340054004716 allosteric magnesium binding site [ion binding]; other site 340054004717 Schiff base residues; other site 340054004718 Protein of unknown function (DUF615); Region: DUF615; cl01147 340054004719 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl00503 340054004720 Protein of unknown function (DUF1190); Region: DUF1190; cl10031 340054004721 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 340054004722 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 340054004723 S-adenosylmethionine binding site [chemical binding]; other site 340054004724 peptide chain release factor 1; Validated; Region: prfA; PRK00591 340054004725 RF-1 domain; Region: RF-1; cl02875 340054004726 RF-1 domain; Region: RF-1; cl02875 340054004727 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 340054004728 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 340054004729 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 340054004730 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 340054004731 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 340054004732 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 340054004733 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 340054004734 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 340054004735 ABC-ATPase subunit interface; other site 340054004736 dimer interface [polypeptide binding]; other site 340054004737 putative PBP binding regions; other site 340054004738 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 340054004739 ABC-ATPase subunit interface; other site 340054004740 dimer interface [polypeptide binding]; other site 340054004741 putative PBP binding regions; other site 340054004742 manganese/iron transporter ATP-binding protein; Provisional; Region: PRK15056 340054004743 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 340054004744 Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that...; Region: PsaA; cd01137 340054004745 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 340054004746 metal binding site [ion binding]; metal-binding site 340054004747 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 340054004748 putative catalytic site [active] 340054004749 putative metal binding site [ion binding]; other site 340054004750 putative phosphate binding site [ion binding]; other site 340054004751 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 340054004752 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 340054004753 N-acetyl-D-glucosamine binding site [chemical binding]; other site 340054004754 catalytic residue [active] 340054004755 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 340054004756 putative peptidoglycan binding site; other site 340054004757 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 340054004758 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 340054004759 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004760 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 340054004761 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 340054004762 N-terminal plug; other site 340054004763 ligand-binding site [chemical binding]; other site 340054004764 Haem utilisation ChuX/HutX; Region: ChuX_HutX; cl01509 340054004765 Haem utilisation ChuX/HutX; Region: ChuX_HutX; cl01509 340054004766 Hemin binding protein HutB. These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a...; Region: HutB; cd01149 340054004767 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 340054004768 putative hemin binding site; other site 340054004769 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 340054004770 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 340054004771 ABC-ATPase subunit interface; other site 340054004772 dimer interface [polypeptide binding]; other site 340054004773 putative PBP binding regions; other site 340054004774 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 340054004775 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 340054004776 Walker A/P-loop; other site 340054004777 ATP binding site [chemical binding]; other site 340054004778 Q-loop/lid; other site 340054004779 ABC transporter signature motif; other site 340054004780 Walker B; other site 340054004781 D-loop; other site 340054004782 H-loop/switch region; other site 340054004783 BRO family, N-terminal domain; Region: Bro-N; cl10591 340054004784 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054004785 Helix-turn-helix domains; Region: HTH; cl00088 340054004786 Integrase core domain; Region: rve; cl01316 340054004787 Transposase domain (DUF772); Region: DUF772; cl15789 340054004788 Transposase domain (DUF772); Region: DUF772; cl15789 340054004789 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 340054004790 ParG; Region: ParG; pfam09274 340054004791 ParA-like protein; Provisional; Region: PHA02518 340054004792 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 340054004793 P-loop; other site 340054004794 Magnesium ion binding site [ion binding]; other site 340054004795 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 340054004796 oligomeric interface; other site 340054004797 putative active site [active] 340054004798 homodimer interface [polypeptide binding]; other site 340054004799 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 340054004800 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 340054004801 multiple promoter invertase; Provisional; Region: mpi; PRK13413 340054004802 catalytic residues [active] 340054004803 catalytic nucleophile [active] 340054004804 Presynaptic Site I dimer interface [polypeptide binding]; other site 340054004805 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 340054004806 Synaptic Flat tetramer interface [polypeptide binding]; other site 340054004807 Synaptic Site I dimer interface [polypeptide binding]; other site 340054004808 DNA binding site [nucleotide binding] 340054004809 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 340054004810 DNA-binding interface [nucleotide binding]; DNA binding site 340054004811 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 340054004812 Coenzyme A binding pocket [chemical binding]; other site 340054004813 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 