-- dump date 20140619_000938 -- class Genbank::misc_feature -- table misc_feature_note -- id note 634504000001 PEP synthetase regulatory protein; Provisional; Region: PRK05339 634504000002 Maf-like protein; Region: Maf; pfam02545 634504000003 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 634504000004 active site 634504000005 dimer interface [polypeptide binding]; other site 634504000006 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 634504000007 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 634504000008 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 634504000009 shikimate binding site; other site 634504000010 NAD(P) binding site [chemical binding]; other site 634504000011 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 634504000012 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 634504000013 CoA-binding site [chemical binding]; other site 634504000014 ATP-binding [chemical binding]; other site 634504000015 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 634504000016 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 634504000017 active site 634504000018 catalytic site [active] 634504000019 substrate binding site [chemical binding]; other site 634504000020 DNA polymerase I; Provisional; Region: PRK05755 634504000021 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 634504000022 active site 634504000023 metal binding site 1 [ion binding]; metal-binding site 634504000024 putative 5' ssDNA interaction site; other site 634504000025 metal binding site 3; metal-binding site 634504000026 metal binding site 2 [ion binding]; metal-binding site 634504000027 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 634504000028 putative DNA binding site [nucleotide binding]; other site 634504000029 putative metal binding site [ion binding]; other site 634504000030 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 634504000031 active site 634504000032 catalytic site [active] 634504000033 substrate binding site [chemical binding]; other site 634504000034 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 634504000035 active site 634504000036 DNA binding site [nucleotide binding] 634504000037 catalytic site [active] 634504000038 Metal-dependent hydrolase [General function prediction only]; Region: ElsH; COG3568 634504000039 putative catalytic site [active] 634504000040 putative metal binding site [ion binding]; other site 634504000041 putative phosphate binding site [ion binding]; other site 634504000042 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 634504000043 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 634504000044 lipoprotein signal peptidase; Provisional; Region: PRK14795 634504000045 lipoprotein signal peptidase; Provisional; Region: PRK14787 634504000046 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 634504000047 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 634504000048 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 634504000049 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 634504000050 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 634504000051 S-adenosylmethionine binding site [chemical binding]; other site 634504000052 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 634504000053 IHF dimer interface [polypeptide binding]; other site 634504000054 IHF - DNA interface [nucleotide binding]; other site 634504000055 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 634504000056 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 634504000057 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 634504000058 OstA-like protein; Region: OstA; pfam03968 634504000059 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 634504000060 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 634504000061 Walker A/P-loop; other site 634504000062 ATP binding site [chemical binding]; other site 634504000063 Q-loop/lid; other site 634504000064 ABC transporter signature motif; other site 634504000065 Walker B; other site 634504000066 D-loop; other site 634504000067 H-loop/switch region; other site 634504000068 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 634504000069 active site 634504000070 phosphorylation site [posttranslational modification] 634504000071 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 634504000072 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 634504000073 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 634504000074 FeS/SAM binding site; other site 634504000075 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 634504000076 argininosuccinate synthase; Provisional; Region: PRK13820 634504000077 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 634504000078 ANP binding site [chemical binding]; other site 634504000079 Substrate Binding Site II [chemical binding]; other site 634504000080 Substrate Binding Site I [chemical binding]; other site 634504000081 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 634504000082 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 634504000083 active site 634504000084 nucleotide binding site [chemical binding]; other site 634504000085 HIGH motif; other site 634504000086 KMSKS motif; other site 634504000087 Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]; Region: PrfC; COG4108 634504000088 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 634504000089 G1 box; other site 634504000090 putative GEF interaction site [polypeptide binding]; other site 634504000091 GTP/Mg2+ binding site [chemical binding]; other site 634504000092 Switch I region; other site 634504000093 G2 box; other site 634504000094 G3 box; other site 634504000095 Switch II region; other site 634504000096 G4 box; other site 634504000097 G5 box; other site 634504000098 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 634504000099 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 634504000100 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 634504000101 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 634504000102 Part of AAA domain; Region: AAA_19; pfam13245 634504000103 Family description; Region: UvrD_C_2; pfam13538 634504000104 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 634504000105 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 634504000106 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 634504000107 catalytic residues [active] 634504000108 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 634504000109 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 634504000110 PAS domain; Region: PAS_8; pfam13188 634504000111 PAS fold; Region: PAS_7; pfam12860 634504000112 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 634504000113 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 634504000114 dimer interface [polypeptide binding]; other site 634504000115 phosphorylation site [posttranslational modification] 634504000116 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 634504000117 ATP binding site [chemical binding]; other site 634504000118 Mg2+ binding site [ion binding]; other site 634504000119 G-X-G motif; other site 634504000120 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 634504000121 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 634504000122 homotetramer interface [polypeptide binding]; other site 634504000123 ligand binding site [chemical binding]; other site 634504000124 catalytic site [active] 634504000125 NAD binding site [chemical binding]; other site 634504000126 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 634504000127 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 634504000128 putative NAD(P) binding site [chemical binding]; other site 634504000129 active site 634504000130 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 634504000131 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 634504000132 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 634504000133 CysZ-like protein; Reviewed; Region: PRK12768 634504000134 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional; Region: PRK13982 634504000135 Plasmid stability protein [General function prediction only]; Region: StbC; COG4691 634504000136 Flavoprotein; Region: Flavoprotein; pfam02441 634504000137 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 634504000138 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 634504000139 ABC1 family; Region: ABC1; pfam03109 634504000140 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 634504000141 active site 634504000142 ATP binding site [chemical binding]; other site 634504000143 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 634504000144 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 634504000145 S-adenosylmethionine binding site [chemical binding]; other site 634504000146 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 634504000147 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 634504000148 Mg2+ binding site [ion binding]; other site 634504000149 G-X-G motif; other site 634504000150 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 634504000151 anchoring element; other site 634504000152 dimer interface [polypeptide binding]; other site 634504000153 ATP binding site [chemical binding]; other site 634504000154 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 634504000155 active site 634504000156 putative metal-binding site [ion binding]; other site 634504000157 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 634504000158 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 634504000159 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 634504000160 substrate binding pocket [chemical binding]; other site 634504000161 membrane-bound complex binding site; other site 634504000162 hinge residues; other site 634504000163 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 634504000164 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 634504000165 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 634504000166 Walker A motif; other site 634504000167 ATP binding site [chemical binding]; other site 634504000168 Walker B motif; other site 634504000169 arginine finger; other site 634504000170 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 634504000171 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 634504000172 Surface antigen; Region: Bac_surface_Ag; pfam01103 634504000173 Family of unknown function (DUF490); Region: DUF490; pfam04357 634504000174 Family of unknown function (DUF490); Region: DUF490; pfam04357 634504000175 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 634504000176 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 634504000177 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 634504000178 Walker A/P-loop; other site 634504000179 ATP binding site [chemical binding]; other site 634504000180 Q-loop/lid; other site 634504000181 ABC transporter signature motif; other site 634504000182 Walker B; other site 634504000183 D-loop; other site 634504000184 H-loop/switch region; other site 634504000185 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 634504000186 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 634504000187 catalytic site [active] 634504000188 Protein of unknown function DUF45; Region: DUF45; pfam01863 634504000189 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 634504000190 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 634504000191 metal binding site [ion binding]; metal-binding site 634504000192 dimer interface [polypeptide binding]; other site 634504000193 coproporphyrinogen III oxidase; Provisional; Region: PRK09057 634504000194 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 634504000195 FeS/SAM binding site; other site 634504000196 HemN C-terminal domain; Region: HemN_C; pfam06969 634504000197 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 634504000198 active site 634504000199 dimerization interface [polypeptide binding]; other site 634504000200 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 634504000201 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 634504000202 heat shock protein GrpE; Provisional; Region: PRK14141 634504000203 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 634504000204 dimer interface [polypeptide binding]; other site 634504000205 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 634504000206 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 634504000207 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 634504000208 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 634504000209 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 634504000210 dimerization domain swap beta strand [polypeptide binding]; other site 634504000211 regulatory protein interface [polypeptide binding]; other site 634504000212 active site 634504000213 regulatory phosphorylation site [posttranslational modification]; other site 634504000214 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 634504000215 active pocket/dimerization site; other site 634504000216 active site 634504000217 phosphorylation site [posttranslational modification] 634504000218 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 634504000219 Hpr binding site; other site 634504000220 active site 634504000221 homohexamer subunit interaction site [polypeptide binding]; other site 634504000222 Sensor N-terminal transmembrane domain; Region: Sensor_TM1; pfam13755 634504000223 Stimulus-sensing domain; Region: Stimulus_sens_1; pfam13756 634504000224 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 634504000225 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 634504000226 dimerization interface [polypeptide binding]; other site 634504000227 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 634504000228 dimer interface [polypeptide binding]; other site 634504000229 phosphorylation site [posttranslational modification] 634504000230 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 634504000231 ATP binding site [chemical binding]; other site 634504000232 Mg2+ binding site [ion binding]; other site 634504000233 G-X-G motif; other site 634504000234 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 634504000235 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 634504000236 active site 634504000237 phosphorylation site [posttranslational modification] 634504000238 intermolecular recognition site; other site 634504000239 dimerization interface [polypeptide binding]; other site 634504000240 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 634504000241 DNA binding site [nucleotide binding] 634504000242 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 634504000243 BON domain; Region: BON; pfam04972 634504000244 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 634504000245 Protein of unknown function (DUF461); Region: DUF461; pfam04314 634504000246 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 634504000247 Nucleotide-binding domain of human HSPA9, Escherichia coli DnaK, and similar proteins; Region: HSPA9-like_NBD; cd11733 634504000248 nucleotide binding site [chemical binding]; other site 634504000249 NEF interaction site [polypeptide binding]; other site 634504000250 SBD interface [polypeptide binding]; other site 634504000251 chaperone protein DnaJ; Provisional; Region: PRK10767 634504000252 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 634504000253 HSP70 interaction site [polypeptide binding]; other site 634504000254 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 634504000255 substrate binding site [polypeptide binding]; other site 634504000256 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 634504000257 Zn binding sites [ion binding]; other site 634504000258 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 634504000259 dimer interface [polypeptide binding]; other site 634504000260 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 634504000261 homohexameric interface [polypeptide binding]; other site 634504000262 feedback inhibition sensing region; other site 634504000263 nucleotide binding site [chemical binding]; other site 634504000264 N-acetyl-L-glutamate binding site [chemical binding]; other site 634504000265 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 634504000266 EamA-like transporter family; Region: EamA; pfam00892 634504000267 GTP-binding protein LepA; Provisional; Region: PRK05433 634504000268 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 634504000269 G1 box; other site 634504000270 putative GEF interaction site [polypeptide binding]; other site 634504000271 GTP/Mg2+ binding site [chemical binding]; other site 634504000272 Switch I region; other site 634504000273 G2 box; other site 634504000274 G3 box; other site 634504000275 Switch II region; other site 634504000276 G4 box; other site 634504000277 G5 box; other site 634504000278 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 634504000279 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 634504000280 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 634504000281 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 634504000282 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 634504000283 trimer interface [polypeptide binding]; other site 634504000284 active site 634504000285 substrate binding site [chemical binding]; other site 634504000286 CoA binding site [chemical binding]; other site 634504000287 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 634504000288 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 634504000289 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 634504000290 dimerization interface 3.5A [polypeptide binding]; other site 634504000291 active site 634504000292 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 634504000293 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 634504000294 putative active site [active] 634504000295 substrate binding site [chemical binding]; other site 634504000296 putative cosubstrate binding site; other site 634504000297 catalytic site [active] 634504000298 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 634504000299 substrate binding site [chemical binding]; other site 634504000300 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 634504000301 active site 634504000302 catalytic residues [active] 634504000303 metal binding site [ion binding]; metal-binding site 634504000304 RmuC family; Region: RmuC; pfam02646 634504000305 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...; Region: LT_GEWL; cd00254 634504000306 N-acetyl-D-glucosamine binding site [chemical binding]; other site 634504000307 catalytic residue [active] 634504000308 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4530 634504000309 Protein of unknown function (FYDLN_acid); Region: FYDLN_acid; pfam09538 634504000310 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 634504000311 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 634504000312 hinge; other site 634504000313 active site 634504000314 cytidylate kinase; Provisional; Region: cmk; PRK00023 634504000315 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 634504000316 CMP-binding site; other site 634504000317 The sites determining sugar specificity; other site 634504000318 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 634504000319 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 634504000320 RNA binding site [nucleotide binding]; other site 634504000321 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 634504000322 RNA binding site [nucleotide binding]; other site 634504000323 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...; Region: S1_RPS1_repeat_ec3; cd05688 634504000324 RNA binding site [nucleotide binding]; other site 634504000325 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 634504000326 RNA binding site [nucleotide binding]; other site 634504000327 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 634504000328 RNA binding site [nucleotide binding]; other site 634504000329 S1_RPS1_repeat_ec6: 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_ec6; cd05691 634504000330 RNA binding site [nucleotide binding]; other site 634504000331 Protein of unknown function (DUF3131); Region: DUF3131; pfam11329 634504000332 Putative glucoamylase; Region: Glycoamylase; pfam10091 634504000333 Second GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains; Region: GH94N_ChvB_NdvB_2_like; cd11753 634504000334 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 634504000335 First GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains; Region: GH94N_ChvB_NdvB_1_like; cd11756 634504000336 Protein of unknown function, DUF608; Region: DUF608; pfam04685 634504000337 Nicotinic acid phosphoribosyltransferase [Coenzyme metabolism]; Region: PncB; COG1488 634504000338 nicotinate phosphoribosyltransferase; Provisional; Region: PRK05321 634504000339 active site 634504000340 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2832 634504000341 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 634504000342 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 634504000343 ABC-ATPase subunit interface; other site 634504000344 dimer interface [polypeptide binding]; other site 634504000345 putative PBP binding regions; other site 634504000346 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 634504000347 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 634504000348 ABC-ATPase subunit interface; other site 634504000349 dimer interface [polypeptide binding]; other site 634504000350 putative PBP binding regions; other site 634504000351 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 634504000352 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 634504000353 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 634504000354 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 634504000355 metal binding site [ion binding]; metal-binding site 634504000356 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 634504000357 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 634504000358 putative tRNA-binding site [nucleotide binding]; other site 634504000359 B3/4 domain; Region: B3_4; pfam03483 634504000360 tRNA synthetase B5 domain; Region: B5; smart00874 634504000361 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 634504000362 dimer interface [polypeptide binding]; other site 634504000363 motif 1; other site 634504000364 motif 3; other site 634504000365 motif 2; other site 634504000366 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; smart00896 634504000367 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 634504000368 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 634504000369 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 634504000370 dimer interface [polypeptide binding]; other site 634504000371 motif 1; other site 634504000372 active site 634504000373 motif 2; other site 634504000374 motif 3; other site 634504000375 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 634504000376 23S rRNA binding site [nucleotide binding]; other site 634504000377 L21 binding site [polypeptide binding]; other site 634504000378 L13 binding site [polypeptide binding]; other site 634504000379 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 634504000380 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 634504000381 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 634504000382 minor groove reading motif; other site 634504000383 helix-hairpin-helix signature motif; other site 634504000384 substrate binding pocket [chemical binding]; other site 634504000385 active site 634504000386 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 634504000387 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 634504000388 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 634504000389 putative dimer interface [polypeptide binding]; other site 634504000390 Uncharacterized small protein [Function unknown]; Region: COG5568 634504000391 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 634504000392 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 634504000393 MutS domain I; Region: MutS_I; pfam01624 634504000394 MutS domain II; Region: MutS_II; pfam05188 634504000395 MutS domain III; Region: MutS_III; pfam05192 634504000396 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 634504000397 Walker A/P-loop; other site 634504000398 ATP binding site [chemical binding]; other site 634504000399 Q-loop/lid; other site 634504000400 ABC transporter signature motif; other site 634504000401 Walker B; other site 634504000402 D-loop; other site 634504000403 H-loop/switch region; other site 634504000404 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 634504000405 Malic enzyme, N-terminal domain; Region: malic; pfam00390 634504000406 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 634504000407 putative NAD(P) binding site [chemical binding]; other site 634504000408 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 634504000409 preprotein translocase subunit SecB; Validated; Region: PRK05751 634504000410 SecA binding site; other site 634504000411 Preprotein binding site; other site 634504000412 FxsA cytoplasmic membrane protein; Region: FxsA; pfam04186 634504000413 Tim44-like domain; Region: Tim44; pfam04280 634504000414 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 634504000415 Smr domain; Region: Smr; pfam01713 634504000416 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5352 634504000417 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 634504000418 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 634504000419 inhibitor-cofactor binding pocket; inhibition site 634504000420 pyridoxal 5'-phosphate binding site [chemical binding]; other site 634504000421 catalytic residue [active] 634504000422 ornithine carbamoyltransferase; Provisional; Region: PRK00779 634504000423 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 634504000424 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 634504000425 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 634504000426 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 634504000427 dimerization interface [polypeptide binding]; other site 634504000428 domain crossover interface; other site 634504000429 redox-dependent activation switch; other site 634504000430 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 634504000431 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 634504000432 catalytic residues [active] 634504000433 central insert; other site 634504000434 Heme exporter protein D (CcmD); Region: CcmD; cl11475 634504000435 heme exporter protein CcmC; Region: ccmC; TIGR01191 634504000436 heme exporter protein CcmB; Region: ccmB; TIGR01190 634504000437 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13539 634504000438 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 634504000439 Walker A/P-loop; other site 634504000440 ATP binding site [chemical binding]; other site 634504000441 Q-loop/lid; other site 634504000442 ABC transporter signature motif; other site 634504000443 Walker B; other site 634504000444 D-loop; other site 634504000445 H-loop/switch region; other site 634504000446 aconitate hydratase; Validated; Region: PRK09277 634504000447 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 634504000448 substrate binding site [chemical binding]; other site 634504000449 ligand binding site [chemical binding]; other site 634504000450 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 634504000451 substrate binding site [chemical binding]; other site 634504000452 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 634504000453 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 634504000454 DnaA N-terminal domain; Region: DnaA_N; pfam11638 634504000455 Bacterial dnaA protein; Region: Bac_DnaA; pfam00308 634504000456 Walker A motif; other site 634504000457 ATP binding site [chemical binding]; other site 634504000458 Walker B motif; other site 634504000459 arginine finger; other site 634504000460 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 634504000461 DnaA box-binding interface [nucleotide binding]; other site 634504000462 DNA polymerase III subunit beta; Validated; Region: PRK05643 634504000463 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 634504000464 putative DNA binding surface [nucleotide binding]; other site 634504000465 dimer interface [polypeptide binding]; other site 634504000466 beta-clamp/clamp loader binding surface; other site 634504000467 beta-clamp/translesion DNA polymerase binding surface; other site 634504000468 recombination protein F; Reviewed; Region: recF; PRK00064 634504000469 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 634504000470 Walker A/P-loop; other site 634504000471 ATP binding site [chemical binding]; other site 634504000472 Q-loop/lid; other site 634504000473 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 634504000474 ABC transporter signature motif; other site 634504000475 Walker B; other site 634504000476 D-loop; other site 634504000477 H-loop/switch region; other site 634504000478 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 634504000479 Dehydroquinase class II; Region: DHquinase_II; pfam01220 634504000480 trimer interface [polypeptide binding]; other site 634504000481 active site 634504000482 dimer interface [polypeptide binding]; other site 634504000483 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 634504000484 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 634504000485 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 634504000486 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 634504000487 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 634504000488 D-pathway; other site 634504000489 Putative ubiquinol binding site [chemical binding]; other site 634504000490 Low-spin heme (heme b) binding site [chemical binding]; other site 634504000491 Putative water exit pathway; other site 634504000492 Binuclear center (heme o3/CuB) [ion binding]; other site 634504000493 K-pathway; other site 634504000494 Putative proton exit pathway; other site 634504000495 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 634504000496 Subunit I/III interface [polypeptide binding]; other site 634504000497 Subunit III/IV interface [polypeptide binding]; other site 634504000498 cytochrome o ubiquinol oxidase subunit IV; Region: CyoD; TIGR02847 634504000499 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 634504000500 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 634504000501 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 634504000502 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06505 634504000503 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 634504000504 NAD binding site [chemical binding]; other site 634504000505 homotetramer interface [polypeptide binding]; other site 634504000506 homodimer interface [polypeptide binding]; other site 634504000507 substrate binding site [chemical binding]; other site 634504000508 active site 634504000509 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 634504000510 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 634504000511 dimer interface [polypeptide binding]; other site 634504000512 active site 634504000513 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 634504000514 active site 1 [active] 634504000515 dimer interface [polypeptide binding]; other site 634504000516 active site 2 [active] 634504000517 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 634504000518 metal binding site 2 [ion binding]; metal-binding site 634504000519 putative DNA binding helix; other site 634504000520 metal binding site 1 [ion binding]; metal-binding site 634504000521 dimer interface [polypeptide binding]; other site 634504000522 structural Zn2+ binding site [ion binding]; other site 634504000523 Bacterial SH3 domain; Region: SH3_4; pfam06347 634504000524 Bacterial SH3 domain; Region: SH3_4; pfam06347 634504000525 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 634504000526 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 634504000527 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 634504000528 Potassium binding sites [ion binding]; other site 634504000529 Cesium cation binding sites [ion binding]; other site 634504000530 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 634504000531 HlyD family secretion protein; Region: HlyD_3; pfam13437 634504000532 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 634504000533 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 634504000534 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 634504000535 active site 634504000536 dimer interface [polypeptide binding]; other site 634504000537 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 634504000538 dimer interface [polypeptide binding]; other site 634504000539 active site 634504000540 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 634504000541 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 634504000542 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 634504000543 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 634504000544 active site 634504000545 phosphorylation site [posttranslational modification] 634504000546 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 634504000547 dimerization domain swap beta strand [polypeptide binding]; other site 634504000548 regulatory protein interface [polypeptide binding]; other site 634504000549 active site 634504000550 regulatory phosphorylation site [posttranslational modification]; other site 634504000551 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 634504000552 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 634504000553 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 634504000554 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 634504000555 H+ Antiporter protein; Region: 2A0121; TIGR00900 634504000556 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 634504000557 H+ Antiporter protein; Region: 2A0121; TIGR00900 634504000558 putative substrate translocation pore; other site 634504000559 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 634504000560 non-specific DNA binding site [nucleotide binding]; other site 634504000561 salt bridge; other site 634504000562 sequence-specific DNA binding site [nucleotide binding]; other site 634504000563 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 634504000564 trimer interface [polypeptide binding]; other site 634504000565 Haemagglutinin; Region: HIM; pfam05662 634504000566 YadA-like C-terminal region; Region: YadA; pfam03895 634504000567 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 634504000568 trimer interface [polypeptide binding]; other site 634504000569 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 634504000570 YadA-like C-terminal region; Region: YadA; pfam03895 634504000571 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 634504000572 trimer interface [polypeptide binding]; other site 634504000573 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 634504000574 trimer interface [polypeptide binding]; other site 634504000575 YadA-like C-terminal region; Region: YadA; pfam03895 634504000576 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 634504000577 trimer interface [polypeptide binding]; other site 634504000578 Autotransporter adhesin [Intracellular trafficking and secretion / Extracellular structures]; Region: Hia; COG5295 634504000579 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 634504000580 trimer interface [polypeptide binding]; other site 634504000581 Haemagglutinin; Region: HIM; pfam05662 634504000582 YadA-like C-terminal region; Region: YadA; pfam03895 634504000583 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 634504000584 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 634504000585 trimer interface [polypeptide binding]; other site 634504000586 YadA-like C-terminal region; Region: YadA; pfam03895 634504000587 Invasion associated locus B (IalB) protein; Region: IalB; pfam06776 634504000588 exopolyphosphatase; Region: exo_poly_only; TIGR03706 634504000589 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 634504000590 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 634504000591 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 634504000592 S-adenosylmethionine binding site [chemical binding]; other site 634504000593 GTPase CgtA; Reviewed; Region: obgE; PRK12299 634504000594 GTP1/OBG; Region: GTP1_OBG; pfam01018 634504000595 Obg GTPase; Region: Obg; cd01898 634504000596 G1 box; other site 634504000597 GTP/Mg2+ binding site [chemical binding]; other site 634504000598 Switch I region; other site 634504000599 G2 box; other site 634504000600 G3 box; other site 634504000601 Switch II region; other site 634504000602 G4 box; other site 634504000603 G5 box; other site 634504000604 gamma-glutamyl kinase; Provisional; Region: PRK05429 634504000605 AAK_G5K_ProB: Glutamate-5-kinase (G5K) catalyzes glutamate-dependent ATP cleavage; G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, in the first and controlling step of proline (and, in mammals, ornithine)...; Region: AAK_G5K_ProB; cd04242 634504000606 nucleotide binding site [chemical binding]; other site 634504000607 homotetrameric interface [polypeptide binding]; other site 634504000608 putative phosphate binding site [ion binding]; other site 634504000609 putative allosteric binding site; other site 634504000610 PUA domain; Region: PUA; pfam01472 634504000611 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 634504000612 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 634504000613 putative catalytic cysteine [active] 634504000614 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 634504000615 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 634504000616 active site 634504000617 (T/H)XGH motif; other site 634504000618 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 634504000619 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 634504000620 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 634504000621 Peptidase family M23; Region: Peptidase_M23; pfam01551 634504000622 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 634504000623 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 634504000624 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 634504000625 protein binding site [polypeptide binding]; other site 634504000626 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 634504000627 Catalytic dyad [active] 634504000628 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 634504000629 putative active site [active] 634504000630 Ap4A binding site [chemical binding]; other site 634504000631 nudix motif; other site 634504000632 putative metal binding site [ion binding]; other site 634504000633 Invasion associated locus B (IalB) protein; Region: IalB; pfam06776 634504000634 YGGT family; Region: YGGT; pfam02325 634504000635 Uncharacterized ACR, YggU family COG1872; Region: DUF167; pfam02594 634504000636 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 634504000637 dimer interface [polypeptide binding]; other site 634504000638 substrate binding site [chemical binding]; other site 634504000639 metal binding sites [ion binding]; metal-binding site 634504000640 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 634504000641 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 634504000642 G1 box; other site 634504000643 putative GEF interaction site [polypeptide binding]; other site 634504000644 GTP/Mg2+ binding site [chemical binding]; other site 634504000645 Switch I region; other site 634504000646 G2 box; other site 634504000647 G3 box; other site 634504000648 Switch II region; other site 634504000649 G4 box; other site 634504000650 G5 box; other site 634504000651 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 634504000652 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 634504000653 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 634504000654 MgtE intracellular N domain; Region: MgtE_N; pfam03448 634504000655 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 634504000656 Divalent cation transporter; Region: MgtE; pfam01769 634504000657 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 634504000658 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 634504000659 active site 634504000660 Zn binding site [ion binding]; other site 634504000661 SGNH_peri2; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known...; Region: SGNH_hydrolase_peri2; cd01829 634504000662 active site 634504000663 catalytic triad [active] 634504000664 oxyanion hole [active] 634504000665 Transglycosylase SLT domain; Region: SLT_2; pfam13406 634504000666 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...; Region: LT_GEWL; cd00254 634504000667 N-acetyl-D-glucosamine binding site [chemical binding]; other site 634504000668 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 634504000669 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 634504000670 active site 634504000671 tetramer interface; other site 634504000672 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 634504000673 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 634504000674 putative active site [active] 634504000675 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 634504000676 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 634504000677 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 634504000678 active site 634504000679 phosphorylation site [posttranslational modification] 634504000680 intermolecular recognition site; other site 634504000681 dimerization interface [polypeptide binding]; other site 634504000682 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 634504000683 Walker A motif; other site 634504000684 ATP binding site [chemical binding]; other site 634504000685 Walker B motif; other site 634504000686 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 634504000687 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 634504000688 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 634504000689 putative active site [active] 634504000690 catalytic site [active] 634504000691 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 634504000692 putative active site [active] 634504000693 catalytic site [active] 634504000694 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 634504000695 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; cl17186 634504000696 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...; Region: CBS_pair_IMPDH; cd04601 634504000697 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...; Region: IMPDH; cd00381 634504000698 active site 634504000699 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 634504000700 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 634504000701 S-adenosylmethionine binding site [chemical binding]; other site 634504000702 GMP synthase; Reviewed; Region: guaA; PRK00074 634504000703 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 634504000704 AMP/PPi binding site [chemical binding]; other site 634504000705 candidate oxyanion hole; other site 634504000706 catalytic triad [active] 634504000707 potential glutamine specificity residues [chemical binding]; other site 634504000708 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 634504000709 ATP Binding subdomain [chemical binding]; other site 634504000710 Ligand Binding sites [chemical binding]; other site 634504000711 Dimerization subdomain; other site 634504000712 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 634504000713 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 634504000714 active site 634504000715 catalytic site [active] 634504000716 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 634504000717 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 634504000718 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 634504000719 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 634504000720 dimer interface [polypeptide binding]; other site 634504000721 conserved gate region; other site 634504000722 putative PBP binding loops; other site 634504000723 ABC-ATPase subunit interface; other site 634504000724 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 634504000725 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 634504000726 dimer interface [polypeptide binding]; other site 634504000727 conserved gate region; other site 634504000728 putative PBP binding loops; other site 634504000729 ABC-ATPase subunit interface; other site 634504000730 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 634504000731 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 634504000732 Walker A/P-loop; other site 634504000733 ATP binding site [chemical binding]; other site 634504000734 Q-loop/lid; other site 634504000735 ABC transporter signature motif; other site 634504000736 Walker B; other site 634504000737 D-loop; other site 634504000738 H-loop/switch region; other site 634504000739 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 634504000740 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 634504000741 metal binding site [ion binding]; metal-binding site 634504000742 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 634504000743 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 634504000744 ABC-ATPase subunit interface; other site 634504000745 dimer interface [polypeptide binding]; other site 634504000746 putative PBP binding regions; other site 634504000747 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 634504000748 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 634504000749 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 634504000750 catalytic residues [active] 634504000751 ribonucleotide reductase stimulatory protein; Reviewed; Region: nrdI; PRK03600 634504000752 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08188 634504000753 Ribonucleotide reductase N-terminal; Region: RNR_N; pfam08343 634504000754 Class I ribonucleotide reductase; Region: RNR_I; cd01679 634504000755 active site 634504000756 dimer interface [polypeptide binding]; other site 634504000757 catalytic residues [active] 634504000758 effector binding site; other site 634504000759 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 634504000760 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 634504000761 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 634504000762 dimer interface [polypeptide binding]; other site 634504000763 putative radical transfer pathway; other site 634504000764 diiron center [ion binding]; other site 634504000765 tyrosyl radical; other site 634504000766 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 634504000767 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 634504000768 S-adenosylmethionine binding site [chemical binding]; other site 634504000769 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 634504000770 peptide chain release factor 1; Validated; Region: prfA; PRK00591 634504000771 This domain is found in peptide chain release factors; Region: PCRF; smart00937 634504000772 RF-1 domain; Region: RF-1; pfam00472 634504000773 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 634504000774 metal binding site 2 [ion binding]; metal-binding site 634504000775 putative DNA binding helix; other site 634504000776 metal binding site 1 [ion binding]; metal-binding site 634504000777 dimer interface [polypeptide binding]; other site 634504000778 structural Zn2+ binding site [ion binding]; other site 634504000779 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 634504000780 DEAD/DEAH box helicase; Region: DEAD; pfam00270 634504000781 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 634504000782 SEC-C motif; Region: SEC-C; pfam02810 634504000783 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03002 634504000784 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 634504000785 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 634504000786 heterotetramer interface [polypeptide binding]; other site 634504000787 active site pocket [active] 634504000788 cleavage site 634504000789 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 634504000790 active site 634504000791 8-oxo-dGMP binding site [chemical binding]; other site 634504000792 nudix motif; other site 634504000793 metal binding site [ion binding]; metal-binding site 634504000794 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 634504000795 NlpC/P60 family; Region: NLPC_P60; cl17555 634504000796 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 634504000797 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 634504000798 interface (dimer of trimers) [polypeptide binding]; other site 634504000799 Substrate-binding/catalytic site; other site 634504000800 Zn-binding sites [ion binding]; other site 634504000801 pantothenate kinase; Provisional; Region: PRK05439 634504000802 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...; Region: PanK; cd02025 634504000803 ATP-binding site [chemical binding]; other site 634504000804 CoA-binding site [chemical binding]; other site 634504000805 Mg2+-binding site [ion binding]; other site 634504000806 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 634504000807 active site 634504000808 homotetramer interface [polypeptide binding]; other site 634504000809 homodimer interface [polypeptide binding]; other site 634504000810 ATP-dependent protease subunit HslV; Provisional; Region: PRK05456 634504000811 active site 634504000812 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 634504000813 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 634504000814 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 634504000815 Walker A motif; other site 634504000816 ATP binding site [chemical binding]; other site 634504000817 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 634504000818 Walker B motif; other site 634504000819 arginine finger; other site 634504000820 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 634504000821 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 634504000822 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 634504000823 S-adenosylmethionine binding site [chemical binding]; other site 634504000824 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 634504000825 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 634504000826 RNase E interface [polypeptide binding]; other site 634504000827 trimer interface [polypeptide binding]; other site 634504000828 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 634504000829 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 634504000830 RNase E interface [polypeptide binding]; other site 634504000831 trimer interface [polypeptide binding]; other site 634504000832 active site 634504000833 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 634504000834 putative nucleic acid binding region [nucleotide binding]; other site 634504000835 G-X-X-G motif; other site 634504000836 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 634504000837 RNA binding site [nucleotide binding]; other site 634504000838 domain interface; other site 634504000839 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 634504000840 16S/18S rRNA binding site [nucleotide binding]; other site 634504000841 S13e-L30e interaction site [polypeptide binding]; other site 634504000842 25S rRNA binding site [nucleotide binding]; other site 634504000843 Transmembrane secretion effector; Region: MFS_3; pfam05977 634504000844 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 634504000845 putative substrate translocation pore; other site 634504000846 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05389 634504000847 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 634504000848 RNA binding site [nucleotide binding]; other site 634504000849 active site 634504000850 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 634504000851 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 634504000852 translation initiation factor IF-2; Validated; Region: infB; PRK05306 634504000853 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 634504000854 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 634504000855 G1 box; other site 634504000856 putative GEF interaction site [polypeptide binding]; other site 634504000857 GTP/Mg2+ binding site [chemical binding]; other site 634504000858 Switch I region; other site 634504000859 G2 box; other site 634504000860 G3 box; other site 634504000861 Switch II region; other site 634504000862 G4 box; other site 634504000863 G5 box; other site 634504000864 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 634504000865 Translation-initiation factor 2; Region: IF-2; pfam11987 634504000866 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 634504000867 hypothetical protein; Provisional; Region: PRK09190 634504000868 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cd00279 634504000869 putative RNA binding cleft [nucleotide binding]; other site 634504000870 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 634504000871 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 634504000872 NusA N-terminal domain; Region: NusA_N; pfam08529 634504000873 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 634504000874 RNA binding site [nucleotide binding]; other site 634504000875 homodimer interface [polypeptide binding]; other site 634504000876 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 634504000877 G-X-X-G motif; other site 634504000878 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 634504000879 G-X-X-G motif; other site 634504000880 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 634504000881 Sm and related proteins; Region: Sm_like; cl00259 634504000882 ribosome maturation protein RimP; Reviewed; Region: PRK00092 634504000883 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 634504000884 putative oligomer interface [polypeptide binding]; other site 634504000885 putative RNA binding site [nucleotide binding]; other site 634504000886 tRNA (guanine-N(7)-)-methyltransferase; Reviewed; Region: trmB; PRK00121 634504000887 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 634504000888 S-adenosylmethionine synthetase; Validated; Region: PRK05250 634504000889 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 634504000890 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 634504000891 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 634504000892 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 634504000893 non-specific DNA binding site [nucleotide binding]; other site 634504000894 salt bridge; other site 634504000895 sequence-specific DNA binding site [nucleotide binding]; other site 634504000896 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 634504000897 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 634504000898 putative active site [active] 634504000899 catalytic triad [active] 634504000900 putative dimer interface [polypeptide binding]; other site 634504000901 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 634504000902 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 634504000903 Transporter associated domain; Region: CorC_HlyC; smart01091 634504000904 Uncharacterized protein family UPF0054; Region: UPF0054; pfam02130 634504000905 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 634504000906 PhoH-like protein; Region: PhoH; pfam02562 634504000907 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 634504000908 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 634504000909 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 634504000910 FeS/SAM binding site; other site 634504000911 TRAM domain; Region: TRAM; cl01282 634504000912 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 634504000913 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 634504000914 Coenzyme A binding pocket [chemical binding]; other site 634504000915 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 634504000916 Glycoprotease family; Region: Peptidase_M22; pfam00814 634504000917 Predicted membrane protein [Function unknown]; Region: COG2855 634504000918 recombination protein RecR; Reviewed; Region: recR; PRK00076 634504000919 RecR protein; Region: RecR; pfam02132 634504000920 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 634504000921 putative active site [active] 634504000922 putative metal-binding site [ion binding]; other site 634504000923 tetramer interface [polypeptide binding]; other site 634504000924 hypothetical protein; Validated; Region: PRK00153 634504000925 DNA polymerase III subunits gamma and tau; Validated; Region: PRK09111 634504000926 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 634504000927 Walker A motif; other site 634504000928 ATP binding site [chemical binding]; other site 634504000929 Walker B motif; other site 634504000930 arginine finger; other site 634504000931 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 634504000932 DNA polymerase III gamma and tau subunits C terminal; Region: DUF3646; pfam12362 634504000933 prephenate dehydratase; Provisional; Region: PRK11899 634504000934 Prephenate dehydratase; Region: PDT; pfam00800 634504000935 C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme; Region: ACT_CM-PDT; cd04905 634504000936 putative L-Phe binding site [chemical binding]; other site 634504000937 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 634504000938 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 634504000939 Ligand binding site; other site 634504000940 oligomer interface; other site 634504000941 Cytochrome c2 [Energy production and conversion]; Region: COG3474 634504000942 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 634504000943 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 634504000944 ATP binding site [chemical binding]; other site 634504000945 substrate interface [chemical binding]; other site 634504000946 glutathione synthetase; Provisional; Region: PRK05246 634504000947 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 634504000948 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 634504000949 PBP superfamily domain; Region: PBP_like_2; pfam12849 634504000950 Phosphate ATP-binding cassette transporter; Region: DUF3708; pfam12501 634504000951 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 634504000952 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 634504000953 dimer interface [polypeptide binding]; other site 634504000954 conserved gate region; other site 634504000955 putative PBP binding loops; other site 634504000956 ABC-ATPase subunit interface; other site 634504000957 Domain of unknown function (DUF3333); Region: DUF3333; pfam11812 634504000958 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 634504000959 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 634504000960 dimer interface [polypeptide binding]; other site 634504000961 conserved gate region; other site 634504000962 putative PBP binding loops; other site 634504000963 ABC-ATPase subunit interface; other site 634504000964 phosphate transporter ATP-binding protein; Provisional; Region: PRK14235 634504000965 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 634504000966 Walker A/P-loop; other site 634504000967 ATP binding site [chemical binding]; other site 634504000968 Q-loop/lid; other site 634504000969 ABC transporter signature motif; other site 634504000970 Walker B; other site 634504000971 D-loop; other site 634504000972 H-loop/switch region; other site 634504000973 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 634504000974 PhoU domain; Region: PhoU; pfam01895 634504000975 PhoU domain; Region: PhoU; pfam01895 634504000976 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 634504000977 Thermophilic metalloprotease (M29); Region: Peptidase_M29; pfam02073 634504000978 Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism]; Region: AmpS; COG2309 634504000979 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 634504000980 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 634504000981 DNA binding site [nucleotide binding] 634504000982 catalytic residue [active] 634504000983 H2TH interface [polypeptide binding]; other site 634504000984 putative catalytic residues [active] 634504000985 turnover-facilitating residue; other site 634504000986 intercalation triad [nucleotide binding]; other site 634504000987 8OG recognition residue [nucleotide binding]; other site 634504000988 putative reading head residues; other site 634504000989 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 634504000990 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 634504000991 hypothetical protein; Validated; Region: PRK09104 634504000992 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_3; cd05680 634504000993 metal binding site [ion binding]; metal-binding site 634504000994 putative dimer interface [polypeptide binding]; other site 634504000995 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 634504000996 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 634504000997 catalytic site [active] 634504000998 putative active site [active] 634504000999 putative substrate binding site [chemical binding]; other site 634504001000 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 634504001001 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 634504001002 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 634504001003 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 634504001004 isoleucyl-tRNA synthetase; Provisional; Region: ileS; PRK13804 634504001005 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 634504001006 active site 634504001007 HIGH motif; other site 634504001008 nucleotide binding site [chemical binding]; other site 634504001009 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 634504001010 active site 634504001011 KMSKS motif; other site 634504001012 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 634504001013 tRNA binding surface [nucleotide binding]; other site 634504001014 anticodon binding site; other site 634504001015 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 634504001016 nucleoside/Zn binding site; other site 634504001017 dimer interface [polypeptide binding]; other site 634504001018 catalytic motif [active] 634504001019 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 634504001020 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 634504001021 RNA binding surface [nucleotide binding]; other site 634504001022 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 634504001023 active site 634504001024 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 634504001025 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 634504001026 S-adenosylmethionine binding site [chemical binding]; other site 634504001027 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 634504001028 hydrophobic ligand binding site; other site 634504001029 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 634504001030 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 634504001031 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 634504001032 active site 634504001033 Domain of unknown function (DUF4170); Region: DUF4170; pfam13773 634504001034 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 634504001035 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 634504001036 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 634504001037 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 634504001038 Uncharacterized protein conserved in bacteria (DUF2093); Region: DUF2093; pfam09866 634504001039 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 634504001040 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 634504001041 ATP binding site [chemical binding]; other site 634504001042 Mg2+ binding site [ion binding]; other site 634504001043 G-X-G motif; other site 634504001044 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 634504001045 ATP binding site [chemical binding]; other site 634504001046 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 634504001047 2'-deoxycytidine 5'-triphosphate deaminase; Provisional; Region: PRK07559 634504001048 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 634504001049 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 634504001050 trimer interface [polypeptide binding]; other site 634504001051 active site 634504001052 Deoxycytidine deaminase [Nucleotide transport and metabolism]; Region: Dcd; COG0717 634504001053 trimer interface [polypeptide binding]; other site 634504001054 active site 634504001055 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 634504001056 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; cl17186 634504001057 phosphate binding site [ion binding]; other site 634504001058 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 634504001059 catalytic residues [active] 634504001060 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 634504001061 SlyX; Region: SlyX; cl01090 634504001062 Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]; Region: AnsP; COG1113 634504001063 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 634504001064 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 634504001065 Walker A/P-loop; other site 634504001066 ATP binding site [chemical binding]; other site 634504001067 Q-loop/lid; other site 634504001068 ABC transporter signature motif; other site 634504001069 Walker B; other site 634504001070 D-loop; other site 634504001071 H-loop/switch region; other site 634504001072 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 634504001073 BioY family; Region: BioY; pfam02632 634504001074 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 634504001075 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 634504001076 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 634504001077 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504001078 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504001079 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 634504001080 major tropism determinant; Region: mtd; PHA00653 634504001081 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 634504001082 catalytic residues [active] 634504001083 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 634504001084 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 634504001085 non-specific DNA binding site [nucleotide binding]; other site 634504001086 salt bridge; other site 634504001087 sequence-specific DNA binding site [nucleotide binding]; other site 634504001088 putatively functional bacteriophage; functionality not clear; exact boundaries not determined 634504001089 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 634504001090 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 634504001091 active site 634504001092 Int/Topo IB signature motif; other site 634504001093 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 634504001094 catalytic residues [active] 634504001095 putative addiction module killer protein; Region: upstrm_HI1419; TIGR02683 634504001096 probable addiction module antidote protein; Region: dnstrm_HI1420; TIGR02684 634504001097 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 634504001098 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 634504001099 Phage Tail Protein X; Region: Phage_tail_X; cl02088 634504001100 Phage P2 GpU; Region: Phage_P2_GpU; pfam06995 634504001101 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 634504001102 Mu-like prophage FluMu protein gp41; Region: FluMu_gp41; pfam10109 634504001103 Phage tail tube protein FII; Region: Phage_tube; pfam04985 634504001104 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 634504001105 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 634504001106 Phage tail repeat like; Region: PTR; pfam12789 634504001107 Phage Tail Collar Domain; Region: Collar; pfam07484 634504001108 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; cl01817 634504001109 Baseplate J-like protein; Region: Baseplate_J; cl01294 634504001110 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 634504001111 phage baseplate assembly protein V; Region: phage_P2_V; TIGR01644 634504001112 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 634504001113 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 634504001114 Protein of unknown function (DUF497); Region: DUF497; cl01108 634504001115 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 634504001116 HicB family; Region: HicB; pfam05534 634504001117 AntA/AntB antirepressor; Region: AntA; pfam08346 634504001118 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 634504001119 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 634504001120 Bacteriophage lambda head decoration protein D; Region: HDPD; pfam02924 634504001121 Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_36K_type; cd07022 634504001122 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 634504001123 tandem repeat interface [polypeptide binding]; other site 634504001124 oligomer interface [polypeptide binding]; other site 634504001125 active site residues [active] 634504001126 Phage portal protein, lambda family; Region: Phage_portal_2; pfam05136 634504001127 phage portal protein, lambda family; Region: portal_lambda; TIGR01539 634504001128 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 634504001129 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 634504001130 YcfA-like protein; Region: YcfA; pfam07927 634504001131 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 634504001132 dimer interface [polypeptide binding]; other site 634504001133 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 634504001134 ssDNA binding site [nucleotide binding]; other site 634504001135 tetramer (dimer of dimers) interface [polypeptide binding]; other site 634504001136 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 634504001137 AntA/AntB antirepressor; Region: AntA; pfam08346 634504001138 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 634504001139 3-oxoacyl-[acyl-carrier-protein] synthase II; Region: PLN02787 634504001140 Protein of unknown function (DUF1376); Region: DUF1376; cl01531 634504001141 Protein of unknown function (DUF1376); Region: DUF1376; cl01531 634504001142 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...; Region: RuvC_resolvase; cl17280 634504001143 active site 634504001144 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 634504001145 non-specific DNA binding site [nucleotide binding]; other site 634504001146 salt bridge; other site 634504001147 sequence-specific DNA binding site [nucleotide binding]; other site 634504001148 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; cd06462 634504001149 Catalytic site [active] 634504001150 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; pfam09669 634504001151 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 634504001152 ERF superfamily; Region: ERF; pfam04404 634504001153 YqaJ-like viral recombinase domain; Region: YqaJ; pfam09588 634504001154 Helix-turn-helix domain; Region: HTH_17; pfam12728 634504001155 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; cd01494 634504001156 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 634504001157 catalytic residue [active] 634504001158 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 634504001159 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 634504001160 GDP-binding site [chemical binding]; other site 634504001161 ACT binding site; other site 634504001162 IMP binding site; other site 634504001163 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 634504001164 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 634504001165 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 634504001166 DNA binding residues [nucleotide binding] 634504001167 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 634504001168 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 634504001169 RNA binding surface [nucleotide binding]; other site 634504001170 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 634504001171 active site 634504001172 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 634504001173 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 634504001174 NAD binding site [chemical binding]; other site 634504001175 catalytic residues [active] 634504001176 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 634504001177 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 634504001178 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 634504001179 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 634504001180 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 634504001181 putative active site [active] 634504001182 heme pocket [chemical binding]; other site 634504001183 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 634504001184 dimer interface [polypeptide binding]; other site 634504001185 phosphorylation site [posttranslational modification] 634504001186 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 634504001187 ATP binding site [chemical binding]; other site 634504001188 Mg2+ binding site [ion binding]; other site 634504001189 G-X-G motif; other site 634504001190 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 634504001191 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 634504001192 