340054004814 Transposase; Region: DEDD_Tnp_IS110; pfam01548 340054004815 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 340054004816 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 340054004817 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 340054004818 Sulfatase; Region: Sulfatase; cl10460 340054004819 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 340054004820 active site 340054004821 catalytic site [active] 340054004822 potential protein location (conserved hypothetical protein) that overlaps protein (addiction module) 340054004823 Plasmid stability protein [General function prediction only]; Region: StbC; COG4691 340054004824 Protein of unknown function (DUF342); Region: DUF342; pfam03961 340054004825 DDE domain; Region: DDE_Tnp_IS240; pfam13610 340054004826 Integrase core domain; Region: rve; cl01316 340054004827 ParA-like protein; Provisional; Region: PHA02518 340054004828 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 340054004829 Magnesium ion binding site [ion binding]; other site 340054004830 conjugal transfer relaxosome component TraJ; Provisional; Region: PRK13877 340054004831 Integrase core domain; Region: rve; cl01316 340054004832 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054004833 Domain of unknown function (DUF4415); Region: DUF4415; cl01401 340054004834 Phage-related tail fibre protein [General function prediction only]; Region: COG5301 340054004835 Integrase core domain; Region: rve; cl01316 340054004836 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054004837 Domain of unknown function (DUF4415); Region: DUF4415; cl01401 340054004838 Phage-related tail fibre protein [General function prediction only]; Region: COG5301 340054004839 Integrase core domain; Region: rve; cl01316 340054004840 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054004841 Domain of unknown function (DUF4415); Region: DUF4415; cl01401 340054004842 Phage-related tail fibre protein [General function prediction only]; Region: COG5301 340054004843 Integrase core domain; Region: rve; cl01316 340054004844 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054004845 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; cl01817 340054004846 Baseplate J-like protein; Region: Baseplate_J; cl01294 340054004847 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 340054004848 Phage P2 baseplate assembly protein gpV [General function prediction only]; Region: gpV; COG4540 340054004849 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 340054004850 Bacteriophage Mu Gp45 protein; Region: Phage_Mu_Gp45; cl15410 340054004851 Domain of unknown function (DUF1834); Region: DUF1834; cl02087 340054004852 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 340054004853 Protein of unknown function (DUF1320); Region: DUF1320; cl01818 340054004854 Mu-like prophage I protein [General function prediction only]; Region: COG4388 340054004855 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 340054004856 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 340054004857 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 340054004858 Protein of unknown function (DUF935); Region: DUF935; pfam06074 340054004859 Methyltransferase domain; Region: Methyltransf_31; pfam13847 340054004860 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 340054004861 S-adenosylmethionine binding site [chemical binding]; other site 340054004862 benzoate transport; Region: 2A0115; TIGR00895 340054004863 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 340054004864 putative substrate translocation pore; other site 340054004865 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 340054004866 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 340054004867 active site 340054004868 NAD binding site [chemical binding]; other site 340054004869 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054004870 DNA binding residues [nucleotide binding] 340054004871 dimerization interface [polypeptide binding]; other site 340054004872 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 340054004873 DNA binding residues [nucleotide binding] 340054004874 dimerization interface [polypeptide binding]; other site 340054004875 Protein of unknown function (DUF3955); Region: DUF3955; pfam13127 340054004876 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 340054004877 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 340054004878 SelR domain; Region: SelR; pfam01641 340054004879 VIP2; A family of actin-ADP-ribosylating toxin. A member of the Bacillus-prodiced vegetative insecticidal proteins (VIPs) possesses high specificity against the major insect pest, corn rootworms, and belongs to a classs of binary toxins and regulators of...; Region: VIP2; cl00173 340054004880 Transposase; Region: HTH_Tnp_IS630; pfam01710 340054004881 Integrase core domain; Region: rve; cl01316 340054004882 Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction; Region: HP_HAP_like; cd07061 340054004883 glucose-1-phosphatase/inositol phosphatase; Provisional; Region: PRK10173 340054004884 catalytic core [active] 340054004885 Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction; Region: HP_HAP_like; cd07061 340054004886 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 340054004887 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 340054004888 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 340054004889 DNA binding site [nucleotide binding] 340054004890 active site 340054004891 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 340054004892 Aspartase; Region: Aspartase; cd01357 340054004893 active sites [active] 340054004894 tetramer interface [polypeptide binding]; other site 340054004895 secretion system apparatus protein SsaU; Reviewed; Region: PRK12721 340054004896 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 340054004897 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 340054004898 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 340054004899 FliP family; Region: FliP; cl00593 340054004900 transcriptional regulator PhoU; Provisional; Region: PRK11115 340054004901 PhoU domain; Region: PhoU; pfam01895 