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 634504001193 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 634504001194 quinone interaction residues [chemical binding]; other site 634504001195 active site 634504001196 catalytic residues [active] 634504001197 FMN binding site [chemical binding]; other site 634504001198 substrate binding site [chemical binding]; other site 634504001199 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 634504001200 active site 2 [active] 634504001201 active site 1 [active] 634504001202 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 634504001203 DNA methylase; Region: N6_N4_Mtase; pfam01555 634504001204 DNA methylase; Region: N6_N4_Mtase; pfam01555 634504001205 Restriction endonuclease [Defense mechanisms]; Region: COG3587 634504001206 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 634504001207 ATP binding site [chemical binding]; other site 634504001208 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 634504001209 Major Facilitator Superfamily; Region: MFS_1; pfam07690 634504001210 putative substrate translocation pore; other site 634504001211 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 634504001212 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 634504001213 FeS/SAM binding site; other site 634504001214 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 634504001215 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 634504001216 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 634504001217 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 634504001218 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 634504001219 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 634504001220 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 634504001221 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 634504001222 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 634504001223 putative active site [active] 634504001224 phosphogluconate dehydratase; Validated; Region: PRK09054 634504001225 6-phosphogluconate dehydratase; Region: edd; TIGR01196 634504001226 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14188 634504001227 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 634504001228 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 634504001229 homodimer interface [polypeptide binding]; other site 634504001230 NADP binding site [chemical binding]; other site 634504001231 substrate binding site [chemical binding]; other site 634504001232 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 634504001233 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 634504001234 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 634504001235 Gamma-glutamylcysteine synthetase [Coenzyme metabolism]; Region: GshA; COG3572 634504001236 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 634504001237 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 634504001238 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 634504001239 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; cl17173 634504001240 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 634504001241 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 634504001242 GSH binding site [chemical binding]; other site 634504001243 catalytic residues [active] 634504001244 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 634504001245 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 634504001246 S-adenosylmethionine binding site [chemical binding]; other site 634504001247 aspartate kinase; Reviewed; Region: PRK06635 634504001248 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 634504001249 putative nucleotide binding site [chemical binding]; other site 634504001250 putative catalytic residues [active] 634504001251 putative Mg ion binding site [ion binding]; other site 634504001252 putative aspartate binding site [chemical binding]; other site 634504001253 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 634504001254 putative allosteric regulatory site; other site 634504001255 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 634504001256 putative allosteric regulatory residue; other site 634504001257 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 634504001258 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; cl17221 634504001259 transmembrane helices; other site 634504001260 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 634504001261 TrkA-C domain; Region: TrkA_C; pfam02080 634504001262 TrkA-C domain; Region: TrkA_C; pfam02080 634504001263 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; cl17221 634504001264 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4649 634504001265 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 634504001266 GTP-binding protein Der; Reviewed; Region: PRK00093 634504001267 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 634504001268 G1 box; other site 634504001269 GTP/Mg2+ binding site [chemical binding]; other site 634504001270 Switch I region; other site 634504001271 G2 box; other site 634504001272 Switch II region; other site 634504001273 G3 box; other site 634504001274 G4 box; other site 634504001275 G5 box; other site 634504001276 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 634504001277 G1 box; other site 634504001278 GTP/Mg2+ binding site [chemical binding]; other site 634504001279 Switch I region; other site 634504001280 G2 box; other site 634504001281 G3 box; other site 634504001282 Switch II region; other site 634504001283 G4 box; other site 634504001284 G5 box; other site 634504001285 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 634504001286 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 634504001287 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 634504001288 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 634504001289 F0F1 ATP synthase subunit B'; Validated; Region: PRK09174 634504001290 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 634504001291 F0F1 ATP synthase subunit B; Validated; Region: PRK09173 634504001292 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 634504001293 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 634504001294 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 634504001295 dimer interface [polypeptide binding]; other site 634504001296 motif 1; other site 634504001297 active site 634504001298 motif 2; other site 634504001299 motif 3; other site 634504001300 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 634504001301 binding surface 634504001302 TPR motif; other site 634504001303 TPR repeat; Region: TPR_11; pfam13414 634504001304 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 634504001305 binding surface 634504001306 TPR motif; other site 634504001307 TPR repeat; Region: TPR_11; pfam13414 634504001308 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 634504001309 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 634504001310 substrate binding pocket [chemical binding]; other site 634504001311 chain length determination region; other site 634504001312 substrate-Mg2+ binding site; other site 634504001313 catalytic residues [active] 634504001314 aspartate-rich region 1; other site 634504001315 active site lid residues [active] 634504001316 aspartate-rich region 2; other site 634504001317 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 634504001318 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 634504001319 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 634504001320 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 634504001321 tandem repeat interface [polypeptide binding]; other site 634504001322 oligomer interface [polypeptide binding]; other site 634504001323 active site residues [active] 634504001324 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14608 634504001325 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 634504001326 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 634504001327 RNA/DNA hybrid binding site [nucleotide binding]; other site 634504001328 active site 634504001329 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 634504001330 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 634504001331 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 634504001332 FAD binding domain; Region: FAD_binding_4; pfam01565 634504001333 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 634504001334 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 634504001335 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 634504001336 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 634504001337 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12878 634504001338 UbiA prenyltransferase family; Region: UbiA; pfam01040 634504001339 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 634504001340 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 634504001341 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 634504001342 chaperone protein DnaJ; Provisional; Region: PRK14299 634504001343 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 634504001344 HSP70 interaction site [polypeptide binding]; other site 634504001345 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 634504001346 dimer interface [polypeptide binding]; other site 634504001347 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08159 634504001348 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 634504001349 NAD binding site [chemical binding]; other site 634504001350 homotetramer interface [polypeptide binding]; other site 634504001351 homodimer interface [polypeptide binding]; other site 634504001352 substrate binding site [chemical binding]; other site 634504001353 active site 634504001354 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 634504001355 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 634504001356 Tetramer interface [polypeptide binding]; other site 634504001357 active site 634504001358 FMN-binding site [chemical binding]; other site 634504001359 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 634504001360 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 634504001361 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 634504001362 dimerization interface [polypeptide binding]; other site 634504001363 active site 634504001364 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 634504001365 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 634504001366 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 634504001367 TPP-binding site; other site 634504001368 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 634504001369 PYR/PP interface [polypeptide binding]; other site 634504001370 dimer interface [polypeptide binding]; other site 634504001371 TPP binding site [chemical binding]; other site 634504001372 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 634504001373 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 634504001374 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 634504001375 RNA binding surface [nucleotide binding]; other site 634504001376 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 634504001377 S-adenosylmethionine binding site [chemical binding]; other site 634504001378 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 634504001379 Methyltransferase domain; Region: Methyltransf_26; pfam13659 634504001380 protease TldD; Provisional; Region: tldD; PRK10735 634504001381 Invasion associated locus B (IalB) protein; Region: IalB; pfam06776 634504001382 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 634504001383 UbiA prenyltransferase family; Region: UbiA; pfam01040 634504001384 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 634504001385 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 634504001386 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 634504001387 Homoserine Kinase, type II. Homoserine kinase 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: HomoserineK_II; cd05153 634504001388 putative active site [active] 634504001389 putative substrate binding site [chemical binding]; other site 634504001390 ATP binding site [chemical binding]; other site 634504001391 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 634504001392 RNA/DNA hybrid binding site [nucleotide binding]; other site 634504001393 active site 634504001394 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 634504001395 hypothetical protein; Validated; Region: PRK00228 634504001396 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 634504001397 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 634504001398 PAS fold; Region: PAS_3; pfam08447 634504001399 putative active site [active] 634504001400 heme pocket [chemical binding]; other site 634504001401 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 634504001402 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 634504001403 metal binding site [ion binding]; metal-binding site 634504001404 active site 634504001405 I-site; other site 634504001406 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 634504001407 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 634504001408 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 634504001409 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 634504001410 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 634504001411 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 634504001412 pyridoxal 5'-phosphate binding site [chemical binding]; other site 634504001413 catalytic residue [active] 634504001414 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 634504001415 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 634504001416 motif II; other site 634504001417 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 634504001418 DNA methylase; Region: N6_N4_Mtase; pfam01555 634504001419 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 634504001420 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 634504001421 minor groove reading motif; other site 634504001422 helix-hairpin-helix signature motif; other site 634504001423 substrate binding pocket [chemical binding]; other site 634504001424 active site 634504001425 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 634504001426 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 634504001427 DNA binding and oxoG recognition site [nucleotide binding] 634504001428 Protein of unknown function (DUF721); Region: DUF721; cl02324 634504001429 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 634504001430 Thioredoxin; Region: Thioredoxin_4; pfam13462 634504001431 pyruvate phosphate dikinase; Provisional; Region: PRK09279 634504001432 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 634504001433 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 634504001434 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 634504001435 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 634504001436 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 634504001437 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 634504001438 Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]; Region: sufE; COG2166 634504001439 Predicted transcriptional regulator [Transcription]; Region: COG4957 634504001440 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 634504001441 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 634504001442 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 634504001443 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 634504001444 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 634504001445 RTX toxin acyltransferase family; Region: HlyC; cl01131 634504001446 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 634504001447 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 634504001448 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 634504001449 Walker A/P-loop; other site 634504001450 ATP binding site [chemical binding]; other site 634504001451 Q-loop/lid; other site 634504001452 ABC transporter signature motif; other site 634504001453 Walker B; other site 634504001454 D-loop; other site 634504001455 H-loop/switch region; other site 634504001456 Protein of unknown function (DUF1499); Region: DUF1499; pfam07386 634504001457 Predicted integral membrane protein [Function unknown]; Region: COG5436 634504001458 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 634504001459 Transglycosylase; Region: Transgly; pfam00912 634504001460 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 634504001461 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 634504001462 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 634504001463 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 634504001464 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 634504001465 active site 634504001466 phosphorylation site [posttranslational modification] 634504001467 intermolecular recognition site; other site 634504001468 dimerization interface [polypeptide binding]; other site 634504001469 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 634504001470 DNA binding site [nucleotide binding] 634504001471 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 634504001472 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; cl00080 634504001473 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 634504001474 ATP binding site [chemical binding]; other site 634504001475 Mg2+ binding site [ion binding]; other site 634504001476 G-X-G motif; other site 634504001477 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 634504001478 TPR motif; other site 634504001479 binding surface 634504001480 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 634504001481 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 634504001482 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 634504001483 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 634504001484 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 634504001485 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 634504001486 protein binding site [polypeptide binding]; other site 634504001487 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 634504001488 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 634504001489 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 634504001490 active site 634504001491 phosphorylation site [posttranslational modification] 634504001492 intermolecular recognition site; other site 634504001493 dimerization interface [polypeptide binding]; other site 634504001494 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 634504001495 DNA binding site [nucleotide binding] 634504001496 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 634504001497 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 634504001498 dimerization interface [polypeptide binding]; other site 634504001499 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 634504001500 dimer interface [polypeptide binding]; other site 634504001501 phosphorylation site [posttranslational modification] 634504001502 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 634504001503 ATP binding site [chemical binding]; other site 634504001504 Mg2+ binding site [ion binding]; other site 634504001505 G-X-G motif; other site 634504001506 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional; Region: PRK14108 634504001507 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 634504001508 metal binding triad; other site 634504001509 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 634504001510 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 634504001511 metal binding triad; other site 634504001512 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 634504001513 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 634504001514 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 634504001515 active site 634504001516 metal binding site [ion binding]; metal-binding site 634504001517 Protein of unknown function (DUF1355); Region: DUF1355; pfam07090 634504001518 A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain; Region: A4_beta-galactosidase_middle_domain; cd03143 634504001519 Domain of unknown function (DUF4159); Region: DUF4159; pfam13709 634504001520 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 634504001521 Protein of unknown function DUF58; Region: DUF58; pfam01882 634504001522 MoxR-like ATPases [General function prediction only]; Region: COG0714 634504001523 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 634504001524 Walker A motif; other site 634504001525 ATP binding site [chemical binding]; other site 634504001526 Walker B motif; other site 634504001527 arginine finger; other site 634504001528 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 634504001529 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 634504001530 active site 634504001531 NTP binding site [chemical binding]; other site 634504001532 metal binding triad [ion binding]; metal-binding site 634504001533 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 634504001534 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 634504001535 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 634504001536 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 634504001537 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 634504001538 [2Fe-2S] cluster binding site [ion binding]; other site 634504001539 cytochrome b; Provisional; Region: CYTB; MTH00191 634504001540 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 634504001541 Qi binding site; other site 634504001542 intrachain domain interface; other site 634504001543 interchain domain interface [polypeptide binding]; other site 634504001544 heme bH binding site [chemical binding]; other site 634504001545 heme bL binding site [chemical binding]; other site 634504001546 Qo binding site; other site 634504001547 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cd00290 634504001548 interchain domain interface [polypeptide binding]; other site 634504001549 intrachain domain interface; other site 634504001550 Qi binding site; other site 634504001551 Qo binding site; other site 634504001552 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 634504001553 Cytochrome c; Region: Cytochrom_C; cl11414 634504001554 PRC-barrel domain; Region: PRC; pfam05239 634504001555 GTP-binding protein YchF; Reviewed; Region: PRK09601 634504001556 YchF GTPase; Region: YchF; cd01900 634504001557 G1 box; other site 634504001558 GTP/Mg2+ binding site [chemical binding]; other site 634504001559 Switch I region; other site 634504001560 G2 box; other site 634504001561 Switch II region; other site 634504001562 G3 box; other site 634504001563 G4 box; other site 634504001564 G5 box; other site 634504001565 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 634504001566 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 634504001567 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 634504001568 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 634504001569 putative active site [active] 634504001570 catalytic residue [active] 634504001571 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 634504001572 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 634504001573 5S rRNA interface [nucleotide binding]; other site 634504001574 CTC domain interface [polypeptide binding]; other site 634504001575 L16 interface [polypeptide binding]; other site 634504001576 HerA helicase [Replication, recombination, and repair]; Region: COG0433 634504001577 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; cl17189 634504001578 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 634504001579 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 634504001580 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 634504001581 active site 634504001582 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 634504001583 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 634504001584 Uncharacterized conserved protein [Function unknown]; Region: COG1565 634504001585 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 634504001586 Membrane fusogenic activity; Region: BMFP; pfam04380 634504001587 Putative bacterial sensory transduction regulator; Region: YbjN; cl15834 634504001588 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 634504001589 HAMP domain; Region: HAMP; pfam00672 634504001590 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; cl00080 634504001591 dimer interface [polypeptide binding]; other site 634504001592 phosphorylation site [posttranslational modification] 634504001593 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 634504001594 ATP binding site [chemical binding]; other site 634504001595 Mg2+ binding site [ion binding]; other site 634504001596 G-X-G motif; other site 634504001597 osmolarity response regulator; Provisional; Region: ompR; PRK09468 634504001598 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 634504001599 active site 634504001600 phosphorylation site [posttranslational modification] 634504001601 intermolecular recognition site; other site 634504001602 dimerization interface [polypeptide binding]; other site 634504001603 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 634504001604 DNA binding site [nucleotide binding] 634504001605 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 634504001606 BA14K-like protein; Region: BA14K; pfam07886 634504001607 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 634504001608 nucleotide binding region [chemical binding]; other site 634504001609 ATP-binding site [chemical binding]; other site 634504001610 Ultra-violet resistance protein B; Region: UvrB; pfam12344 634504001611 UvrB/uvrC motif; Region: UVR; pfam02151 634504001612 BA14K-like protein; Region: BA14K; pfam07886 634504001613 excinuclease ABC subunit B; Provisional; Region: PRK05298 634504001614 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 634504001615 ATP binding site [chemical binding]; other site 634504001616 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 634504001617 nucleotide binding region [chemical binding]; other site 634504001618 ATP-binding site [chemical binding]; other site 634504001619 Ultra-violet resistance protein B; Region: UvrB; pfam12344 634504001620 UvrB/uvrC motif; Region: UVR; pfam02151 634504001621 Bacterial SH3 domain; Region: SH3_3; pfam08239 634504001622 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 634504001623 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 634504001624 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 634504001625 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 634504001626 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 634504001627 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 634504001628 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 634504001629 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 634504001630 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 634504001631 Transcriptional regulator [Transcription]; Region: LysR; COG0583 634504001632 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 634504001633 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 634504001634 putative effector binding pocket; other site 634504001635 dimerization interface [polypeptide binding]; other site 634504001636 aspartate aminotransferase; Provisional; Region: PRK05764 634504001637 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 634504001638 pyridoxal 5'-phosphate binding site [chemical binding]; other site 634504001639 homodimer interface [polypeptide binding]; other site 634504001640 catalytic residue [active] 634504001641 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...; Region: CSP_CDS; cd04458 634504001642 DNA-binding site [nucleotide binding]; DNA binding site 634504001643 RNA-binding motif; other site 634504001644 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 634504001645 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 634504001646 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 634504001647 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 634504001648 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 634504001649 ATP-grasp domain; Region: ATP-grasp_4; cl17255 634504001650 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 634504001651 IMP binding site; other site 634504001652 dimer interface [polypeptide binding]; other site 634504001653 interdomain contacts; other site 634504001654 partial ornithine binding site; other site 634504001655 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 634504001656 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 634504001657 DNA binding site [nucleotide binding] 634504001658 active site 634504001659 PAS fold; Region: PAS_3; pfam08447 634504001660 PAS fold; Region: PAS_7; pfam12860 634504001661 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 634504001662 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 634504001663 dimer interface [polypeptide binding]; other site 634504001664 phosphorylation site [posttranslational modification] 634504001665 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 634504001666 ATP binding site [chemical binding]; other site 634504001667 Mg2+ binding site [ion binding]; other site 634504001668 G-X-G motif; other site 634504001669 aminopeptidase N; Provisional; Region: pepN; PRK14015 634504001670 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 634504001671 active site 634504001672 Zn binding site [ion binding]; other site 634504001673 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 634504001674 Fe-S cluster binding site [ion binding]; other site 634504001675 active site 634504001676 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 634504001677 substrate binding site [chemical binding]; other site 634504001678 dimer interface [polypeptide binding]; other site 634504001679 ATP binding site [chemical binding]; other site 634504001680 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 634504001681 thiamine phosphate binding site [chemical binding]; other site 634504001682 active site 634504001683 pyrophosphate binding site [ion binding]; other site 634504001684 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 634504001685 ThiS interaction site; other site 634504001686 putative active site [active] 634504001687 tetramer interface [polypeptide binding]; other site 634504001688 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 634504001689 thiS-thiF/thiG interaction site; other site 634504001690 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 634504001691 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 634504001692 ThiC-associated domain; Region: ThiC-associated; pfam13667 634504001693 ThiC family; Region: ThiC; pfam01964 634504001694 Phage Tail Collar Domain; Region: Collar; pfam07484 634504001695 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 634504001696 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 634504001697 Walker A/P-loop; other site 634504001698 ATP binding site [chemical binding]; other site 634504001699 Q-loop/lid; other site 634504001700 ABC transporter signature motif; other site 634504001701 Walker B; other site 634504001702 D-loop; other site 634504001703 H-loop/switch region; other site 634504001704 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 634504001705 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 634504001706 ABC-ATPase subunit interface; other site 634504001707 dimer interface [polypeptide binding]; other site 634504001708 putative PBP binding regions; other site 634504001709 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 634504001710 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 634504001711 putative hemin binding site; other site 634504001712 Putative heme degradation protein [Inorganic ion transport and metabolism]; Region: HemS; COG3720 634504001713 Haemin-degrading HemS.ChuX domain; Region: HemS; pfam05171 634504001714 Haemin-degrading HemS.ChuX domain; Region: HemS; pfam05171 634504001715 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 634504001716 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 634504001717 N-terminal plug; other site 634504001718 ligand-binding site [chemical binding]; other site 634504001719 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 634504001720 TonB C terminal; Region: TonB_2; pfam13103 634504001721 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 634504001722 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...; Region: LT_GEWL; cd00254 634504001723 N-acetyl-D-glucosamine binding site [chemical binding]; other site 634504001724 catalytic residue [active] 634504001725 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 634504001726 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 634504001727 dimer interface [polypeptide binding]; other site 634504001728 active site 634504001729 catalytic residue [active] 634504001730 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 634504001731 SmpB-tmRNA interface; other site 634504001732 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 634504001733 Fe-S cluster binding site [ion binding]; other site 634504001734 DNA binding site [nucleotide binding] 634504001735 active site 634504001736 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 634504001737 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 634504001738 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 634504001739 Zn2+ binding site [ion binding]; other site 634504001740 Mg2+ binding site [ion binding]; other site 634504001741 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 634504001742 synthetase active site [active] 634504001743 NTP binding site [chemical binding]; other site 634504001744 metal binding site [ion binding]; metal-binding site 634504001745 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 634504001746 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 634504001747 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 634504001748 active site 634504001749 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 634504001750 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 634504001751 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 634504001752 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 634504001753 Catalytic site [active] 634504001754 ribonuclease III; Reviewed; Region: PRK12371 634504001755 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 634504001756 dimerization interface [polypeptide binding]; other site 634504001757 active site 634504001758 metal binding site [ion binding]; metal-binding site 634504001759 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 634504001760 dsRNA binding site [nucleotide binding]; other site 634504001761 GTPase Era; Reviewed; Region: era; PRK00089 634504001762 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 634504001763 G1 box; other site 634504001764 GTP/Mg2+ binding site [chemical binding]; other site 634504001765 Switch I region; other site 634504001766 G2 box; other site 634504001767 Switch II region; other site 634504001768 G3 box; other site 634504001769 G4 box; other site 634504001770 G5 box; other site 634504001771 KH domain; Region: KH_2; pfam07650 634504001772 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 634504001773 Recombination protein O N terminal; Region: RecO_N; pfam11967 634504001774 Recombination protein O C terminal; Region: RecO_C; pfam02565 634504001775 pantoate--beta-alanine ligase; Region: panC; TIGR00018 634504001776 Pantoate-beta-alanine ligase; Region: PanC; cd00560 634504001777 active site 634504001778 ATP-binding site [chemical binding]; other site 634504001779 pantoate-binding site; other site 634504001780 HXXH motif; other site 634504001781 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 634504001782 active site 634504001783 oligomerization interface [polypeptide binding]; other site 634504001784 metal binding site [ion binding]; metal-binding site 634504001785 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 634504001786 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 634504001787 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 634504001788 dihydroorotase; Validated; Region: PRK09060 634504001789 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 634504001790 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 634504001791 active site 634504001792 Protein of unknown function (DUF2385); Region: DUF2385; pfam09539 634504001793 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 634504001794 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 634504001795 active site 634504001796 HIGH motif; other site 634504001797 nucleotide binding site [chemical binding]; other site 634504001798 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 634504001799 KMSKS motif; other site 634504001800 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 634504001801 tRNA binding surface [nucleotide binding]; other site 634504001802 anticodon binding site; other site 634504001803 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 634504001804 Predicted membrane protein [Function unknown]; Region: COG2323 634504001805 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 634504001806 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 634504001807 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 634504001808 Walker A/P-loop; other site 634504001809 ATP binding site [chemical binding]; other site 634504001810 Q-loop/lid; other site 634504001811 ABC transporter signature motif; other site 634504001812 Walker B; other site 634504001813 D-loop; other site 634504001814 H-loop/switch region; other site 634504001815 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 634504001816 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 634504001817 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 634504001818 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 634504001819 classical (c) SDRs; Region: SDR_c; cd05233 634504001820 NAD(P) binding site [chemical binding]; other site 634504001821 active site 634504001822 amidophosphoribosyltransferase; Provisional; Region: PRK09123 634504001823 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 634504001824 active site 634504001825 tetramer interface [polypeptide binding]; other site 634504001826 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 634504001827 active site 634504001828 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 634504001829 Colicin V production protein; Region: Colicin_V; pfam02674 634504001830 DNA repair protein RadA; Provisional; Region: PRK11823 634504001831 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 634504001832 Walker A motif/ATP binding site; other site 634504001833 ATP binding site [chemical binding]; other site 634504001834 Walker B motif; other site 634504001835 replicative DNA helicase; Provisional; Region: PRK09165 634504001836 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 634504001837 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 634504001838 Walker A motif; other site 634504001839 ATP binding site [chemical binding]; other site 634504001840 Walker B motif; other site 634504001841 DNA binding loops [nucleotide binding] 634504001842 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 634504001843 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 634504001844 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 634504001845 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 634504001846 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 634504001847 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 634504001848 PAP2_like proteins, BcrC_like subfamily. Several members of this family have been annotated as bacitracin transport permeases, as it was suspected that they form the permease component of an ABC transporter system. It was shown, however, that BcrC from...; Region: PAP2_BcrC_like; cd03385 634504001849 active site 634504001850 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 634504001851 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 634504001852 3-ketoacyl-(acyl-carrier-protein) reductase NodG; Reviewed; Region: PRK12936 634504001853 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 634504001854 NAD(P) binding site [chemical binding]; other site 634504001855 homotetramer interface [polypeptide binding]; other site 634504001856 homodimer interface [polypeptide binding]; other site 634504001857 active site 634504001858 acyl carrier protein; Provisional; Region: acpP; PRK00982 634504001859 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 634504001860 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 634504001861 dimer interface [polypeptide binding]; other site 634504001862 active site 634504001863 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 634504001864 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 634504001865 dimerization interface [polypeptide binding]; other site 634504001866 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 634504001867 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 634504001868 catalytic site [active] 634504001869 G-X2-G-X-G-K; other site 634504001870 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 634504001871 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 634504001872 S-adenosylmethionine binding site [chemical binding]; other site 634504001873 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK05312 634504001874 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 634504001875 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 634504001876 SurA N-terminal domain; Region: SurA_N; pfam09312 634504001877 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 634504001878 OstA-like protein; Region: OstA; cl00844 634504001879 Organic solvent tolerance protein; Region: OstA_C; pfam04453 634504001880 Predicted permeases [General function prediction only]; Region: COG0795 634504001881 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 634504001882 Predicted permeases [General function prediction only]; Region: COG0795 634504001883 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 634504001884 DNA polymerase III subunit chi; Validated; Region: PRK05728 634504001885 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 634504001886 metabolite-proton symporter; Region: 2A0106; TIGR00883 634504001887 putative substrate translocation pore; other site 634504001888 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 634504001889 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 634504001890 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 634504001891 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504001892 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 634504001893 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 634504001894 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504001895 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 634504001896 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504001897 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 634504001898 active site 634504001899 multimer interface [polypeptide binding]; other site 634504001900 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 634504001901 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 634504001902 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 634504001903 GIY-YIG motif/motif A; other site 634504001904 active site 634504001905 catalytic site [active] 634504001906 putative DNA binding site [nucleotide binding]; other site 634504001907 metal binding site [ion binding]; metal-binding site 634504001908 UvrB/uvrC motif; Region: UVR; pfam02151 634504001909 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 634504001910 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 634504001911 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; cl17173 634504001912 twin arginine translocase protein A; Provisional; Region: tatA; PRK00720 634504001913 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 634504001914 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 634504001915 seryl-tRNA synthetase; Provisional; Region: PRK05431 634504001916 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 634504001917 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 634504001918 dimer interface [polypeptide binding]; other site 634504001919 active site 634504001920 motif 1; other site 634504001921 motif 2; other site 634504001922 motif 3; other site 634504001923 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 634504001924 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 634504001925 S-adenosylmethionine binding site [chemical binding]; other site 634504001926 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 634504001927 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 634504001928 Peptidase family M23; Region: Peptidase_M23; pfam01551 634504001929 Preprotein translocase subunit YajC [Intracellular trafficking and secretion]; Region: YajC; COG1862 634504001930 Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a...; Region: Mth938-like; cd00248 634504001931 Squalene/phytoene synthase; Region: SQS_PSY; pfam00494 634504001932 substrate binding pocket [chemical binding]; other site 634504001933 substrate-Mg2+ binding site; other site 634504001934 aspartate-rich region 1; other site 634504001935 aspartate-rich region 2; other site 634504001936 periplasmic folding chaperone; Provisional; Region: PRK10788 634504001937 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 634504001938 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 634504001939 triosephosphate isomerase; Provisional; Region: PRK14565 634504001940 substrate binding site [chemical binding]; other site 634504001941 dimer interface [polypeptide binding]; other site 634504001942 catalytic triad [active] 634504001943 preprotein translocase subunit SecG; Reviewed; Region: secG; PRK06870 634504001944 CTP synthetase; Validated; Region: pyrG; PRK05380 634504001945 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 634504001946 Catalytic site [active] 634504001947 active site 634504001948 UTP binding site [chemical binding]; other site 634504001949 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 634504001950 active site 634504001951 putative oxyanion hole; other site 634504001952 catalytic triad [active] 634504001953 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 634504001954 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 634504001955 enolase; Provisional; Region: eno; PRK00077 634504001956 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 634504001957 dimer interface [polypeptide binding]; other site 634504001958 metal binding site [ion binding]; metal-binding site 634504001959 substrate binding pocket [chemical binding]; other site 634504001960 TM2 domain; Region: TM2; pfam05154 634504001961 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 634504001962 Septum formation initiator; Region: DivIC; pfam04977 634504001963 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 634504001964 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 634504001965 tetramer interface [polypeptide binding]; other site 634504001966 TPP-binding site [chemical binding]; other site 634504001967 heterodimer interface [polypeptide binding]; other site 634504001968 phosphorylation loop region [posttranslational modification] 634504001969 pyruvate dehydrogenase subunit beta; Provisional; Region: PRK11892 634504001970 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 634504001971 E3 interaction surface; other site 634504001972 lipoyl attachment site [posttranslational modification]; other site 634504001973 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 634504001974 alpha subunit interface [polypeptide binding]; other site 634504001975 TPP binding site [chemical binding]; other site 634504001976 heterodimer interface [polypeptide binding]; other site 634504001977 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 634504001978 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 634504001979 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 634504001980 E3 interaction surface; other site 634504001981 lipoyl attachment site [posttranslational modification]; other site 634504001982 e3 binding domain; Region: E3_binding; pfam02817 634504001983 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 634504001984 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 634504001985 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 634504001986 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 634504001987 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 634504001988 lipoyl synthase; Provisional; Region: PRK05481 634504001989 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 634504001990 FeS/SAM binding site; other site 634504001991 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 634504001992 putative coenzyme Q binding site [chemical binding]; other site 634504001993 Competence-damaged protein; Region: CinA; pfam02464 634504001994 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 634504001995 substrate binding site; other site 634504001996 dimer interface; other site 634504001997 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 634504001998 homotrimer interaction site [polypeptide binding]; other site 634504001999 zinc binding site [ion binding]; other site 634504002000 CDP-binding sites; other site 634504002001 iron-responsive transcriptional regulator; Reviewed; Region: rirA; PRK11920 634504002002 Predicted transcriptional regulator [Transcription]; Region: COG1959 634504002003 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 634504002004 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 634504002005 dimerization interface [polypeptide binding]; other site 634504002006 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 634504002007 dimer interface [polypeptide binding]; other site 634504002008 phosphorylation site [posttranslational modification] 634504002009 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 634504002010 ATP binding site [chemical binding]; other site 634504002011 Mg2+ binding site [ion binding]; other site 634504002012 G-X-G motif; other site 634504002013 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 634504002014 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 634504002015 active site 634504002016 phosphorylation site [posttranslational modification] 634504002017 intermolecular recognition site; other site 634504002018 dimerization interface [polypeptide binding]; other site 634504002019 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 634504002020 Walker A motif; other site 634504002021 ATP binding site [chemical binding]; other site 634504002022 Walker B motif; other site 634504002023 arginine finger; other site 634504002024 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 634504002025 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 634504002026 TrkA-N domain; Region: TrkA_N; pfam02254 634504002027 TrkA-C domain; Region: TrkA_C; pfam02080 634504002028 TrkA-N domain; Region: TrkA_N; pfam02254 634504002029 TrkA-C domain; Region: TrkA_C; pfam02080 634504002030 Capsular polysaccharide synthesis protein; Region: Caps_synth; pfam05704 634504002031 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 634504002032 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 634504002033 oligomer interface [polypeptide binding]; other site 634504002034 active site residues [active] 634504002035 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 634504002036 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 634504002037 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 634504002038 Walker A motif; other site 634504002039 ATP binding site [chemical binding]; other site 634504002040 Walker B motif; other site 634504002041 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 634504002042 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 634504002043 Found in ATP-dependent protease La (LON); Region: LON; smart00464 634504002044 Found in ATP-dependent protease La (LON); Region: LON; smart00464 634504002045 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 634504002046 Walker A motif; other site 634504002047 ATP binding site [chemical binding]; other site 634504002048 Walker B motif; other site 634504002049 arginine finger; other site 634504002050 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 634504002051 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 634504002052 IHF dimer interface [polypeptide binding]; other site 634504002053 IHF - DNA interface [nucleotide binding]; other site 634504002054 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 634504002055 Glucose inhibited division protein A; Region: GIDA; pfam01134 634504002056 trigger factor; Provisional; Region: tig; PRK01490 634504002057 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 634504002058 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 634504002059 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 634504002060 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 634504002061 GatB domain; Region: GatB_Yqey; smart00845 634504002062 NADH dehydrogenase; Validated; Region: PRK08183 634504002063 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 634504002064 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 634504002065 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 634504002066 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 634504002067 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 634504002068 elongation factor Tu; Reviewed; Region: PRK00049 634504002069 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 634504002070 G1 box; other site 634504002071 GEF interaction site [polypeptide binding]; other site 634504002072 GTP/Mg2+ binding site [chemical binding]; other site 634504002073 Switch I region; other site 634504002074 G2 box; other site 634504002075 G3 box; other site 634504002076 Switch II region; other site 634504002077 G4 box; other site 634504002078 G5 box; other site 634504002079 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 634504002080 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 634504002081 Antibiotic Binding Site [chemical binding]; other site 634504002082 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 634504002083 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 634504002084 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 634504002085 putative homodimer interface [polypeptide binding]; other site 634504002086 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 634504002087 heterodimer interface [polypeptide binding]; other site 634504002088 homodimer interface [polypeptide binding]; other site 634504002089 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 634504002090 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 634504002091 23S rRNA interface [nucleotide binding]; other site 634504002092 L7/L12 interface [polypeptide binding]; other site 634504002093 putative thiostrepton binding site; other site 634504002094 L25 interface [polypeptide binding]; other site 634504002095 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 634504002096 mRNA/rRNA interface [nucleotide binding]; other site 634504002097 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 634504002098 23S rRNA interface [nucleotide binding]; other site 634504002099 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 634504002100 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 634504002101 L11 interface [polypeptide binding]; other site 634504002102 putative EF-Tu interaction site [polypeptide binding]; other site 634504002103 putative EF-G interaction site [polypeptide binding]; other site 634504002104 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 634504002105 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; cl17585 634504002106 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 634504002107 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 634504002108 RPB11 interaction site [polypeptide binding]; other site 634504002109 RPB12 interaction site [polypeptide binding]; other site 634504002110 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 634504002111 RPB1 interaction site [polypeptide binding]; other site 634504002112 RPB11 interaction site [polypeptide binding]; other site 634504002113 RPB10 interaction site [polypeptide binding]; other site 634504002114 RPB3 interaction site [polypeptide binding]; other site 634504002115 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 634504002116 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 634504002117 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 634504002118 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 634504002119 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 634504002120 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 634504002121 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 634504002122 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 634504002123 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 634504002124 Rpb1 - Rpb5 interaction site [polypeptide binding]; other site 634504002125 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 634504002126 DNA binding site [nucleotide binding] 634504002127 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 634504002128 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 634504002129 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 634504002130 DNA binding residues [nucleotide binding] 634504002131 putative dimer interface [polypeptide binding]; other site 634504002132 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source...; Region: Nitroreductase; cd02136 634504002133 putative FMN binding site [chemical binding]; other site 634504002134 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 634504002135 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 634504002136 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 634504002137 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 634504002138 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 634504002139 Sporulation related domain; Region: SPOR; pfam05036 634504002140 Uncharacterized conserved protein [Function unknown]; Region: COG2127 634504002141 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 634504002142 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 634504002143 Walker A motif; other site 634504002144 ATP binding site [chemical binding]; other site 634504002145 Walker B motif; other site 634504002146 arginine finger; other site 634504002147 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 634504002148 Walker A motif; other site 634504002149 ATP binding site [chemical binding]; other site 634504002150 Walker B motif; other site 634504002151 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 634504002152 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 634504002153 HIT family signature motif; other site 634504002154 catalytic residue [active] 634504002155 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_1; cd02199 634504002156 homotrimer interaction site [polypeptide binding]; other site 634504002157 putative active site [active] 634504002158 Domain of unknown function (DUF1849); Region: DUF1849; pfam08904 634504002159 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 634504002160 rRNA interaction site [nucleotide binding]; other site 634504002161 S8 interaction site; other site 634504002162 putative laminin-1 binding site; other site 634504002163 elongation factor Ts; Provisional; Region: tsf; PRK09377 634504002164 UBA/TS-N domain; Region: UBA; pfam00627 634504002165 Elongation factor TS; Region: EF_TS; pfam00889 634504002166 Elongation factor TS; Region: EF_TS; pfam00889 634504002167 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 634504002168 putative nucleotide binding site [chemical binding]; other site 634504002169 uridine monophosphate binding site [chemical binding]; other site 634504002170 homohexameric interface [polypeptide binding]; other site 634504002171 ribosome recycling factor; Reviewed; Region: frr; PRK00083 634504002172 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...; Region: RRF; cd00520 634504002173 hinge region; other site 634504002174 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 634504002175 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 634504002176 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 634504002177 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 634504002178 active site 634504002179 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 634504002180 protein binding site [polypeptide binding]; other site 634504002181 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 634504002182 putative substrate binding region [chemical binding]; other site 634504002183 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 634504002184 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 634504002185 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 634504002186 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 634504002187 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 634504002188 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 634504002189 Surface antigen; Region: Bac_surface_Ag; pfam01103 634504002190 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 634504002191 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 634504002192 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 634504002193 trimer interface [polypeptide binding]; other site 634504002194 active site 634504002195 UDP-GlcNAc binding site [chemical binding]; other site 634504002196 lipid binding site [chemical binding]; lipid-binding site 634504002197 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 634504002198 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 634504002199 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 634504002200 active site 634504002201 Protein of unknown function (DUF1009); Region: DUF1009; cl09182 634504002202 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 634504002203 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 634504002204 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 634504002205 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 634504002206 Walker A/P-loop; other site 634504002207 ATP binding site [chemical binding]; other site 634504002208 Q-loop/lid; other site 634504002209 ABC transporter signature motif; other site 634504002210 Walker B; other site 634504002211 D-loop; other site 634504002212 H-loop/switch region; other site 634504002213 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 634504002214 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 634504002215 dimer interface [polypeptide binding]; other site 634504002216 conserved gate region; other site 634504002217 putative PBP binding loops; other site 634504002218 ABC-ATPase subunit interface; other site 634504002219 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 634504002220 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 634504002221 dimer interface [polypeptide binding]; other site 634504002222 conserved gate region; other site 634504002223 putative PBP binding loops; other site 634504002224 ABC-ATPase subunit interface; other site 634504002225 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 634504002226 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 634504002227 substrate binding pocket [chemical binding]; other site 634504002228 membrane-bound complex binding site; other site 634504002229 hinge residues; other site 634504002230 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 634504002231 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 634504002232 substrate binding pocket [chemical binding]; other site 634504002233 membrane-bound complex binding site; other site 634504002234 hinge residues; other site 634504002235 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 634504002236 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 634504002237 dimer interface [polypeptide binding]; other site 634504002238 active site 634504002239 citrylCoA binding site [chemical binding]; other site 634504002240 NADH binding [chemical binding]; other site 634504002241 cationic pore residues; other site 634504002242 oxalacetate/citrate binding site [chemical binding]; other site 634504002243 coenzyme A binding site [chemical binding]; other site 634504002244 catalytic triad [active] 634504002245 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 634504002246 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 634504002247 active site 634504002248 HIGH motif; other site 634504002249 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 634504002250 active site 634504002251 KMSKS motif; other site 634504002252 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 634504002253 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 634504002254 Competence protein; Region: Competence; pfam03772 634504002255 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 634504002256 tetramer (dimer of dimers) interface [polypeptide binding]; other site 634504002257 active site 634504002258 dimer interface [polypeptide binding]; other site 634504002259 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; cl01243 634504002260 glutathione reductase; Validated; Region: PRK06116 634504002261 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 634504002262 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 634504002263 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 634504002264 NAD synthetase; Provisional; Region: PRK13981 634504002265 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 634504002266 multimer interface [polypeptide binding]; other site 634504002267 active site 634504002268 catalytic triad [active] 634504002269 protein interface 1 [polypeptide binding]; other site 634504002270 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 634504002271 homodimer interface [polypeptide binding]; other site 634504002272 NAD binding pocket [chemical binding]; other site 634504002273 ATP binding pocket [chemical binding]; other site 634504002274 Mg binding site [ion binding]; other site 634504002275 active-site loop [active] 634504002276 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 634504002277 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 634504002278 active site 634504002279 HIGH motif; other site 634504002280 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 634504002281 active site 634504002282 KMSKS motif; other site 634504002283 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 634504002284 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 634504002285 ATP binding site [chemical binding]; other site 634504002286 Mg++ binding site [ion binding]; other site 634504002287 motif III; other site 634504002288 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 634504002289 nucleotide binding region [chemical binding]; other site 634504002290 ATP-binding site [chemical binding]; other site 634504002291 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 634504002292 ATP-NAD kinase; Region: NAD_kinase; pfam01513 634504002293 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 634504002294 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 634504002295 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 634504002296 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 634504002297 Transporter associated domain; Region: CorC_HlyC; smart01091 634504002298 Predicted integral membrane protein [Function unknown]; Region: COG0392 634504002299 putative cation:proton antiport protein; Provisional; Region: PRK10669 634504002300 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 634504002301 TrkA-N domain; Region: TrkA_N; pfam02254 634504002302 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 634504002303 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 634504002304 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 634504002305 Protein export membrane protein; Region: SecD_SecF; pfam02355 634504002306 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 634504002307 Mechanosensitive ion channel; Region: MS_channel; pfam00924 634504002308 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 634504002309 putative addiction module killer protein; Region: upstrm_HI1419; TIGR02683 634504002310 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 634504002311 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 634504002312 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 634504002313 active site 634504002314 catalytic residues [active] 634504002315 DNA binding site [nucleotide binding] 634504002316 Int/Topo IB signature motif; other site 634504002317 Sugar fermentation stimulation protein; Region: SfsA; cl00647 634504002318 Protein of unknown function, DUF488; Region: DUF488; pfam04343 634504002319 YqaJ-like viral recombinase domain; Region: YqaJ; pfam09588 634504002320 RecT family; Region: RecT; pfam03837 634504002321 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002322 putative trimer interface [polypeptide binding]; other site 634504002323 putative CoA binding site [chemical binding]; other site 634504002324 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002325 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002326 putative trimer interface [polypeptide binding]; other site 634504002327 putative CoA binding site [chemical binding]; other site 634504002328 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 634504002329 sequence-specific DNA binding site [nucleotide binding]; other site 634504002330 salt bridge; other site 634504002331 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 634504002332 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...; Region: RuvC_resolvase; cl17280 634504002333 active site 634504002334 Protein of unknown function (DUF1376); Region: DUF1376; cl01531 634504002335 Protein of unknown function (DUF1376); Region: DUF1376; cl01531 634504002336 AntA/AntB antirepressor; Region: AntA; cl01430 634504002337 replicative DNA helicase; Provisional; Region: PRK09165 634504002338 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 634504002339 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 634504002340 Walker A motif; other site 634504002341 ATP binding site [chemical binding]; other site 634504002342 Walker B motif; other site 634504002343 DNA binding loops [nucleotide binding] 634504002344 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 634504002345 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 634504002346 dimer interface [polypeptide binding]; other site 634504002347 ssDNA binding site [nucleotide binding]; other site 634504002348 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002349 putative trimer interface [polypeptide binding]; other site 634504002350 putative CoA binding site [chemical binding]; other site 634504002351 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002352 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002353 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002354 Predicted helicase [General function prediction only]; Region: COG4889 634504002355 Restriction endonuclease; Region: Mrr_cat_2; pfam13156 634504002356 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 634504002357 ATP binding site [chemical binding]; other site 634504002358 putative Mg++ binding site [ion binding]; other site 634504002359 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 634504002360 nucleotide binding region [chemical binding]; other site 634504002361 ATP-binding site [chemical binding]; other site 634504002362 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 634504002363 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 634504002364 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 634504002365 haemagglutination activity domain; Region: Haemagg_act; pfam05860 634504002366 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 634504002367 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 634504002368 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 634504002369 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 634504002370 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 634504002371 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 634504002372 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 634504002373 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 634504002374 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 634504002375 active site 634504002376 Int/Topo IB signature motif; other site 634504002377 Phage terminase large subunit; Region: Terminase_3; cl12054 634504002378 Protein of unknown function (DUF4043); Region: DUF4043; pfam13252 634504002379 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002380 UDP-3-O-[3-hydroxymyristoyl]; Region: LpxD; COG1044 634504002381 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002382 putative trimer interface [polypeptide binding]; other site 634504002383 putative CoA binding site [chemical binding]; other site 634504002384 Predicted helicase [General function prediction