340054004902 PhoU domain; Region: PhoU; pfam01895 340054004903 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 340054004904 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 340054004905 Walker A/P-loop; other site 340054004906 ATP binding site [chemical binding]; other site 340054004907 Q-loop/lid; other site 340054004908 ABC transporter signature motif; other site 340054004909 Walker B; other site 340054004910 D-loop; other site 340054004911 H-loop/switch region; other site 340054004912 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 340054004913 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 340054004914 dimer interface [polypeptide binding]; other site 340054004915 conserved gate region; other site 340054004916 putative PBP binding loops; other site 340054004917 ABC-ATPase subunit interface; other site 340054004918 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 340054004919 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 340054004920 dimer interface [polypeptide binding]; other site 340054004921 conserved gate region; other site 340054004922 putative PBP binding loops; other site 340054004923 ABC-ATPase subunit interface; other site 340054004924 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 340054004925 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 340054004926 substrate binding pocket [chemical binding]; other site 340054004927 membrane-bound complex binding site; other site 340054004928 hinge residues; other site 340054004929 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 340054004930 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 340054004931 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 340054004932 Protein of unknown function (DUF2531); Region: DUF2531; pfam10748 340054004933 putative outer membrane porin HofQ; Provisional; Region: hofQ; PRK13568 340054004934 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 340054004935 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 340054004936 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 340054004937 Family description; Region: VCBS; pfam13517 340054004938 Family description; Region: VCBS; pfam13517 340054004939 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004940 Peptidase C80 family; Region: Peptidase_C80; pfam11713 340054004941 BON domain; Region: BON; cl02771 340054004942 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 340054004943 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 340054004944 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 340054004945 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 340054004946 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 340054004947 probable active site [active] 340054004948 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 340054004949 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 340054004950 G1 box; other site 340054004951 putative GEF interaction site [polypeptide binding]; other site 340054004952 GTP/Mg2+ binding site [chemical binding]; other site 340054004953 Switch I region; other site 340054004954 G2 box; other site 340054004955 G3 box; other site 340054004956 Switch II region; other site 340054004957 G4 box; other site 340054004958 G5 box; other site 340054004959 RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the...; Region: RF3_II; cd03689 340054004960 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 340054004961 methyltransferase, MtaA/CmuA family; Region: mtaA_cmuA; TIGR01463 340054004962 substrate binding site [chemical binding]; other site 340054004963 active site 340054004964 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 340054004965 trimer interface [polypeptide binding]; other site 340054004966 eyelet of channel; other site 340054004967 BRO family, N-terminal domain; Region: Bro-N; cl10591 340054004968 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 340054004969 Integrase core domain; Region: rve; cl01316 340054004970 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054004971 TIGR01777 family protein; Region: yfcH 340054004972 NAD(P) binding site [chemical binding]; other site 340054004973 active site 340054004974 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 340054004975 ferric uptake regulator; Provisional; Region: fur; PRK09462 340054004976 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 340054004977 metal binding site 2 [ion binding]; metal-binding site 340054004978 putative DNA binding helix; other site 340054004979 metal binding site 1 [ion binding]; metal-binding site 340054004980 dimer interface [polypeptide binding]; other site 340054004981 structural Zn2+ binding site [ion binding]; other site 340054004982 RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when...; Region: RhoGAP; cd00159 340054004983 GTPase-activator protein for Rho-like GTPases; Region: RhoGAP; smart00324 340054004984 GTPase interaction site; other site 340054004985 catalytic residue [active] 340054004986 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 340054004987 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the...; Region: PNPsynthase; cd00003 340054004988 active site 340054004989 hydrophilic channel; other site 340054004990 dimerization interface [polypeptide binding]; other site 340054004991 catalytic residues [active] 340054004992 active site lid [active] 340054004993 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 340054004994 Peptidase C80 family; Region: Peptidase_C80; pfam11713 340054004995 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 340054004996 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 340054004997 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 340054004998 active site 1 [active] 340054004999 dimer interface [polypeptide binding]; other site 340054005000 active site 2 [active] 340054005001 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 340054005002 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 340054005003 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 340054005004 S-adenosylmethionine binding site [chemical binding]; other site 340054005005 ATP-dependent DNA helicase Rep; Provisional; Region: PRK10919 340054005006 