only]; Region: COG4889 634504002385 Restriction endonuclease; Region: Mrr_cat_2; pfam13156 634504002386 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 634504002387 ATP binding site [chemical binding]; other site 634504002388 putative Mg++ binding site [ion binding]; other site 634504002389 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 634504002390 nucleotide binding region [chemical binding]; other site 634504002391 ATP-binding site [chemical binding]; other site 634504002392 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 634504002393 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 634504002394 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 634504002395 haemagglutination activity domain; Region: Haemagg_act; pfam05860 634504002396 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 634504002397 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 634504002398 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 634504002399 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 634504002400 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 634504002401 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 634504002402 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 634504002403 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 634504002404 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 634504002405 active site 634504002406 Int/Topo IB signature motif; other site 634504002407 Helix-turn-helix domain; Region: HTH_37; pfam13744 634504002408 non-specific DNA binding site [nucleotide binding]; other site 634504002409 salt bridge; other site 634504002410 sequence-specific DNA binding site [nucleotide binding]; other site 634504002411 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 634504002412 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002413 UDP-3-O-[3-hydroxymyristoyl]; Region: LpxD; COG1044 634504002414 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002415 putative trimer interface [polypeptide binding]; other site 634504002416 putative CoA binding site [chemical binding]; other site 634504002417 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 634504002418 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 634504002419 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 634504002420 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 634504002421 haemagglutination activity domain; Region: Haemagg_act; pfam05860 634504002422 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 634504002423 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 634504002424 A nuclease of the HNH/ENDO VII superfamily with conserved LHH; Region: LHH; pfam14411 634504002425 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504002426 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 634504002427 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504002428 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 634504002429 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 634504002430 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 634504002431 Predicted transcriptional regulator [Transcription]; Region: COG3905 634504002432 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 634504002433 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 634504002434 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 634504002435 active site 634504002436 Int/Topo IB signature motif; other site 634504002437 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...; Region: LT_GEWL; cd00254 634504002438 N-acetyl-D-glucosamine binding site [chemical binding]; other site 634504002439 catalytic residue [active] 634504002440 Phage Tail Collar Domain; Region: Collar; pfam07484 634504002441 Phage Tail Collar Domain; Region: Collar; pfam07484 634504002442 Phage Tail Collar Domain; Region: Collar; pfam07484 634504002443 major tropism determinant; Region: mtd; PHA00653 634504002444 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 634504002445 catalytic residues [active] 634504002446 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 634504002447 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 634504002448 putatively functional bacteriophage; functionality not clear; exact boundaries not determined 634504002449 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 634504002450 active site 634504002451 Int/Topo IB signature motif; other site 634504002452 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 634504002453 catalytic residues [active] 634504002454 putative addiction module killer protein; Region: upstrm_HI1419; TIGR02683 634504002455 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 634504002456 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 634504002457 Mnt; Region: mnt; PHA01513 634504002458 Arc-like DNA binding domain; Region: Arc; pfam03869 634504002459 AntA/AntB antirepressor; Region: AntA; pfam08346 634504002460 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 634504002461 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 634504002462 Phage Tail Protein X; Region: Phage_tail_X; cl02088 634504002463 Phage P2 GpU; Region: Phage_P2_GpU; pfam06995 634504002464 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 634504002465 Mu-like prophage FluMu protein gp41; Region: FluMu_gp41; pfam10109 634504002466 Phage tail tube protein FII; Region: Phage_tube; pfam04985 634504002467 major tail sheath protein; Provisional; Region: FI; PHA02560 634504002468 AntA/AntB antirepressor; Region: AntA; pfam08346 634504002469 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 634504002470 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 634504002471 non-specific DNA binding site [nucleotide binding]; other site 634504002472 salt bridge; other site 634504002473 sequence-specific DNA binding site [nucleotide binding]; other site 634504002474 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 634504002475 Phage tail repeat like; Region: PTR; pfam12789 634504002476 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; cl01817 634504002477 Baseplate J-like protein; Region: Baseplate_J; cl01294 634504002478 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 634504002479 phage baseplate assembly protein V; Region: phage_P2_V; TIGR01644 634504002480 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 634504002481 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 634504002482 Protein of unknown function (DUF497); Region: DUF497; cl01108 634504002483 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 634504002484 HicB family; Region: HicB; pfam05534 634504002485 AntA/AntB antirepressor; Region: AntA; cl01430 634504002486 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 634504002487 UDP-3-O-[3-hydroxymyristoyl]; Region: LpxD; COG1044 634504002488 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002489 putative trimer interface [polypeptide binding]; other site 634504002490 putative CoA binding site [chemical binding]; other site 634504002491 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 634504002492 Bacteriophage lambda head decoration protein D; Region: HDPD; pfam02924 634504002493 Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_36K_type; cd07022 634504002494 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 634504002495 tandem repeat interface [polypeptide binding]; other site 634504002496 oligomer interface [polypeptide binding]; other site 634504002497 active site residues [active] 634504002498 Phage portal protein, lambda family; Region: Phage_portal_2; pfam05136 634504002499 phage portal protein, lambda family; Region: portal_lambda; TIGR01539 634504002500 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 634504002501 YcfA-like protein; Region: YcfA; pfam07927 634504002502 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 634504002503 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 634504002504 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 634504002505 dimer interface [polypeptide binding]; other site 634504002506 ssDNA binding site [nucleotide binding]; other site 634504002507 tetramer (dimer of dimers) interface [polypeptide binding]; other site 634504002508 Helix-turn-helix domain; Region: HTH_19; pfam12844 634504002509 non-specific DNA binding site [nucleotide binding]; other site 634504002510 salt bridge; other site 634504002511 sequence-specific DNA binding site [nucleotide binding]; other site 634504002512 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 634504002513 Protein of unknown function (DUF1376); Region: DUF1376; cl01531 634504002514 Protein of unknown function (DUF1376); Region: DUF1376; cl01531 634504002515 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...; Region: RuvC_resolvase; cl17280 634504002516 active site 634504002517 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 634504002518 non-specific DNA binding site [nucleotide binding]; other site 634504002519 salt bridge; other site 634504002520 sequence-specific DNA binding site [nucleotide binding]; other site 634504002521 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 634504002522 non-specific DNA binding site [nucleotide binding]; other site 634504002523 salt bridge; other site 634504002524 sequence-specific DNA binding site [nucleotide binding]; other site 634504002525 AntA/AntB antirepressor; Region: AntA; cl01430 634504002526 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; pfam09669 634504002527 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 634504002528 ERF superfamily; Region: ERF; pfam04404 634504002529 YqaJ-like viral recombinase domain; Region: YqaJ; pfam09588 634504002530 Helix-turn-helix domain; Region: HTH_17; pfam12728 634504002531 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 634504002532 catalytic core [active] 634504002533 dihydrodipicolinate reductase; Provisional; Region: PRK00048 634504002534 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 634504002535 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 634504002536 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 634504002537 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 634504002538 C-terminal domain interface [polypeptide binding]; other site 634504002539 GSH binding site (G-site) [chemical binding]; other site 634504002540 dimer interface [polypeptide binding]; other site 634504002541 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 634504002542 N-terminal domain interface [polypeptide binding]; other site 634504002543 dimer interface [polypeptide binding]; other site 634504002544 substrate binding pocket (H-site) [chemical binding]; other site 634504002545 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 634504002546 G1 box; other site 634504002547 GTP/Mg2+ binding site [chemical binding]; other site 634504002548 Switch I region; other site 634504002549 G2 box; other site 634504002550 G3 box; other site 634504002551 Switch II region; other site 634504002552 G4 box; other site 634504002553 G5 box; other site 634504002554 membrane protein insertase; Provisional; Region: PRK01318 634504002555 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 634504002556 ribonuclease P; Reviewed; Region: rnpA; PRK01313 634504002557 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 634504002558 antiporter inner membrane protein; Provisional; Region: PRK11670 634504002559 Domain of unknown function DUF59; Region: DUF59; pfam01883 634504002560 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 634504002561 Walker A motif; other site 634504002562 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK06476 634504002563 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; pfam03807 634504002564 hypothetical protein; Reviewed; Region: PRK12497 634504002565 Predicted methyltransferases [General function prediction only]; Region: COG0313 634504002566 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 634504002567 putative SAM binding site [chemical binding]; other site 634504002568 putative homodimer interface [polypeptide binding]; other site 634504002569 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 634504002570 hydroxyglutarate oxidase; Provisional; Region: PRK11728 634504002571 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 634504002572 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 634504002573 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 634504002574 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 634504002575 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 634504002576 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 634504002577 Ligand binding site [chemical binding]; other site 634504002578 Electron transfer flavoprotein domain; Region: ETF; pfam01012 634504002579 Predicted permeases [General function prediction only]; Region: COG0730 634504002580 Putative transmembrane protein (Alph_Pro_TM); Region: Alph_Pro_TM; pfam09608 634504002581 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_7; cd08512 634504002582 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 634504002583 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_7; cd08512 634504002584 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 634504002585 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_7; cd08512 634504002586 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 634504002587 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 634504002588 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 634504002589 generic binding surface II; other site 634504002590 generic binding surface I; other site 634504002591 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 634504002592 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_7; cd08512 634504002593 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 634504002594 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_7; cd08512 634504002595 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 634504002596 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 634504002597 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 634504002598 dimer interface [polypeptide binding]; other site 634504002599 conserved gate region; other site 634504002600 putative PBP binding loops; other site 634504002601 ABC-ATPase subunit interface; other site 634504002602 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 634504002603 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 634504002604 dimer interface [polypeptide binding]; other site 634504002605 conserved gate region; other site 634504002606 ABC-ATPase subunit interface; other site 634504002607 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 634504002608 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 634504002609 Walker A/P-loop; other site 634504002610 ATP binding site [chemical binding]; other site 634504002611 Q-loop/lid; other site 634504002612 ABC transporter signature motif; other site 634504002613 Walker B; other site 634504002614 D-loop; other site 634504002615 H-loop/switch region; other site 634504002616 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 634504002617 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 634504002618 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 634504002619 Walker A/P-loop; other site 634504002620 ATP binding site [chemical binding]; other site 634504002621 Q-loop/lid; other site 634504002622 ABC transporter signature motif; other site 634504002623 Walker B; other site 634504002624 D-loop; other site 634504002625 H-loop/switch region; other site 634504002626 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 634504002627 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 634504002628 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504002629 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 634504002630 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 634504002631 Phage P2 GpU; Region: Phage_P2_GpU; cl01391 634504002632 Phage Tail Protein X; Region: Phage_tail_X; cl02088 634504002633 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 634504002634 replicative DNA helicase; Provisional; Region: PRK09165 634504002635 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 634504002636 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 634504002637 Walker A motif; other site 634504002638 ATP binding site [chemical binding]; other site 634504002639 Walker B motif; other site 634504002640 DNA binding loops [nucleotide binding] 634504002641 Plasmid maintenance system killer protein; Region: Plasmid_killer; pfam05015 634504002642 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 634504002643 non-specific DNA binding site [nucleotide binding]; other site 634504002644 salt bridge; other site 634504002645 sequence-specific DNA binding site [nucleotide binding]; other site 634504002646 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 634504002647 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 634504002648 active site 634504002649 catalytic residues [active] 634504002650 DNA binding site [nucleotide binding] 634504002651 Int/Topo IB signature motif; other site 634504002652 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504002653 putative trimer interface [polypeptide binding]; other site 634504002654 putative CoA binding site [chemical binding]; other site 634504002655 Protein of unknown function, DUF488; Region: DUF488; pfam04343 634504002656 YqaJ-like viral recombinase domain; Region: YqaJ; pfam09588 634504002657 ERF superfamily; Region: ERF; pfam04404 634504002658 AntA/AntB antirepressor; Region: AntA; pfam08346 634504002659 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 634504002660 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 634504002661 non-specific DNA binding site [nucleotide binding]; other site 634504002662 salt bridge; other site 634504002663 sequence-specific DNA binding site [nucleotide binding]; other site 634504002664 Predicted transcriptional regulator [Transcription]; Region: COG2932 634504002665 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 634504002666 Catalytic site [active] 634504002667 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 634504002668 non-specific DNA binding site [nucleotide binding]; other site 634504002669 salt bridge; other site 634504002670 sequence-specific DNA binding site [nucleotide binding]; other site 634504002671 Protein of unknown function (DUF1376); Region: DUF1376; pfam07120 634504002672 3-oxoacyl-[acyl-carrier-protein] synthase II; Region: PLN02787 634504002673 Domain of unknown function (DUF4415); Region: DUF4415; pfam14384 634504002674 Protein of unknown function (DUF497); Region: DUF497; pfam04365 634504002675 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 634504002676 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 634504002677 dimer interface [polypeptide binding]; other site 634504002678 ssDNA binding site [nucleotide binding]; other site 634504002679 tetramer (dimer of dimers) interface [polypeptide binding]; other site 634504002680 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 634504002681 Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]; Region: RelE; COG2026 634504002682 Phage terminase large subunit; Region: Terminase_3; cl12054 634504002683 Protein of unknown function (DUF4043); Region: DUF4043; pfam13252 634504002684 ATP synthase (F/14-kDa) subunit; Region: ATP-synt_F; cl00632 634504002685 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 634504002686 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...; Region: LT_GEWL; cd00254 634504002687 N-acetyl-D-glucosamine binding site [chemical binding]; other site 634504002688 catalytic residue [active] 634504002689 Phage Tail Collar Domain; Region: Collar; pfam07484 634504002690 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 634504002691 catalytic residues [active] 634504002692 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 634504002693 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 634504002694 Helix-turn-helix domain; Region: HTH_19; pfam12844 634504002695 non-specific DNA binding site [nucleotide binding]; other site 634504002696 salt bridge; other site 634504002697 sequence-specific DNA binding site [nucleotide binding]; other site 634504002698 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 634504002699 NADH dehydrogenase subunit B; Validated; Region: PRK06411 634504002700 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 634504002701 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 634504002702 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 634504002703 NADH dehydrogenase subunit D; Validated; Region: PRK06075 634504002704 NADH dehydrogenase subunit E; Validated; Region: PRK07539 634504002705 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 634504002706 putative dimer interface [polypeptide binding]; other site 634504002707 [2Fe-2S] cluster binding site [ion binding]; other site 634504002708 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 634504002709 SLBB domain; Region: SLBB; pfam10531 634504002710 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 634504002711 NADH dehydrogenase subunit G; Validated; Region: PRK09130 634504002712 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 634504002713 catalytic loop [active] 634504002714 iron binding site [ion binding]; other site 634504002715 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 634504002716 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase...; Region: MopB_Res-Cmplx1_Nad11; cd02773 634504002717 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 634504002718 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 634504002719 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 634504002720 4Fe-4S binding domain; Region: Fer4; pfam00037 634504002721 4Fe-4S binding domain; Region: Fer4; pfam00037 634504002722 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 634504002723 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 634504002724 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 634504002725 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 634504002726 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 634504002727 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 634504002728 NADH dehydrogenase subunit 5 C-terminus; Region: NADH5_C; pfam06455 634504002729 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 634504002730 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 634504002731 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 634504002732 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 634504002733 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 634504002734 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 634504002735 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 634504002736 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 634504002737 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 634504002738 prolyl-tRNA synthetase; Provisional; Region: PRK12325 634504002739 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...; Region: ProRS_core_prok; cd00779 634504002740 dimer interface [polypeptide binding]; other site 634504002741 motif 1; other site 634504002742 active site 634504002743 motif 2; other site 634504002744 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 634504002745 active site 634504002746 motif 3; other site 634504002747 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 634504002748 anticodon binding site; other site 634504002749 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 634504002750 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 634504002751 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 634504002752 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 634504002753 Walker A/P-loop; other site 634504002754 ATP binding site [chemical binding]; other site 634504002755 Q-loop/lid; other site 634504002756 ABC transporter signature motif; other site 634504002757 Walker B; other site 634504002758 D-loop; other site 634504002759 H-loop/switch region; other site 634504002760 Uncharacterized conserved protein [Function unknown]; Region: COG2938 634504002761 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 634504002762 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 634504002763 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 634504002764 ATP binding site [chemical binding]; other site 634504002765 putative Mg++ binding site [ion binding]; other site 634504002766 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 634504002767 nucleotide binding region [chemical binding]; other site 634504002768 ATP-binding site [chemical binding]; other site 634504002769 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 634504002770 Invasion associated locus B (IalB) protein; Region: IalB; pfam06776 634504002771 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 634504002772 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 634504002773 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 634504002774 RNA binding site [nucleotide binding]; other site 634504002775 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 634504002776 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 634504002777 active site 634504002778 metal binding site [ion binding]; metal-binding site 634504002779 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 634504002780 Transglycosylase; Region: Transgly; pfam00912 634504002781 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 634504002782 peptide chain release factor 2; Provisional; Region: PRK07342 634504002783 This domain is found in peptide chain release factors; Region: PCRF; smart00937 634504002784 RF-1 domain; Region: RF-1; pfam00472 634504002785 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 634504002786 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 634504002787 catalytic triad [active] 634504002788 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 634504002789 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 634504002790 active site 634504002791 HIGH motif; other site 634504002792 dimer interface [polypeptide binding]; other site 634504002793 KMSKS motif; other site 634504002794 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 634504002795 RNA binding surface [nucleotide binding]; other site 634504002796 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 634504002797 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 634504002798 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 634504002799 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 634504002800 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 634504002801 catalytic residue [active] 634504002802 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 634504002803 putative ABC transporter; Region: ycf24; CHL00085 634504002804 Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]; Region: sufC; COG0396 634504002805 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 634504002806 Walker A/P-loop; other site 634504002807 ATP binding site [chemical binding]; other site 634504002808 Q-loop/lid; other site 634504002809 ABC transporter signature motif; other site 634504002810 Walker B; other site 634504002811 D-loop; other site 634504002812 H-loop/switch region; other site 634504002813 Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]; Region: SufB; COG0719 634504002814 FeS assembly protein SufD; Region: sufD; TIGR01981 634504002815 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 634504002816 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 634504002817 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 634504002818 catalytic residue [active] 634504002819 FeS assembly SUF system protein; Region: SUF_assoc; TIGR02945 634504002820 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 634504002821 DNA methylase; Region: N6_N4_Mtase; pfam01555 634504002822 DNA methylase; Region: N6_N4_Mtase; pfam01555 634504002823 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 634504002824 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 634504002825 Protein of unknown function (DUF511); Region: DUF511; pfam04373 634504002826 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 634504002827 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 634504002828 E-class dimer interface [polypeptide binding]; other site 634504002829 P-class dimer interface [polypeptide binding]; other site 634504002830 active site 634504002831 Cu2+ binding site [ion binding]; other site 634504002832 Zn2+ binding site [ion binding]; other site 634504002833 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional; Region: PRK07494 634504002834 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 634504002835 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 634504002836 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 634504002837 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 634504002838 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 634504002839 substrate binding site [chemical binding]; other site 634504002840 oxyanion hole (OAH) forming residues; other site 634504002841 trimer interface [polypeptide binding]; other site 634504002842 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 634504002843 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 634504002844 putative hydrolase; Provisional; Region: PRK02113 634504002845 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 634504002846 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 634504002847 active site 634504002848 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 634504002849 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 634504002850 active site 634504002851 HIGH motif; other site 634504002852 KMSKS motif; other site 634504002853 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 634504002854 tRNA binding surface [nucleotide binding]; other site 634504002855 anticodon binding site; other site 634504002856 DNA polymerase III subunit delta'; Validated; Region: PRK09112 634504002857 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 634504002858 Walker A motif; other site 634504002859 ATP binding site [chemical binding]; other site 634504002860 Walker B motif; other site 634504002861 arginine finger; other site 634504002862 thymidylate kinase; Validated; Region: tmk; PRK00698 634504002863 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 634504002864 TMP-binding site; other site 634504002865 ATP-binding site [chemical binding]; other site 634504002866 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 634504002867 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 634504002868 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 634504002869 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 634504002870 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 634504002871 LexA repressor; Validated; Region: PRK00215 634504002872 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 634504002873 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 634504002874 Catalytic site [active] 634504002875 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 634504002876 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 634504002877 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 634504002878 FeS/SAM binding site; other site 634504002879 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 634504002880 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 634504002881 Ligand Binding Site [chemical binding]; other site 634504002882 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 634504002883 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 634504002884 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 634504002885 RNA binding surface [nucleotide binding]; other site 634504002886 glutamate racemase; Provisional; Region: PRK00865 634504002887 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 634504002888 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 634504002889 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 634504002890 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 634504002891 active site 634504002892 hypothetical protein; Reviewed; Region: PRK00024 634504002893 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 634504002894 MPN+ (JAMM) motif; other site 634504002895 Zinc-binding site [ion binding]; other site 634504002896 Protein of unknown function (DUF3126); Region: DUF3126; pfam11324 634504002897 proline-specific peptidase, Bacillus coagulans-type subfamily; Region: pro_imino_pep_2; TIGR01250 634504002898 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 634504002899 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 634504002900 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...; Region: CSP_CDS; cd04458 634504002901 DNA-binding site [nucleotide binding]; DNA binding site 634504002902 RNA-binding motif; other site 634504002903 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...; Region: CSP_CDS; cd04458 634504002904 DNA-binding site [nucleotide binding]; DNA binding site 634504002905 RNA-binding motif; other site 634504002906 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 634504002907 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_12; cd06347 634504002908 putative ligand binding site [chemical binding]; other site 634504002909 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 634504002910 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 634504002911 TM-ABC transporter signature motif; other site 634504002912 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 634504002913 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 634504002914 TM-ABC transporter signature motif; other site 634504002915 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 634504002916 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 634504002917 Walker A/P-loop; other site 634504002918 ATP binding site [chemical binding]; other site 634504002919 Q-loop/lid; other site 634504002920 ABC transporter signature motif; other site 634504002921 Walker B; other site 634504002922 D-loop; other site 634504002923 H-loop/switch region; other site 634504002924 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 634504002925 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 634504002926 Walker A/P-loop; other site 634504002927 ATP binding site [chemical binding]; other site 634504002928 Q-loop/lid; other site 634504002929 ABC transporter signature motif; other site 634504002930 Walker B; other site 634504002931 D-loop; other site 634504002932 H-loop/switch region; other site 634504002933 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 634504002934 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 634504002935 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 634504002936 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 634504002937 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 634504002938 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 634504002939 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 634504002940 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 634504002941 dihydroorotase; Validated; Region: PRK09059 634504002942 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 634504002943 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 634504002944 active site 634504002945 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 634504002946 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 634504002947 DNA protecting protein DprA; Region: dprA; TIGR00732 634504002948 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 634504002949 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 634504002950 active site 634504002951 interdomain interaction site; other site 634504002952 putative metal-binding site [ion binding]; other site 634504002953 nucleotide binding site [chemical binding]; other site 634504002954 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 634504002955 domain I; other site 634504002956 DNA binding groove [nucleotide binding] 634504002957 phosphate binding site [ion binding]; other site 634504002958 domain II; other site 634504002959 domain III; other site 634504002960 nucleotide binding site [chemical binding]; other site 634504002961 catalytic site [active] 634504002962 domain IV; other site 634504002963 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 634504002964 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 634504002965 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 634504002966 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 