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054005007 Family description; Region: UvrD_C_2; cl15862 340054005008 isocitrate dehydrogenase; Validated; Region: PRK07362 340054005009 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 340054005010 FtsX-like permease family; Region: FtsX; cl15850 340054005011 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 340054005012 cell division protein FtsE; Provisional; Region: PRK10908 340054005013 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 340054005014 Walker A/P-loop; other site 340054005015 ATP binding site [chemical binding]; other site 340054005016 Q-loop/lid; other site 340054005017 ABC transporter signature motif; other site 340054005018 Walker B; other site 340054005019 D-loop; other site 340054005020 H-loop/switch region; other site 340054005021 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 340054005022 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 340054005023 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 340054005024 P loop; other site 340054005025 GTP binding site [chemical binding]; other site 340054005026 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 340054005027 S-adenosylmethionine binding site [chemical binding]; other site 340054005028 putative hydrolase; Provisional; Region: PRK10976 340054005029 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 340054005030 active site 340054005031 motif I; other site 340054005032 motif II; other site 340054005033 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 340054005034 PAS fold; Region: PAS_4; pfam08448 340054005035 Helix-turn-helix domains; Region: HTH; cl00088 340054005036 ATP-dependent helicase HepA; Validated; Region: PRK04914 340054005037 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 340054005038 ATP binding site [chemical binding]; other site 340054005039 putative Mg++ binding site [ion binding]; other site 340054005040 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 340054005041 nucleotide binding region [chemical binding]; other site 340054005042 ATP-binding site [chemical binding]; other site 340054005043 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 340054005044 Flavoprotein; Region: Flavoprotein; cl08021 340054005045 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 340054005046 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 340054005047 trimer interface [polypeptide binding]; other site 340054005048 active site 340054005049 TcdA/TcdB catalytic glycosyltransferase domain; Region: TcdA_TcdB; pfam12919 340054005050 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 340054005051 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 340054005052 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 340054005053 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 340054005054 putative active site [active] 340054005055 putative NTP binding site [chemical binding]; other site 340054005056 putative nucleic acid binding site [nucleotide binding]; other site 340054005057 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 340054005058 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 340054005059 active site 340054005060 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 340054005061 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 340054005062 RimM N-terminal domain; Region: RimM; pfam01782 340054005063 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 340054005064 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 340054005065 signal recognition particle protein; Provisional; Region: PRK10867 340054005066 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 340054005067 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 340054005068 P loop; other site 340054005069 GTP binding site [chemical binding]; other site 340054005070 Signal peptide binding domain; Region: SRP_SPB; pfam02978 340054005071 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 340054005072 hypothetical protein; Provisional; Region: PRK11573 340054005073 Domain of unknown function DUF21; Region: DUF21; pfam01595 340054005074 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 340054005075 Transporter associated domain; Region: CorC_HlyC; cl08393 340054005076 Glutamate-cysteine ligase; Region: Glu_cys_ligase; cl15791 340054005077 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 340054005078 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 340054005079 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 340054005080 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 340054005081 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 340054005082 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 340054005083 F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a...; Region: F1-ATPase_beta; cd01133 340054005084 alpha subunit interaction interface [polypeptide binding]; other site 340054005085 Walker A motif; other site 340054005086 ATP binding site [chemical binding]; other site 340054005087 Walker B motif; other site 340054005088 inhibitor binding site; inhibition site 340054005089 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 340054005090 ATP synthase; Region: ATP-synt; cl00365 340054005091 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 340054005092 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 340054005093 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 340054005094 F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to...; Region: F1_ATPase_alpha; cd01132 340054005095 beta subunit interaction interface [polypeptide binding]; other site 340054005096 Walker A motif; other site 340054005097 ATP binding site [chemical binding]; other site 340054005098 Walker B motif; other site 340054005099 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 340054005100 Plant ATP synthase F0; Region: YMF19; cl07975 340054005101 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 340054005102 Plant ATP synthase F0; Region: YMF19; cl07975 340054005103 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 340054005104 ATP synthase subunit C; Region: ATP-synt_C; cl00466 340054005105 ATP synthase A chain; Region: ATP-synt_A; cl00413 