634504002967 ribonuclease R; Region: RNase_R; TIGR02063 634504002968 RNB domain; Region: RNB; pfam00773 634504002969 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...; Region: S1_RNase_R; cd04471 634504002970 RNA binding site [nucleotide binding]; other site 634504002971 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 634504002972 Major Facilitator Superfamily; Region: MFS_1; pfam07690 634504002973 putative substrate translocation pore; other site 634504002974 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 634504002975 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]; Region: COG1525 634504002976 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 634504002977 Catalytic site; other site 634504002978 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 634504002979 putative uracil binding site [chemical binding]; other site 634504002980 putative active site [active] 634504002981 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 634504002982 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 634504002983 putative DNA binding site [nucleotide binding]; other site 634504002984 putative Zn2+ binding site [ion binding]; other site 634504002985 AsnC family; Region: AsnC_trans_reg; pfam01037 634504002986 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 634504002987 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 634504002988 active site pocket [active] 634504002989 putative dimer interface [polypeptide binding]; other site 634504002990 putative cataytic base [active] 634504002991 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 634504002992 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 634504002993 FMN binding site [chemical binding]; other site 634504002994 active site 634504002995 catalytic residues [active] 634504002996 substrate binding site [chemical binding]; other site 634504002997 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 634504002998 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 634504002999 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 634504003000 catalytic residues [active] 634504003001 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 634504003002 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 634504003003 carboxyltransferase (CT) interaction site; other site 634504003004 biotinylation site [posttranslational modification]; other site 634504003005 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 634504003006 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 634504003007 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 634504003008 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 634504003009 Alpha/beta hydrolase of unknown function (DUF900); Region: DUF900; pfam05990 634504003010 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 634504003011 GTP cyclohydrolase I; Provisional; Region: PLN03044 634504003012 active site 634504003013 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 634504003014 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 634504003015 trimerization site [polypeptide binding]; other site 634504003016 active site 634504003017 hypothetical protein; Validated; Region: PRK00041 634504003018 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 634504003019 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 634504003020 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 634504003021 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 634504003022 active site 634504003023 dimer interface [polypeptide binding]; other site 634504003024 motif 1; other site 634504003025 motif 2; other site 634504003026 motif 3; other site 634504003027 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 634504003028 anticodon binding site; other site 634504003029 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 634504003030 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 634504003031 DNA binding residues [nucleotide binding] 634504003032 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 634504003033 IHF dimer interface [polypeptide binding]; other site 634504003034 IHF - DNA interface [nucleotide binding]; other site 634504003035 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 634504003036 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 634504003037 dimer interface [polypeptide binding]; other site 634504003038 active site 634504003039 CoA binding pocket [chemical binding]; other site 634504003040 putative phosphate acyltransferase; Provisional; Region: PRK05331 634504003041 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 634504003042 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 634504003043 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 634504003044 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 634504003045 putative RNA binding site [nucleotide binding]; other site 634504003046 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 634504003047 homopentamer interface [polypeptide binding]; other site 634504003048 active site 634504003049 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 634504003050 Lumazine binding domain; Region: Lum_binding; pfam00677 634504003051 Lumazine binding domain; Region: Lum_binding; pfam00677 634504003052 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 634504003053 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 634504003054 catalytic motif [active] 634504003055 Zn binding site [ion binding]; other site 634504003056 RibD C-terminal domain; Region: RibD_C; cl17279 634504003057 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 634504003058 ATP cone domain; Region: ATP-cone; pfam03477 634504003059 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 634504003060 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 634504003061 dimer interface [polypeptide binding]; other site 634504003062 active site 634504003063 glycine-pyridoxal phosphate binding site [chemical binding]; other site 634504003064 folate binding site [chemical binding]; other site 634504003065 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 634504003066 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 634504003067 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 634504003068 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 634504003069 AAA domain; Region: AAA_31; pfam13614 634504003070 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 634504003071 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 634504003072 HflX GTPase family; Region: HflX; cd01878 634504003073 G1 box; other site 634504003074 GTP/Mg2+ binding site [chemical binding]; other site 634504003075 Switch I region; other site 634504003076 G2 box; other site 634504003077 G3 box; other site 634504003078 Switch II region; other site 634504003079 G4 box; other site 634504003080 G5 box; other site 634504003081 bacterial Hfq-like; Region: Hfq; cd01716 634504003082 hexamer interface [polypeptide binding]; other site 634504003083 Sm1 motif; other site 634504003084 RNA binding site [nucleotide binding]; other site 634504003085 Sm2 motif; other site 634504003086 malic enzyme; Reviewed; Region: PRK12862 634504003087 Malic enzyme, N-terminal domain; Region: malic; pfam00390 634504003088 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 634504003089 putative NAD(P) binding site [chemical binding]; other site 634504003090 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 634504003091 acyl carrier protein; Provisional; Region: PRK06508 634504003092 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06519 634504003093 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 634504003094 active site 634504003095 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06501 634504003096 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 634504003097 dimer interface [polypeptide binding]; other site 634504003098 active site 634504003099 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 634504003100 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH_like1; cd08266 634504003101 putative NAD(P) binding site [chemical binding]; other site 634504003102 structural Zn binding site [ion binding]; other site 634504003103 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 634504003104 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 634504003105 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 634504003106 putative acyl-acceptor binding pocket; other site 634504003107 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 634504003108 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 634504003109 homodimer interface [polypeptide binding]; other site 634504003110 metal binding site [ion binding]; metal-binding site 634504003111 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 634504003112 homodimer interface [polypeptide binding]; other site 634504003113 active site 634504003114 putative chemical substrate binding site [chemical binding]; other site 634504003115 metal binding site [ion binding]; metal-binding site 634504003116 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 634504003117 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 634504003118 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 634504003119 putative dimer interface [polypeptide binding]; other site 634504003120 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 634504003121 Response regulator receiver domain; Region: Response_reg; pfam00072 634504003122 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 634504003123 active site 634504003124 phosphorylation site [posttranslational modification] 634504003125 intermolecular recognition site; other site 634504003126 dimerization interface [polypeptide binding]; other site 634504003127 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 634504003128 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 634504003129 hypothetical protein; Validated; Region: PRK09087 634504003130 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 634504003131 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 634504003132 Domain of unknown function DUF20; Region: UPF0118; pfam01594 634504003133 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 634504003134 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 634504003135 dimerization interface [polypeptide binding]; other site 634504003136 putative ATP binding site [chemical binding]; other site 634504003137 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 634504003138 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 634504003139 active site 634504003140 substrate binding site [chemical binding]; other site 634504003141 cosubstrate binding site; other site 634504003142 catalytic site [active] 634504003143 PAS domain S-box; Region: sensory_box; TIGR00229 634504003144 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 634504003145 PAS domain; Region: PAS; smart00091 634504003146 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 634504003147 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 634504003148 dimer interface [polypeptide binding]; other site 634504003149 phosphorylation site [posttranslational modification] 634504003150 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 634504003151 ATP binding site [chemical binding]; other site 634504003152 Mg2+ binding site [ion binding]; other site 634504003153 G-X-G motif; other site 634504003154 Response regulator receiver domain; Region: Response_reg; pfam00072 634504003155 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 634504003156 active site 634504003157 phosphorylation site [posttranslational modification] 634504003158 intermolecular recognition site; other site 634504003159 dimerization interface [polypeptide binding]; other site 634504003160 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 634504003161 Flavin Reductases; Region: FlaRed; cl00801 634504003162 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 634504003163 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 634504003164 substrate binding site [chemical binding]; other site 634504003165 hexamer interface [polypeptide binding]; other site 634504003166 metal binding site [ion binding]; metal-binding site 634504003167 adenylosuccinate lyase; Provisional; Region: PRK07492 634504003168 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 634504003169 tetramer interface [polypeptide binding]; other site 634504003170 active site 634504003171 Serine hydrolase; Region: Ser_hydrolase; pfam06821 634504003172 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 634504003173 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 634504003174 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 634504003175 ATP binding site [chemical binding]; other site 634504003176 active site 634504003177 substrate binding site [chemical binding]; other site 634504003178 phosphoribosylformylglycinamidine synthase subunit PurS; Reviewed; Region: PRK05974 634504003179 phosphoribosylformylglycinamidine synthase I; Provisional; Region: PRK03619 634504003180 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 634504003181 putative active site [active] 634504003182 catalytic triad [active] 634504003183 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 634504003184 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 634504003185 dimerization interface [polypeptide binding]; other site 634504003186 ATP binding site [chemical binding]; other site 634504003187 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat2; cd02204 634504003188 dimerization interface [polypeptide binding]; other site 634504003189 ATP binding site [chemical binding]; other site 634504003190 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 634504003191 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 634504003192 putative GSH binding site [chemical binding]; other site 634504003193 catalytic residues [active] 634504003194 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 634504003195 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 634504003196 putative substrate translocation pore; other site 634504003197 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 634504003198 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...; Region: TOP4c; cd00187 634504003199 CAP-like domain; other site 634504003200 active site 634504003201 primary dimer interface [polypeptide binding]; other site 634504003202 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 634504003203 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 634504003204 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 634504003205 dimer interface [polypeptide binding]; other site 634504003206 anticodon binding site; other site 634504003207 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...; Region: AspRS_core; cd00777 634504003208 homodimer interface [polypeptide binding]; other site 634504003209 motif 1; other site 634504003210 active site 634504003211 motif 2; other site 634504003212 GAD domain; Region: GAD; pfam02938 634504003213 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 634504003214 active site 634504003215 motif 3; other site 634504003216 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 634504003217 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 634504003218 catalytic site [active] 634504003219 putative active site [active] 634504003220 putative substrate binding site [chemical binding]; other site 634504003221 HRDC domain; Region: HRDC; pfam00570 634504003222 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 634504003223 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 634504003224 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 634504003225 polyphosphate kinase; Provisional; Region: PRK05443 634504003226 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 634504003227 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 634504003228 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 634504003229 putative domain interface [polypeptide binding]; other site 634504003230 putative active site [active] 634504003231 catalytic site [active] 634504003232 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 634504003233 putative domain interface [polypeptide binding]; other site 634504003234 putative active site [active] 634504003235 catalytic site [active] 634504003236 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4391 634504003237 salicylate hydroxylase; Provisional; Region: PRK06475 634504003238 salicylate hydroxylase; Provisional; Region: PRK08163 634504003239 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 634504003240 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 634504003241 putative active site [active] 634504003242 putative PHP Thumb interface [polypeptide binding]; other site 634504003243 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 634504003244 generic binding surface II; other site 634504003245 generic binding surface I; other site 634504003246 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 634504003247 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 634504003248 generic binding surface II; other site 634504003249 ssDNA binding site; other site 634504003250 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 634504003251 ATP binding site [chemical binding]; other site 634504003252 putative Mg++ binding site [ion binding]; other site 634504003253 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 634504003254 nucleotide binding region [chemical binding]; other site 634504003255 ATP-binding site [chemical binding]; other site 634504003256 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 634504003257 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 634504003258 glutaminase active site [active] 634504003259 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 634504003260 dimer interface [polypeptide binding]; other site 634504003261 active site 634504003262 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 634504003263 dimer interface [polypeptide binding]; other site 634504003264 active site 634504003265 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14353 634504003266 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 634504003267 Substrate binding site; other site 634504003268 Mg++ binding site; other site 634504003269 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 634504003270 active site 634504003271 substrate binding site [chemical binding]; other site 634504003272 CoA binding site [chemical binding]; other site 634504003273 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 634504003274 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 634504003275 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 634504003276 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 634504003277 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 634504003278 Zn2+ binding site [ion binding]; other site 634504003279 Mg2+ binding site [ion binding]; other site 634504003280 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 634504003281 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 634504003282 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 634504003283 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 634504003284 active site 634504003285 HIGH motif; other site 634504003286 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 634504003287 KMSK motif region; other site 634504003288 tRNA binding surface [nucleotide binding]; other site 634504003289 DALR anticodon binding domain; Region: DALR_1; smart00836 634504003290 anticodon binding site; other site 634504003291 Sporulation related domain; Region: SPOR; pfam05036 634504003292 Region of unknown function (DUF2417); Region: DUF2417; pfam10329 634504003293 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 634504003294 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 634504003295 homodimer interface [polypeptide binding]; other site 634504003296 substrate-cofactor binding pocket; other site 634504003297 catalytic residue [active] 634504003298 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 634504003299 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 634504003300 putative active site [active] 634504003301 homoserine dehydrogenase; Provisional; Region: PRK06349 634504003302 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 634504003303 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 634504003304 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 634504003305 isocitrate dehydrogenase; Validated; Region: PRK08299 634504003306 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 634504003307 Major Facilitator Superfamily; Region: MFS_1; pfam07690 634504003308 putative substrate translocation pore; other site 634504003309 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 634504003310 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 634504003311 putative substrate translocation pore; other site 634504003312 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 634504003313 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 634504003314 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 634504003315 active site 634504003316 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 634504003317 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 634504003318 active site 634504003319 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 634504003320 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 634504003321 active site 634504003322 (T/H)XGH motif; other site 634504003323 DNA gyrase subunit A; Validated; Region: PRK05560 634504003324 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...; Region: TOP4c; cd00187 634504003325 CAP-like domain; other site 634504003326 active site 634504003327 primary dimer interface [polypeptide binding]; other site 634504003328 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 634504003329 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 634504003330 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 634504003331 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 634504003332 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 634504003333 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 634504003334 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 634504003335 dimer interface [polypeptide binding]; other site 634504003336 ssDNA binding site [nucleotide binding]; other site 634504003337 tetramer (dimer of dimers) interface [polypeptide binding]; other site 634504003338 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 634504003339 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 634504003340 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 634504003341 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 634504003342 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 634504003343 Nitrogen regulatory protein P-II; Region: P-II; smart00938 634504003344 glutamine synthetase; Provisional; Region: glnA; PRK09469 634504003345 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 634504003346 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 634504003347 ATP12 chaperone protein; Region: ATP12; cl02228 634504003348 EamA-like transporter family; Region: EamA; pfam00892 634504003349 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 634504003350 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 634504003351 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504003352 putative proline-specific permease; Provisional; Region: proY; PRK10580 634504003353 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 634504003354 active sites [active] 634504003355 tetramer interface [polypeptide binding]; other site 634504003356 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 634504003357 S-adenosylmethionine binding site [chemical binding]; other site 634504003358 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 634504003359 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 634504003360 Repair protein; Region: Repair_PSII; pfam04536 634504003361 lipoate-protein ligase B; Provisional; Region: PRK14341 634504003362 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 634504003363 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 634504003364 ATP binding site [chemical binding]; other site 634504003365 Mg2+ binding site [ion binding]; other site 634504003366 G-X-G motif; other site 634504003367 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 634504003368 anchoring element; other site 634504003369 dimer interface [polypeptide binding]; other site 634504003370 ATP binding site [chemical binding]; other site 634504003371 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 634504003372 active site 634504003373 metal binding site [ion binding]; metal-binding site 634504003374 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 634504003375 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 634504003376 DHH family; Region: DHH; pfam01368 634504003377 DHHA1 domain; Region: DHHA1; pfam02272 634504003378 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 634504003379 23S rRNA interface [nucleotide binding]; other site 634504003380 L3 interface [polypeptide binding]; other site 634504003381 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 634504003382 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 634504003383 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 634504003384 active site 634504003385 phosphorylation site [posttranslational modification] 634504003386 intermolecular recognition site; other site 634504003387 dimerization interface [polypeptide binding]; other site 634504003388 ABC-2 family transporter protein; Region: ABC2_membrane_6; cl01496 634504003389 ABC-2 family transporter protein; Region: ABC2_membrane_6; cl01496 634504003390 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 634504003391 daunorubicin resistance ABC transporter ATP-binding subunit; Region: drrA; TIGR01188 634504003392 Walker A/P-loop; other site 634504003393 ATP binding site [chemical binding]; other site 634504003394 Q-loop/lid; other site 634504003395 ABC transporter signature motif; other site 634504003396 Walker B; other site 634504003397 D-loop; other site 634504003398 H-loop/switch region; other site 634504003399 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 634504003400 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 634504003401 active site 634504003402 cyclic beta-1,2-glucan ABC transporter; Provisional; Region: PRK13657 634504003403 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 634504003404 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 634504003405 Walker A/P-loop; other site 634504003406 ATP binding site [chemical binding]; other site 634504003407 Q-loop/lid; other site 634504003408 ABC transporter signature motif; other site 634504003409 Walker B; other site 634504003410 D-loop; other site 634504003411 H-loop/switch region; other site 634504003412 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504003413 putative trimer interface [polypeptide binding]; other site 634504003414 putative CoA binding site [chemical binding]; other site 634504003415 UDP-3-O-[3-hydroxymyristoyl]; Region: LpxD; COG1044 634504003416 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504003417 putative trimer interface [polypeptide binding]; other site 634504003418 putative CoA binding site [chemical binding]; other site 634504003419 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 634504003420 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 634504003421 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 634504003422 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 634504003423 FeS/SAM binding site; other site 634504003424 Radical SAM superfamily; Region: Radical_SAM; pfam04055 634504003425 anaerobic sulfatase-maturating enzyme; Region: sulfatase_rSAM; TIGR03942 634504003426 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 634504003427 active site 634504003428 ATP binding site [chemical binding]; other site 634504003429 Phosphotransferase enzyme family; Region: APH; pfam01636 634504003430 Radical SAM superfamily; Region: Radical_SAM; pfam04055 634504003431 Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion; Region: enolase_like; cl17188 634504003432 metal binding site [ion binding]; metal-binding site 634504003433 substrate binding pocket [chemical binding]; other site 634504003434 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 634504003435 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 634504003436 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...; Region: AlaRS_core; cd00673 634504003437 motif 1; other site 634504003438 active site 634504003439 motif 2; other site 634504003440 motif 3; other site 634504003441 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 634504003442 DHHA1 domain; Region: DHHA1; pfam02272 634504003443 recombinase A; Provisional; Region: recA; PRK09354 634504003444 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 634504003445 hexamer interface [polypeptide binding]; other site 634504003446 Walker A motif; other site 634504003447 ATP binding site [chemical binding]; other site 634504003448 Walker B motif; other site 634504003449 recombination factor protein RarA; Reviewed; Region: PRK13342 634504003450 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 634504003451 Walker A motif; other site 634504003452 ATP binding site [chemical binding]; other site 634504003453 Walker B motif; other site 634504003454 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 634504003455 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 634504003456 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 634504003457 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 634504003458 protein binding site [polypeptide binding]; other site 634504003459 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 634504003460 protein binding site [polypeptide binding]; other site 634504003461 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 634504003462 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 634504003463 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 634504003464 alphaNTD homodimer interface [polypeptide binding]; other site 634504003465 alphaNTD - beta interaction site [polypeptide binding]; other site 634504003466 alphaNTD - beta' interaction site [polypeptide binding]; other site 634504003467 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 634504003468 30S ribosomal protein S11; Validated; Region: PRK05309 634504003469 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 634504003470 30S ribosomal protein S13; Region: bact_S13; TIGR03631 634504003471 adenylate kinase; Reviewed; Region: adk; PRK00279 634504003472 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 634504003473 AMP-binding site [chemical binding]; other site 634504003474 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 634504003475 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 634504003476 SecY translocase; Region: SecY; pfam00344 634504003477 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 634504003478 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 634504003479 23S rRNA binding site [nucleotide binding]; other site 634504003480 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 634504003481 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 634504003482 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 634504003483 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 634504003484 23S rRNA interface [nucleotide binding]; other site 634504003485 5S rRNA interface [nucleotide binding]; other site 634504003486 L27 interface [polypeptide binding]; other site 634504003487 L5 interface [polypeptide binding]; other site 634504003488 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 634504003489 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 634504003490 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 634504003491 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 634504003492 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 634504003493 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 634504003494 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 634504003495 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 634504003496 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 634504003497 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 634504003498 RNA binding site [nucleotide binding]; other site 634504003499 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 634504003500 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 634504003501 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; cd00427 634504003502 23S rRNA interface [nucleotide binding]; other site 634504003503 putative translocon interaction site; other site 634504003504 signal recognition particle (SRP54) interaction site; other site 634504003505 L23 interface [polypeptide binding]; other site 634504003506 trigger factor interaction site; other site 634504003507 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 634504003508 23S rRNA interface [nucleotide binding]; other site 634504003509 5S rRNA interface [nucleotide binding]; other site 634504003510 putative antibiotic binding site [chemical binding]; other site 634504003511 L25 interface [polypeptide binding]; other site 634504003512 L27 interface [polypeptide binding]; other site 634504003513 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 634504003514 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 634504003515 G-X-X-G motif; other site 634504003516 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 634504003517 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 634504003518 putative translocon binding site; other site 634504003519 protein-rRNA interface [nucleotide binding]; other site 634504003520 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 634504003521 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 634504003522 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 634504003523 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 634504003524 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 634504003525 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 634504003526 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 634504003527 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 634504003528 elongation factor Tu; Reviewed; Region: PRK00049 634504003529 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 634504003530 G1 box; other site 634504003531 GEF interaction site [polypeptide binding]; other site 634504003532 GTP/Mg2+ binding site [chemical binding]; other site 634504003533 Switch I region; other site 634504003534 G2 box; other site 634504003535 G3 box; other site 634504003536 Switch II region; other site 634504003537 G4 box; other site 634504003538 G5 box; other site 634504003539 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 634504003540 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 634504003541 Antibiotic Binding Site [chemical binding]; other site 634504003542 elongation factor G; Reviewed; Region: PRK00007 634504003543 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 634504003544 G1 box; other site 634504003545 putative GEF interaction site [polypeptide binding]; other site 634504003546 GTP/Mg2+ binding site [chemical binding]; other site 634504003547 Switch I region; other site 634504003548 G2 box; other site 634504003549 G3 box; other site 634504003550 Switch II region; other site 634504003551 G4 box; other site 634504003552 G5 box; other site 634504003553 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 634504003554 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 634504003555 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 634504003556 30S ribosomal protein S7; Validated; Region: PRK05302 634504003557 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 634504003558 S17 interaction site [polypeptide binding]; other site 634504003559 S8 interaction site; other site 634504003560 16S rRNA interaction site [nucleotide binding]; other site 634504003561 streptomycin interaction site [chemical binding]; other site 634504003562 23S rRNA interaction site [nucleotide binding]; other site 634504003563 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 634504003564 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 634504003565 putative catalytic site [active] 634504003566 putative phosphate binding site [ion binding]; other site 634504003567 active site 634504003568 metal binding site A [ion binding]; metal-binding site 634504003569 DNA binding site [nucleotide binding] 634504003570 putative AP binding site [nucleotide binding]; other site 634504003571 putative metal binding site B [ion binding]; other site 634504003572 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 634504003573 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 634504003574 substrate binding pocket [chemical binding]; other site 634504003575 membrane-bound complex binding site; other site 634504003576 hinge residues; other site 634504003577 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 634504003578 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 634504003579 dimer interface [polypeptide binding]; other site 634504003580 conserved gate region; other site 634504003581 putative PBP binding loops; other site 634504003582 ABC-ATPase subunit interface; other site 634504003583 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 634504003584 dimer interface [polypeptide binding]; other site 634504003585 conserved gate region; other site 634504003586 putative PBP binding loops; other site 634504003587 ABC-ATPase subunit interface; other site 634504003588 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 634504003589 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 634504003590 Walker A/P-loop; other site 634504003591 ATP binding site [chemical binding]; other site 634504003592 Q-loop/lid; other site 634504003593 ABC transporter signature motif; other site 634504003594 Walker B; other site 634504003595 D-loop; other site 634504003596 H-loop/switch region; other site 634504003597 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 634504003598 Sel1-like repeats; Region: SEL1; smart00671 634504003599 Sel1-like repeats; Region: SEL1; smart00671 634504003600 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 634504003601 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 634504003602 HIGH motif; other site 634504003603 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 634504003604 active site 634504003605 KMSKS motif; other site 634504003606 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 634504003607 tRNA binding surface [nucleotide binding]; other site 634504003608 anticodon binding site; other site 634504003609 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 634504003610 Protein of unknown function (DUF2497); Region: DUF2497; pfam10691 634504003611 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 634504003612 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 634504003613 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 634504003614 S-adenosylmethionine binding site [chemical binding]; other site 634504003615 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 634504003616 DEAD-like helicases superfamily; Region: DEXDc; smart00487 634504003617 ATP binding site [chemical binding]; other site 634504003618 Mg++ binding site [ion binding]; other site 634504003619 motif III; other site 634504003620 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 634504003621 nucleotide binding region [chemical binding]; other site 634504003622 ATP-binding site [chemical binding]; other site 634504003623 threonine dehydratase; Validated; Region: PRK08639 634504003624 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 634504003625 tetramer interface [polypeptide binding]; other site 634504003626 pyridoxal 5'-phosphate binding site [chemical binding]; other site 634504003627 catalytic residue [active] 634504003628 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 634504003629 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 634504003630 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 634504003631 D-alanine/D-serine/glycine permease; Provisional; Region: PRK11049 634504003632 D-alanine/D-serine/glycine permease; Provisional; Region: PRK11049 634504003633 ketol-acid reductoisomerase; Provisional; Region: PRK05479 634504003634 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 634504003635 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 634504003636 pyridoxine 5'-phosphate synthase; Provisional; Region: PRK05265 634504003637 active site 634504003638 hydrophilic channel; other site 634504003639 dimerization interface [polypeptide binding]; other site 634504003640 catalytic residues [active] 634504003641 active site lid [active] 634504003642 ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]; Region: RecD; COG0507 634504003643 AAA domain; Region: AAA_30; pfam13604 634504003644 Family description; Region: UvrD_C_2; pfam13538 634504003645 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 634504003646 Putative D-3-Phosphoglycerate Dehydrogenases; Region: PGDH_like_1; cd12169 634504003647 dimerization interface [polypeptide binding]; other site 634504003648 NAD binding site [chemical binding]; other site 634504003649 ligand binding site [chemical binding]; other site 634504003650 catalytic site [active] 634504003651 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK09107 634504003652 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 634504003653 PYR/PP interface [polypeptide binding]; other site 634504003654 dimer interface [polypeptide binding]; other site 634504003655 TPP binding site [chemical binding]; other site 634504003656 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 634504003657 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 634504003658 TPP-binding site [chemical binding]; other site 634504003659 dimer interface [polypeptide binding]; other site 634504003660 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 634504003661 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 634504003662 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 634504003663 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 634504003664 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 634504003665 protein binding site [polypeptide binding]; other site 634504003666 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 634504003667 protein binding site [polypeptide binding]; other site 634504003668 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 634504003669 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 634504003670 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 634504003671 HflK protein; Region: hflK; TIGR01933 634504003672 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 634504003673 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 634504003674 folate binding site [chemical binding]; other site 634504003675 NADP+ binding site [chemical binding]; other site 634504003676 thymidylate synthase; Reviewed; Region: thyA; PRK01827 634504003677 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 634504003678 dimerization interface [polypeptide binding]; other site 634504003679 active site 634504003680 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 634504003681 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 634504003682 putative substrate translocation pore; other site 634504003683 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 634504003684 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 634504003685 putative substrate translocation pore; other site 634504003686 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 634504003687 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 634504003688 putative substrate translocation pore; other site 634504003689 Protein of unknown function (DUF2853); Region: DUF2853; pfam11015 634504003690 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 634504003691 Domain of unknown function (DUF4169); Region: DUF4169; pfam13770 634504003692 Ribbon-helix-helix domain; Region: RHH_4; pfam13467 634504003693 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 634504003694 Part of AAA domain; Region: AAA_19; pfam13245 634504003695 Family description; Region: UvrD_C_2; pfam13538 634504003696 phosphonate metabolim protein, transferase hexapeptide repeat family; Region: phn_thr-fam; TIGR03308 634504003697 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 634504003698 trimer interface [polypeptide binding]; other site 634504003699 active site 634504003700 substrate binding site [chemical binding]; other site 634504003701 CoA binding site [chemical binding]; other site 634504003702 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 634504003703 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 634504003704 Cu(I) binding site [ion binding]; other site 634504003705 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 634504003706 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 634504003707 S-adenosylmethionine binding site [chemical binding]; other site 634504003708 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 634504003709 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 634504003710 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 634504003711 active site 634504003712 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 634504003713 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 634504003714 nucleotide binding pocket [chemical binding]; other site 634504003715 K-X-D-G motif; other site 634504003716 catalytic site [active] 634504003717 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 634504003718 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 634504003719 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 634504003720 Dimer interface [polypeptide binding]; other site 634504003721 BRCT sequence motif; other site 634504003722 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 634504003723 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 634504003724 Walker A/P-loop; other site 634504003725 ATP binding site [chemical binding]; other site 634504003726 Q-loop/lid; other site 634504003727 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 634504003728 ABC transporter signature motif; other site 634504003729 Walker B; other site 634504003730 D-loop; other site 634504003731 H-loop/switch region; other site 634504003732 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 634504003733 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 634504003734 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 634504003735 cell division protein FtsZ; Validated; Region: PRK09330 634504003736 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 634504003737 nucleotide binding site [chemical binding]; other site 634504003738 SulA interaction site; other site 634504003739 cell division protein FtsZ, alphaProteobacterial C-terminal extension; Region: FtsZ_alphas_C; TIGR03483 634504003740 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 634504003741 Cell division protein FtsA; Region: FtsA; smart00842 634504003742 Cell division protein FtsA; Region: FtsA; pfam14450 634504003743 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 634504003744 Cell division protein FtsQ; Region: FtsQ; pfam03799 634504003745 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 634504003746 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 634504003747 ATP-grasp domain; Region: ATP-grasp_4; cl17255 634504003748 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 634504003749 FAD binding domain; Region: FAD_binding_4; pfam01565 634504003750 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 634504003751 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 634504003752 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 634504003753 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 634504003754 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 634504003755 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 634504003756 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 634504003757 active site 634504003758 homodimer interface [polypeptide binding]; other site 634504003759 cell division protein FtsW; Region: ftsW; TIGR02614 634504003760 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01390 634504003761 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 634504003762 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cd01983 634504003763 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 634504003764 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 634504003765 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 634504003766 Mg++ binding site [ion binding]; other site 634504003767 putative catalytic motif [active] 634504003768 putative substrate binding site [chemical binding]; other site 634504003769 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional; Region: PRK14093 634504003770 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 634504003771 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 634504003772 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 634504003773 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 634504003774 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 634504003775 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 634504003776 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 634504003777 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 634504003778 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 634504003779 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 634504003780 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 634504003781 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 634504003782 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 634504003783 S-adenosylmethionine binding site [chemical binding]; other site 634504003784 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 634504003785 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...; Region: LT_GEWL; cd00254 634504003786 N-acetyl-D-glucosamine binding site [chemical binding]; other site 634504003787 catalytic residue [active] 634504003788 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 634504003789 dimerization interface [polypeptide binding]; other site 634504003790 putative DNA binding site [nucleotide binding]; other site 634504003791 putative Zn2+ binding site [ion binding]; other site 634504003792 Methyltransferase domain; Region: Methyltransf_11; pfam08241 634504003793 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 634504003794 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 634504003795 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 634504003796 ABC transporter; Region: ABC_tran_2; pfam12848 634504003797 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 634504003798 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 634504003799 Isochorismatase family; Region: Isochorismatase; pfam00857 634504003800 catalytic triad [active] 634504003801 metal binding site [ion binding]; metal-binding site 634504003802 conserved cis-peptide bond; other site 634504003803 hypothetical protein; Provisional; Region: PRK14013 634504003804 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 634504003805 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 634504003806 non-specific DNA binding site [nucleotide binding]; other site 634504003807 salt bridge; other site 634504003808 sequence-specific DNA binding site [nucleotide binding]; other site 634504003809 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 634504003810 NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the...; Region: NTR_like; cl02512 634504003811 Uncharacterized conserved protein [Function unknown]; Region: COG2968 634504003812 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 634504003813 hypothetical protein; Provisional; Region: PRK05170 634504003814 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 634504003815 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 634504003816 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 634504003817 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 634504003818 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 634504003819 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 634504003820 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 634504003821 DNA binding residues [nucleotide binding] 634504003822 DNA primase; Validated; Region: dnaG; PRK05667 634504003823 CHC2 zinc finger; Region: zf-CHC2; cl17510 634504003824 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 634504003825 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 634504003826 active site 634504003827 metal binding site [ion binding]; metal-binding site 634504003828 interdomain interaction site; other site 634504003829 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 634504003830 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 634504003831 Mechanosensitive ion channel; Region: MS_channel; pfam00924 634504003832 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 634504003833 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 634504003834 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 634504003835 PhoU domain; Region: PhoU; pfam01895 634504003836 chorismate pyruvate lyase; Provisional; Region: ubiC; PRK11655 634504003837 Uncharacterized conserved protein [Function unknown]; Region: COG1610 634504003838 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 634504003839 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 634504003840 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 634504003841 catalytic site [active] 634504003842 subunit interface [polypeptide binding]; other site 634504003843 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 634504003844 Major Facilitator Superfamily; Region: MFS_1; pfam07690 634504003845 putative substrate translocation pore; other site 634504003846 Protein of unknown function (DUF1460); Region: DUF1460; pfam07313 634504003847 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 634504003848 Cation efflux family; Region: Cation_efflux; pfam01545 634504003849 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 634504003850 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 634504003851 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 634504003852 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 634504003853 Ligand Binding Site [chemical binding]; other site 634504003854 Protein of unknown function (DUF1153); Region: DUF1153; pfam06627 634504003855 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 634504003856 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 634504003857 active site 634504003858 phosphorylation site [posttranslational modification] 634504003859 intermolecular recognition site; other site 634504003860 dimerization interface [polypeptide binding]; other site 634504003861 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 634504003862 DNA binding site [nucleotide binding] 634504003863 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5385 634504003864 Protein of unknown function (DUF1134); Region: DUF1134; pfam06577 634504003865 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 634504003866 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 634504003867 inhibitor-cofactor binding pocket; inhibition site 634504003868 pyridoxal 5'-phosphate binding site [chemical binding]; other site 634504003869 catalytic residue [active] 634504003870 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 634504003871 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 634504003872 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 634504003873 replicative DNA helicase; Provisional; Region: PRK09165 634504003874 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 634504003875 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 634504003876 Walker A motif; other site 634504003877 ATP binding site [chemical binding]; other site 634504003878 Walker B motif; other site 634504003879 DNA binding loops [nucleotide binding] 634504003880 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 634504003881 Phage Tail Protein X; Region: Phage_tail_X; cl02088 634504003882 Phage P2 GpU; Region: Phage_P2_GpU; cl01391 634504003883 SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate...; Region: SERPIN; cl00137 634504003884 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 634504003885 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504003886 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 634504003887 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504003888 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 634504003889 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504003890 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 634504003891 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504003892 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504003893 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 634504003894 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 634504003895 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504003896 Bacterial protein of unknown function (DUF948); Region: DUF948; cl01972 634504003897 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 634504003898 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 634504003899 P-loop; other site 634504003900 Magnesium ion binding site [ion binding]; other site 634504003901 Putative phosphatase (DUF442); Region: DUF442; cl17385 634504003902 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 634504003903 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 634504003904 active site 634504003905 Riboflavin kinase; Region: Flavokinase; smart00904 634504003906 Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]; Region: NagD; COG0647 634504003907 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 634504003908 active site 634504003909 motif I; other site 634504003910 motif II; other site 634504003911 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 634504003912 motif II; other site 634504003913 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 634504003914 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 634504003915 non-specific DNA binding site [nucleotide binding]; other site 634504003916 salt bridge; other site 634504003917 sequence-specific DNA binding site [nucleotide binding]; other site 634504003918 hypothetical protein; Provisional; Region: PRK06518 634504003919 Staphylococcal nuclease homologues; Region: SNc; smart00318 634504003920 Catalytic site; other site 634504003921 TrbC/VIRB2 family; Region: TrbC; pfam04956 634504003922 Type IV secretory pathway, VirB3 components [Intracellular trafficking and secretion]; Region: VirB3; COG3702 634504003923 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 634504003924 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 634504003925 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 634504003926 VirB8 protein; Region: VirB8; cl01500 634504003927 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 634504003928 VirB7 interaction site; other site 634504003929 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 634504003930 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 634504003931 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 634504003932 Walker A motif; other site 634504003933 hexamer interface [polypeptide binding]; other site 634504003934 ATP binding site [chemical binding]; other site 634504003935 Walker B motif; other site 634504003936 VbhA antitoxin and related proteins; Region: VbhA_like; cd11586 634504003937 FIC domain binding interface [polypeptide binding]; other site 634504003938 Fic/DOC family; Region: Fic; cl00960 634504003939 conjugal transfer coupling protein TraG; Provisional; Region: PRK13822 634504003940 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 634504003941 Walker A motif; other site 634504003942 ATP binding site [chemical binding]; other site 634504003943 Walker B motif; other site 634504003944 Fic/DOC family; Region: Fic; cl00960 634504003945 Dtr system oriT relaxase; Provisional; Region: PRK13826 634504003946 Fic/DOC family; Region: Fic; cl00960 634504003947 Fic/DOC family; Region: Fic; cl00960 634504003948 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 634504003949 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 634504003950 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 634504003951 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 634504003952 active site 634504003953 HIGH motif; other site 634504003954 dimer interface [polypeptide binding]; other site 634504003955 KMSKS motif; other site 634504003956 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 634504003957 Ligand Binding Site [chemical binding]; other site 634504003958 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 634504003959 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 634504003960 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 634504003961 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 634504003962 PhnA protein; Region: PhnA; pfam03831 634504003963 phosphoglucomutase; Region: PLN02307 634504003964 Phosphoglucomutase 1 (PGM1) catalyzes the bidirectional interconversion of glucose-1-phosphate (G-1-P) and glucose-6-phosphate (G-6-P) via a glucose 1,6-diphosphate intermediate, an important metabolic step in prokaryotes and eukaryotes. In one direction; Region: PGM1; cd03085 634504003965 substrate binding site [chemical binding]; other site 634504003966 dimer interface [polypeptide binding]; other site 634504003967 active site 634504003968 metal binding site [ion binding]; metal-binding site 634504003969 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 634504003970 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 634504003971 catalytic triad [active] 634504003972 dimer interface [polypeptide binding]; other site 634504003973 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 634504003974 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 634504003975 active site 634504003976 Int/Topo IB signature motif; other site 634504003977 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 634504003978 Predicted transcriptional regulator [Transcription]; Region: COG3905 634504003979 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 634504003980 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504003981 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504003982 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504003983 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504003984 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504003985 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504003986 haemagglutination activity domain; Region: Haemagg_act; pfam05860 634504003987 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 634504003988 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 634504003989 A nuclease of the HNH/ENDO VII superfamily with conserved LHH; Region: LHH; pfam14411 634504003990 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 634504003991 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 634504003992 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 634504003993 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 634504003994 UDP-3-O-[3-hydroxymyristoyl]; Region: LpxD; COG1044 634504003995 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504003996 putative trimer interface [polypeptide binding]; other site 634504003997 putative CoA binding site [chemical binding]; other site 634504003998 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504003999 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 634504004000 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...; Region: HisRS-like_core; cd00773 634504004001 dimer interface [polypeptide binding]; other site 634504004002 motif 1; other site 634504004003 active site 634504004004 motif 2; other site 634504004005 motif 3; other site 634504004006 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 634504004007 anticodon binding site; other site 634504004008 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...; Region: OMP_decarboxylase_like; cd04725 634504004009 active site 634504004010 dimer interface [polypeptide binding]; other site 634504004011 putative membrane protein, TIGR04086 family; Region: TIGR04086_membr 634504004012 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 634504004013 Major Facilitator Superfamily; Region: MFS_1; pfam07690 634504004014 putative substrate translocation pore; other site 634504004015 Major Facilitator Superfamily; Region: MFS_1; pfam07690 634504004016 Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]; Region: Fur; COG0735 634504004017 metal binding site 2 [ion binding]; metal-binding site 634504004018 putative DNA binding helix; other site 634504004019 metal binding site 1 [ion binding]; metal-binding site 634504004020 dimer interface [polypeptide binding]; other site 634504004021 structural Zn2+ binding site [ion binding]; other site 634504004022 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 634504004023 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 634504004024 HlyD family secretion protein; Region: HlyD_3; pfam13437 634504004025 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 634504004026 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 634504004027 putative substrate translocation pore; other site 634504004028 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 634504004029 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 634504004030 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 634504004031 Coenzyme A binding pocket [chemical binding]; other site 634504004032 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 634504004033 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 634504004034 dimer interface [polypeptide binding]; other site 634504004035 active site 634504004036 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 634504004037 catalytic residues [active] 634504004038 substrate binding site [chemical binding]; other site 634504004039 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 634504004040 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 634504004041 active site residue [active] 634504004042 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 634504004043 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 634504004044 active site 634504004045 intersubunit interface [polypeptide binding]; other site 634504004046 catalytic residue [active] 634504004047 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 634504004048 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 634504004049 FAD binding pocket [chemical binding]; other site 634504004050 FAD binding motif [chemical binding]; other site 634504004051 phosphate binding motif [ion binding]; other site 634504004052 beta-alpha-beta structure motif; other site 634504004053 NAD binding pocket [chemical binding]; other site 634504004054 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 634504004055 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 634504004056 active site 634504004057 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 634504004058 dimer interface [polypeptide binding]; other site 634504004059 substrate binding site [chemical binding]; other site 634504004060 catalytic residues [active] 634504004061 glycine dehydrogenase; Provisional; Region: PRK05367 634504004062 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 634504004063 tetramer interface [polypeptide binding]; other site 634504004064 pyridoxal 5'-phosphate binding site [chemical binding]; other site 634504004065 catalytic residue [active] 634504004066 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 634504004067 tetramer interface [polypeptide binding]; other site 634504004068 pyridoxal 5'-phosphate binding site [chemical binding]; other site 634504004069 catalytic residue [active] 634504004070 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 634504004071 lipoyl attachment site [posttranslational modification]; other site 634504004072 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 634504004073 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 634504004074 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 634504004075 Uncharacterized conserved protein [Function unknown]; Region: COG2835 634504004076 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504004077 putative trimer interface [polypeptide binding]; other site 634504004078 putative CoA binding site [chemical binding]; other site 634504004079 UDP-3-O-[3-hydroxymyristoyl]; Region: LpxD; COG1044 634504004080 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504004081 putative trimer interface [polypeptide binding]; other site 634504004082 putative CoA binding site [chemical binding]; other site 634504004083 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 634504004084 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 634504004085 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 634504004086 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 634504004087 haemagglutination activity domain; Region: Haemagg_act; pfam05860 634504004088 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 634504004089 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 634504004090 A nuclease of the HNH/ENDO VII superfamily with conserved LHH; Region: LHH; pfam14411 634504004091 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504004092 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504004093 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 634504004094 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 634504004095 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 634504004096 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 634504004097 active site 634504004098 metal binding site [ion binding]; metal-binding site 634504004099 interdomain interaction site; other site 634504004100 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 634504004101 integrase; Provisional; Region: PRK09692 634504004102 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 634504004103 active site 634504004104 Int/Topo IB signature motif; other site 634504004105 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 634504004106 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 634504004107 non-specific DNA binding site [nucleotide binding]; other site 634504004108 salt bridge; other site 634504004109 sequence-specific DNA binding site [nucleotide binding]; other site 634504004110 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 634504004111 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 634504004112 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 634504004113 Bacterial SH3 domain; Region: SH3_3; pfam08239 634504004114 DL-methionine transporter substrate-binding subunit; Provisional; Region: metQ; PRK11063 634504004115 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 634504004116 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 634504004117 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 634504004118 Walker A/P-loop; other site 634504004119 ATP binding site [chemical binding]; other site 634504004120 Q-loop/lid; other site 634504004121 ABC transporter signature motif; other site 634504004122 Walker B; other site 634504004123 D-loop; other site 634504004124 H-loop/switch region; other site 634504004125 NIL domain; Region: NIL; pfam09383 634504004126 ABC-type phosphate/phosphonate transport system, permease component [Inorganic ion transport and metabolism]; Region: COG3639 634504004127 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 634504004128 dimer interface [polypeptide binding]; other site 634504004129 conserved gate region; other site 634504004130 ABC-ATPase subunit interface; other site 634504004131 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 634504004132 putative active site [active] 634504004133 putative catalytic site [active] 634504004134 Predicted homoserine dehydrogenase [Amino acid transport and metabolism]; Region: COG4091 634504004135 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 634504004136 SAF domain of putative dehydrogenases or oxidoreductases; Region: SAF_DH_OX_like; cd11616 634504004137 Creatinine amidohydrolase; Region: Creatininase; pfam02633 634504004138 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 634504004139 The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage...; Region: CobW_like; cd03112 634504004140 P-loop, Walker A motif; other site 634504004141 Base recognition motif; other site 634504004142 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 634504004143 FOG: WD40 repeat [General function prediction only]; Region: COG2319 634504004144 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 