340054005106 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 340054005107 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 340054005108 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054005109 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 340054005110 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 572265005111 IncFII RepA protein family; Region: IncFII_repA; cl11495 572265005112 PAS fold; Region: PAS_4; pfam08448 572265005113 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 572265005114 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 572265005115 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 572265005116 ATP binding site [chemical binding]; other site 572265005117 Mg2+ binding site [ion binding]; other site 572265005118 G-X-G motif; other site 572265005119 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 572265005120 ATP binding site [chemical binding]; other site 572265005121 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 572265005122 Uncharacterized conserved protein [Function unknown]; Region: COG2850 572265005123 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 572265005124 multiple promoter invertase; Provisional; Region: mpi; PRK13413 572265005125 catalytic residues [active] 572265005126 catalytic nucleophile [active] 572265005127 Presynaptic Site I dimer interface [polypeptide binding]; other site 572265005128 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 572265005129 Synaptic Flat tetramer interface [polypeptide binding]; other site 572265005130 Synaptic Site I dimer interface [polypeptide binding]; other site 572265005131 DNA binding site [nucleotide binding] 572265005132 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 572265005133 DNA-binding interface [nucleotide binding]; DNA binding site 572265005134 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 572265005135 oligomeric interface; other site 572265005136 putative active site [active] 572265005137 homodimer interface [polypeptide binding]; other site 572265005138 ParA-like protein; Provisional; Region: PHA02518 572265005139 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 572265005140 Magnesium ion binding site [ion binding]; other site 572265005141 conjugal transfer relaxosome component TraJ; Provisional; Region: PRK13877 572265005142 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 572265005143 conjugal transfer relaxase TraI; Provisional; Region: PRK13878 572265005144 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 572265005145 IHF dimer interface [polypeptide binding]; other site 572265005146 IHF - DNA interface [nucleotide binding]; other site 572265005147 putative transposase; Provisional; Region: PRK09857 572265005148 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 572265005149 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 572265005150 Walker A motif; other site 572265005151 ATP binding site [chemical binding]; other site 572265005152 Walker B motif; other site 572265005153 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 572265005154 catalytic residues [active] 572265005155 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]; Region: VirB4; COG3451 572265005156 AAA-like domain; Region: AAA_10; pfam12846 572265005157 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 572265005158 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 572265005159 Protein of unknown function (DUF3625); Region: DUF3625; pfam12293 572265005160 Macrophage killing protein with similarity to conjugation protein; Region: IcmL; pfam11393 572265005161 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 572265005162 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 572265005163 active site 572265005164 metal binding site [ion binding]; metal-binding site 572265005165 interdomain interaction site; other site 572265005166 plasmid transfer ATPase TraJ; Region: plasmid_TraJ; TIGR02525 572265005167 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 572265005168 Walker A motif; other site 572265005169 ATP binding site [chemical binding]; other site 572265005170 Walker B motif; other site 572265005171 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 572265005172 N-acetyl-D-glucosamine binding site [chemical binding]; other site 572265005173 catalytic residue [active] 572265005174 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 572265005175 PilM; Region: PilM; pfam07419 572265005176 Bacterial shufflon protein, N-terminal constant region; Region: Shufflon_N; pfam04917 572265005177 PilS N terminal; Region: PilS; pfam08805 572265005178 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 572265005179 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 572265005180 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 572265005181 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 572265005182 Walker A motif; other site 572265005183 ATP binding site [chemical binding]; other site 572265005184 Walker B motif; other site 572265005185 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 572265005186 Pilin accessory protein (PilO); Region: PAP_PilO; pfam06864 572265005187 Protein of unknown function (DUF497); Region: DUF497; cl01108 572265005188 Domain of unknown function (DUF4415); Region: DUF4415; cl01401 572265005189 type IVB pilus formation outer membrane protein, R64 PilN family; Region: pilus_B_mal_scr; TIGR02520 572265005190 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 572265005191 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 572265005192 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; Region: NGN_SP_AnfA1; cd09894 572265005193 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 572265005194 DNA binding residues [nucleotide binding] 572265005195 dimerization interface [polypeptide binding]; other site 572265005196 PAS fold; Region: PAS_4; pfam08448 572265005197 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 572265005198 DNA binding residues [nucleotide binding] 572265005199 dimerization interface [polypeptide binding]; other site 572265005200 Predicted membrane-associated trancriptional regulator [Transcription]; Region: COG2512