634504004145 structural tetrad; other site 634504004146 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 634504004147 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504004148 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; cd00253 634504004149 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504004150 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 634504004151 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504004152 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504004153 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 634504004154 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504004155 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 634504004156 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 634504004157 Autotransporter beta-domain; Region: Autotransporter; smart00869 634504004158 ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CeuA; COG4607 634504004159 Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins...; Region: FatB; cd01140 634504004160 putative ligand binding residues [chemical binding]; other site 634504004161 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 634504004162 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 634504004163 ABC-ATPase subunit interface; other site 634504004164 dimer interface [polypeptide binding]; other site 634504004165 putative PBP binding regions; other site 634504004166 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 634504004167 ABC-ATPase subunit interface; other site 634504004168 dimer interface [polypeptide binding]; other site 634504004169 putative PBP binding regions; other site 634504004170 ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CeuD; COG4604 634504004171 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 634504004172 Walker A/P-loop; other site 634504004173 ATP binding site [chemical binding]; other site 634504004174 Q-loop/lid; other site 634504004175 ABC transporter signature motif; other site 634504004176 Walker B; other site 634504004177 D-loop; other site 634504004178 H-loop/switch region; other site 634504004179 replicative DNA helicase; Provisional; Region: PRK09165 634504004180 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 634504004181 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 634504004182 Walker A motif; other site 634504004183 ATP binding site [chemical binding]; other site 634504004184 Walker B motif; other site 634504004185 DNA binding loops [nucleotide binding] 634504004186 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 634504004187 Phage Tail Protein X; Region: Phage_tail_X; cl02088 634504004188 Phage P2 GpU; Region: Phage_P2_GpU; cl01391 634504004189 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 634504004190 Phage tail tube protein FII; Region: Phage_tube; cl01390 634504004191 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 634504004192 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 634504004193 active site 1 [active] 634504004194 dimer interface [polypeptide binding]; other site 634504004195 hexamer interface [polypeptide binding]; other site 634504004196 active site 2 [active] 634504004197 FAD-NAD(P)-binding; Region: NAD_binding_9; pfam13454 634504004198 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 634504004199 Major Facilitator Superfamily; Region: MFS_1; pfam07690 634504004200 putative substrate translocation pore; other site 634504004201 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 634504004202 Porin subfamily; Region: Porin_2; pfam02530 634504004203 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 634504004204 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 634504004205 amidase catalytic site [active] 634504004206 Zn binding residues [ion binding]; other site 634504004207 substrate binding site [chemical binding]; other site 634504004208 tartrate dehydrogenase; Region: TTC; TIGR02089 634504004209 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 634504004210 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 634504004211 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 634504004212 putative MPT binding site; other site 634504004213 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 634504004214 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 634504004215 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 634504004216 putative substrate translocation pore; other site 634504004217 Mu-like prophage FluMu protein gp41; Region: FluMu_gp41; pfam10109 634504004218 putative membrane protein, TIGR04086 family; Region: TIGR04086_membr 634504004219 Abortive infection C-terminus; Region: Abi_C; pfam14355 634504004220 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 634504004221 Peptidase family M23; Region: Peptidase_M23; pfam01551 634504004222 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 634504004223 Histidine kinase; Region: HisKA_2; pfam07568 634504004224 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 634504004225 ATP binding site [chemical binding]; other site 634504004226 Mg2+ binding site [ion binding]; other site 634504004227 G-X-G motif; other site 634504004228 RNA polymerase sigma factor; Provisional; Region: PRK12547 634504004229 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 634504004230 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 634504004231 DNA binding residues [nucleotide binding] 634504004232 two-component response regulator; Provisional; Region: PRK09191 634504004233 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 634504004234 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 634504004235 active site 634504004236 phosphorylation site [posttranslational modification] 634504004237 intermolecular recognition site; other site 634504004238 dimerization interface [polypeptide binding]; other site 634504004239 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 634504004240 HWE histidine kinase; Region: HWE_HK; pfam07536 634504004241 Domain of unknown function (DUF4167); Region: DUF4167; pfam13763 634504004242 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 634504004243 Protein of unknown function (DUF4043); Region: DUF4043; pfam13252 634504004244 Class I aldolases; Region: Aldolase_Class_I; cl17187 634504004245 Phage terminase large subunit; Region: Terminase_3; cl12054 634504004246 Terminase-like family; Region: Terminase_6; pfam03237 634504004247 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 634504004248 putative substrate translocation pore; other site 634504004249 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 634504004250 non-specific DNA binding site [nucleotide binding]; other site 634504004251 salt bridge; other site 634504004252 sequence-specific DNA binding site [nucleotide binding]; other site 634504004253 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 634504004254 non-specific DNA binding site [nucleotide binding]; other site 634504004255 salt bridge; other site 634504004256 sequence-specific DNA binding site [nucleotide binding]; other site 634504004257 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 634504004258 non-specific DNA binding site [nucleotide binding]; other site 634504004259 salt bridge; other site 634504004260 sequence-specific DNA binding site [nucleotide binding]; other site 634504004261 major head protein; Region: PHA00144 634504004262 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 634504004263 Clp amino terminal domain; Region: Clp_N; pfam02861 634504004264 Clp amino terminal domain; Region: Clp_N; pfam02861 634504004265 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 634504004266 Walker A motif; other site 634504004267 ATP binding site [chemical binding]; other site 634504004268 Walker B motif; other site 634504004269 arginine finger; other site 634504004270 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 634504004271 Walker A motif; other site 634504004272 ATP binding site [chemical binding]; other site 634504004273 Walker B motif; other site 634504004274 arginine finger; other site 634504004275 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 634504004276 Domain of unknown function (DUF3472); Region: DUF3472; pfam11958 634504004277 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 634504004278 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 634504004279 non-specific DNA binding site [nucleotide binding]; other site 634504004280 salt bridge; other site 634504004281 sequence-specific DNA binding site [nucleotide binding]; other site 634504004282 UDP-3-O-[3-hydroxymyristoyl]; Region: LpxD; COG1044 634504004283 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504004284 putative trimer interface [polypeptide binding]; other site 634504004285 putative CoA binding site [chemical binding]; other site 634504004286 UDP-3-O-[3-hydroxymyristoyl]; Region: LpxD; COG1044 634504004287 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 634504004288 putative trimer interface [polypeptide binding]; other site 634504004289 putative CoA binding site [chemical binding]; other site 634504004290 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 634504004291 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 634504004292 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 634504004293 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 634504004294 haemagglutination activity domain; Region: Haemagg_act; pfam05860 634504004295 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 634504004296 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 634504004297 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 634504004298 active site 634504004299 metal binding site [ion binding]; metal-binding site 634504004300 interdomain interaction site; other site 634504004301 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 634504004302 integrase; Provisional; Region: PRK09692 634504004303 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 634504004304 active site 634504004305 Int/Topo IB signature motif; other site 634504004306 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 634504004307 non-specific DNA binding site [nucleotide binding]; other site 634504004308 salt bridge; other site 634504004309 sequence-specific DNA binding site [nucleotide binding]; other site 634504004310 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 634504004311 putative substrate translocation pore; other site 634504004312 Major Facilitator Superfamily; Region: MFS_1; pfam07690 634504004313 zinc-binding protein; Provisional; Region: PRK01343 634504004314 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 634504004315 active site 634504004316 dimer interface [polypeptide binding]; other site 634504004317 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 634504004318 rRNA binding site [nucleotide binding]; other site 634504004319 predicted 30S ribosome binding site; other site 634504004320 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 634504004321 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 634504004322 non-specific DNA binding site [nucleotide binding]; other site 634504004323 salt bridge; other site 634504004324 sequence-specific DNA binding site [nucleotide binding]; other site 634504004325 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 634504004326 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 634504004327 non-specific DNA binding site [nucleotide binding]; other site 634504004328 salt bridge; other site 634504004329 sequence-specific DNA binding site [nucleotide binding]; other site 634504004330 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 634504004331 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 634504004332 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 634504004333 ATP-grasp domain; Region: ATP-grasp; pfam02222 634504004334 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 634504004335 TPR repeat; Region: TPR_11; pfam13414 634504004336 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 634504004337 TPR motif; other site 634504004338 TPR repeat; Region: TPR_11; pfam13414 634504004339 binding surface 634504004340 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 634504004341 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 634504004342 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 634504004343 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 634504004344 putative active site [active] 634504004345 metal binding site [ion binding]; metal-binding site 634504004346 homodimer binding site [polypeptide binding]; other site 634504004347 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 634504004348 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 634504004349 non-specific DNA binding site [nucleotide binding]; other site 634504004350 salt bridge; other site 634504004351 sequence-specific DNA binding site [nucleotide binding]; other site 634504004352 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 634504004353 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 634504004354 non-specific DNA binding site [nucleotide binding]; other site 634504004355 salt bridge; other site 634504004356 sequence-specific DNA binding site [nucleotide binding]; other site 634504004357 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 634504004358 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 634504004359 non-specific DNA binding site [nucleotide binding]; other site 634504004360 salt bridge; other site 634504004361 sequence-specific DNA binding site [nucleotide binding]; other site 634504004362 conjugal transfer coupling protein TraG; Provisional; Region: PRK13822 634504004363 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 634504004364 Walker A motif; other site 634504004365 ATP binding site [chemical binding]; other site 634504004366 Walker B motif; other site 634504004367 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 634504004368 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 634504004369 hinge; other site 634504004370 active site 634504004371 YqaJ-like viral recombinase domain; Region: YqaJ; pfam09588 634504004372 Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA; Region: Topoisomer_IB_N; cl02774 634504004373 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 634504004374 Protein of unknown function (DUF1376); Region: DUF1376; pfam07120 634504004375 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 634504004376 active site 634504004377 metal binding site [ion binding]; metal-binding site 634504004378 interdomain interaction site; other site 634504004379 AAA domain; Region: AAA_25; pfam13481 634504004380 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 634504004381 Walker A motif; other site 634504004382 ATP binding site [chemical binding]; other site 634504004383 Walker B motif; other site 634504004384 Predicted flavoprotein [General function prediction only]; Region: COG0431 634504004385 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 634504004386 short chain dehydrogenase; Provisional; Region: PRK08309 634504004387 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 634504004388 effector protein YopJ; Provisional; Region: PRK15371 634504004389 effector protein YopJ; Provisional; Region: PRK15371 634504004390 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 634504004391 catalytic residues [active] 634504004392 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 634504004393 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 634504004394 ring oligomerisation interface [polypeptide binding]; other site 634504004395 ATP/Mg binding site [chemical binding]; other site 634504004396 stacking interactions; other site 634504004397 hinge regions; other site 634504004398 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 634504004399 oligomerisation interface [polypeptide binding]; other site 634504004400 mobile loop; other site 634504004401 roof hairpin; other site 634504004402 fumarate hydratase; Reviewed; Region: fumC; PRK00485 634504004403 Class II fumarases; Region: Fumarase_classII; cd01362 634504004404 active site 634504004405 tetramer interface [polypeptide binding]; other site 634504004406 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 634504004407 Predicted membrane protein [Function unknown]; Region: COG1238 634504004408 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 634504004409 PemK-like protein; Region: PemK; pfam02452 634504004410 Uncharacterized conserved protein [Function unknown]; Region: COG1633 634504004411 CCC1-related protein family; Region: CCC1_like_1; cd02437 634504004412 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 634504004413 trimer interface [polypeptide binding]; other site 634504004414 active site 634504004415 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 634504004416 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 634504004417 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 634504004418 Bacterial protein of unknown function (DUF883); Region: DUF883; pfam05957 634504004419 Protein of unknown function (DUF1266); Region: DUF1266; cl14673 634504004420 hypothetical protein; Provisional; Region: PRK06518 634504004421 Staphylococcal nuclease homologues; Region: SNc; smart00318 634504004422 Catalytic site; other site 634504004423 TrbC/VIRB2 family; Region: TrbC; pfam04956 634504004424 Type IV secretory pathway, VirB3 components [Intracellular trafficking and secretion]; Region: VirB3; COG3702 634504004425 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 634504004426 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 634504004427 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 634504004428 Walker A motif; other site 634504004429 ATP binding site [chemical binding]; other site 634504004430 P-type DNA transfer protein VirB5; Region: VirB5; TIGR02791 634504004431 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 634504004432 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 634504004433 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 634504004434 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 634504004435 VirB7 interaction site; other site 634504004436 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 634504004437 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 634504004438 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 634504004439 Walker A motif; other site 634504004440 hexamer interface [polypeptide binding]; other site 634504004441 ATP binding site [chemical binding]; other site 634504004442 Walker B motif; other site 634504004443 Protein involved in cell division [Cell division and chromosome partitioning]; Region: Fic; COG2184 634504004444 Fic/DOC family; Region: Fic; cl00960 634504004445 VbhA antitoxin and related proteins; Region: VbhA_like; cd11586 634504004446 FIC domain binding interface [polypeptide binding]; other site 634504004447 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14315 634504004448 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 634504004449 active site 634504004450 substrate binding site [chemical binding]; other site 634504004451 metal binding site [ion binding]; metal-binding site 634504004452 FtsH Extracellular; Region: FtsH_ext; pfam06480 634504004453 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 634504004454 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 634504004455 Walker A motif; other site 634504004456 ATP binding site [chemical binding]; other site 634504004457 Walker B motif; other site 634504004458 arginine finger; other site 634504004459 Peptidase family M41; Region: Peptidase_M41; pfam01434 634504004460 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 634504004461 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 634504004462 Ligand Binding Site [chemical binding]; other site 634504004463 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 634504004464 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 634504004465 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 634504004466 ligand binding site [chemical binding]; other site 634504004467 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3820 634504004468 hypothetical protein; Validated; Region: PRK00110 634504004469 translocation protein TolB; Provisional; Region: tolB; PRK05137 634504004470 TolB amino-terminal domain; Region: TolB_N; pfam04052 634504004471 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 634504004472 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 634504004473 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14951 634504004474 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 634504004475 TolR protein; Region: tolR; TIGR02801 634504004476 TolQ protein; Region: tolQ; TIGR02796 634504004477 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 634504004478 active site 634504004479 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 634504004480 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 634504004481 Walker A motif; other site 634504004482 ATP binding site [chemical binding]; other site 634504004483 Walker B motif; other site 634504004484 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 634504004485 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 634504004486 RuvA N terminal domain; Region: RuvA_N; pfam01330 634504004487 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 634504004488 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...; Region: RuvC_resolvase; cd00529 634504004489 active site 634504004490 putative DNA-binding cleft [nucleotide binding]; other site 634504004491 dimer interface [polypeptide binding]; other site 634504004492 Protein of unknown function (DUF1465); Region: DUF1465; pfam07323 634504004493 OpgC protein; Region: OpgC_C; pfam10129 634504004494 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 634504004495 active site 634504004496 thiamine phosphate binding site [chemical binding]; other site 634504004497 pyrophosphate binding site [ion binding]; other site 634504004498 Predicted nucleotide-binding protein containing TIR-like domain; Region: TIR-like; cl17861 634504004499 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 634504004500 sequence-specific DNA binding site [nucleotide binding]; other site 634504004501 salt bridge; other site 634504004502 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 634504004503 sequence-specific DNA binding site [nucleotide binding]; other site 634504004504 salt bridge; other site 634504004505 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 634504004506 sequence-specific DNA binding site [nucleotide binding]; other site 634504004507 salt bridge; other site 634504004508 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 634504004509 Sel1-like repeats; Region: SEL1; smart00671 634504004510 elongation factor P; Validated; Region: PRK00529 634504004511 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 634504004512 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 634504004513 RNA binding site [nucleotide binding]; other site 634504004514 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 634504004515 RNA binding site [nucleotide binding]; other site 634504004516 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 634504004517 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 634504004518 active site 634504004519 dimerization interface [polypeptide binding]; other site 634504004520 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 634504004521 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 634504004522 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 634504004523 Walker A/P-loop; other site 634504004524 ATP binding site [chemical binding]; other site 634504004525 Q-loop/lid; other site 634504004526 ABC transporter signature motif; other site 634504004527 Walker B; other site 634504004528 D-loop; other site 634504004529 H-loop/switch region; other site 634504004530 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00528 634504004531 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 634504004532 Walker B; other site 634504004533 D-loop; other site 634504004534 H-loop/switch region; other site 634504004535 Fructose-1,6-bisphosphate aldolase; Region: FBP_aldolase_I_a; cd00948 634504004536 active site 634504004537 intersubunit interface [polypeptide binding]; other site 634504004538 catalytic residue [active] 634504004539 Phosphoglycerate kinase; Region: PGK; pfam00162 634504004540 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 634504004541 substrate binding site [chemical binding]; other site 634504004542 hinge regions; other site 634504004543 ADP binding site [chemical binding]; other site 634504004544 catalytic site [active] 634504004545 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 634504004546 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 634504004547 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 634504004548 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 634504004549 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 634504004550 TPP-binding site [chemical binding]; other site 634504004551 dimer interface [polypeptide binding]; other site 634504004552 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 634504004553 PYR/PP interface [polypeptide binding]; other site 634504004554 dimer interface [polypeptide binding]; other site 634504004555 TPP binding site [chemical binding]; other site 634504004556 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 634504004557 Domain of unknown function (DUF4164); Region: DUF4164; pfam13747 634504004558 Cell division protein ZapA; Region: ZapA; pfam05164 634504004559 pyruvate kinase; Provisional; Region: PRK06247 634504004560 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; cl17342 634504004561 domain interfaces; other site 634504004562 active site 634504004563 Protein of unknown function (DUF1036); Region: DUF1036; pfam06282 634504004564 hypothetical protein; Provisional; Region: PRK13694 634504004565 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 634504004566 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 634504004567 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 634504004568 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 634504004569 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 634504004570 Thiamine pyrophosphokinase [Coenzyme metabolism]; Region: THI80; COG1564 634504004571 Thiamine pyrophosphokinase; Region: TPK; cd07995 634504004572 active site 634504004573 dimerization interface [polypeptide binding]; other site 634504004574 thiamine binding site [chemical binding]; other site 634504004575 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 634504004576 Peptidase family M48; Region: Peptidase_M48; pfam01435 634504004577 RNA polymerase factor sigma-32; Reviewed; Region: rpoH2; PRK07500 634504004578 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 634504004579 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 634504004580 DNA binding residues [nucleotide binding] 634504004581 Ferredoxin [Energy production and conversion]; Region: COG1146 634504004582 4Fe-4S binding domain; Region: Fer4; pfam00037 634504004583 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 634504004584 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 634504004585 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 634504004586 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 634504004587 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 634504004588 substrate binding pocket [chemical binding]; other site 634504004589 chain length determination region; other site 634504004590 substrate-Mg2+ binding site; other site 634504004591 catalytic residues [active] 634504004592 aspartate-rich region 1; other site 634504004593 active site lid residues [active] 634504004594 aspartate-rich region 2; other site 634504004595 Major Facilitator Superfamily; Region: MFS_1; pfam07690 634504004596 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 634504004597 putative substrate translocation pore; other site 634504004598 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 634504004599 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 634504004600 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 634504004601 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 634504004602 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 634504004603 HlyD family secretion protein; Region: HlyD_3; pfam13437 634504004604 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 634504004605 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 634504004606 gamma subunit interface [polypeptide binding]; other site 634504004607 epsilon subunit interface [polypeptide binding]; other site 634504004608 LBP interface [polypeptide binding]; other site 634504004609 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 634504004610 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 634504004611 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 634504004612 alpha subunit interaction interface [polypeptide binding]; other site 634504004613 Walker A motif; other site 634504004614 ATP binding site [chemical binding]; other site 634504004615 Walker B motif; other site 634504004616 inhibitor binding site; inhibition site 634504004617 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 634504004618 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 634504004619 core domain interface [polypeptide binding]; other site 634504004620 delta subunit interface [polypeptide binding]; other site 634504004621 epsilon subunit interface [polypeptide binding]; other site 634504004622 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 634504004623 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 634504004624 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 634504004625 beta subunit interaction interface [polypeptide binding]; other site 634504004626 Walker A motif; other site 634504004627 ATP binding site [chemical binding]; other site 634504004628 Walker B motif; other site 634504004629 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 634504004630 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 634504004631 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 634504004632 primosome assembly protein PriA; Validated; Region: PRK05580 634504004633 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 634504004634 ATP binding site [chemical binding]; other site 634504004635 putative Mg++ binding site [ion binding]; other site 634504004636 helicase superfamily c-terminal domain; Region: HELICc; smart00490 634504004637 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 634504004638 active site 634504004639 intersubunit interactions; other site 634504004640 catalytic residue [active] 634504004641 Lipopolysaccharide-assembly; Region: LptE; cl01125 634504004642 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 634504004643 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 634504004644 HIGH motif; other site 634504004645 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 634504004646 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 634504004647 active site 634504004648 KMSKS motif; other site 634504004649 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 634504004650 tRNA binding surface [nucleotide binding]; other site 634504004651 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 634504004652 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 634504004653 catalytic residue [active] 634504004654 acetyl-CoA synthetase; Provisional; Region: PRK00174 634504004655 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 634504004656 active site 634504004657 CoA binding site [chemical binding]; other site 634504004658 acyl-activating enzyme (AAE) consensus motif; other site 634504004659 AMP binding site [chemical binding]; other site 634504004660 acetate binding site [chemical binding]; other site 634504004661 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 634504004662 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 634504004663 Walker A/P-loop; other site 634504004664 ATP binding site [chemical binding]; other site 634504004665 Q-loop/lid; other site 634504004666 ABC transporter signature motif; other site 634504004667 Walker B; other site 634504004668 D-loop; other site 634504004669 H-loop/switch region; other site 634504004670 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 634504004671 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 634504004672 Uncharacterized conserved protein [Function unknown]; Region: COG1434 634504004673 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 634504004674 putative active site [active] 634504004675 Predicted helicase [General function prediction only]; Region: COG4889 634504004676 Restriction endonuclease; Region: Mrr_cat_2; pfam13156 634504004677 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 634504004678 ATP binding site [chemical binding]; other site 634504004679 putative Mg++ binding site [ion binding]; other site 634504004680 helicase superfamily c-terminal domain; Region: HELICc; smart00490 634504004681 nucleotide binding region [chemical binding]; other site 634504004682 ATP-binding site [chemical binding]; other site 634504004683 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 634504004684 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 634504004685 Walker A/P-loop; other site 634504004686 ATP binding site [chemical binding]; other site 634504004687 Q-loop/lid; other site 634504004688 ABC transporter signature motif; other site 634504004689 Walker B; other site 634504004690 D-loop; other site 634504004691 H-loop/switch region; other site 634504004692 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 634504004693 FtsX-like permease family; Region: FtsX; pfam02687 634504004694 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 634504004695 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 634504004696 HlyD family secretion protein; Region: HlyD_3; pfam13437 634504004697 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 634504004698 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 634504004699 putative catalytic site [active] 634504004700 putative phosphate binding site [ion binding]; other site 634504004701 active site 634504004702 metal binding site A [ion binding]; metal-binding site 634504004703 DNA binding site [nucleotide binding] 634504004704 putative AP binding site [nucleotide binding]; other site 634504004705 putative metal binding site B [ion binding]; other site 634504004706 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 634504004707 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 634504004708 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 634504004709 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 634504004710 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 634504004711 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 634504004712 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 634504004713 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional; Region: PRK07333 634504004714 H-NS histone family; Region: Histone_HNS; pfam00816 634504004715 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 634504004716 TrbC/VIRB2 family; Region: TrbC; pfam04956 634504004717 TrbC/VIRB2 family; Region: TrbC; pfam04956 634504004718 TrbC/VIRB2 family; Region: TrbC; pfam04956 634504004719 TrbC/VIRB2 family; Region: TrbC; pfam04956 634504004720 TrbC/VIRB2 family; Region: TrbC; pfam04956 634504004721 TrbC/VIRB2 family; Region: TrbC; pfam04956 634504004722 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 634504004723 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 634504004724 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 634504004725 Type IV secretion system proteins; Region: T4SS; pfam07996 634504004726 P-type DNA transfer protein VirB5; Region: VirB5; TIGR02791 634504004727 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 634504004728 Type IV secretion system proteins; Region: T4SS; pfam07996 634504004729 P-type DNA transfer protein VirB5; Region: VirB5; TIGR02791 634504004730 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 634504004731 P-type DNA transfer protein VirB5; Region: VirB5; TIGR02791 634504004732 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 634504004733 Type IV secretion system proteins; Region: T4SS; pfam07996 634504004734 P-type DNA transfer protein VirB5; Region: VirB5; TIGR02791 634504004735 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 634504004736 VirB/Tra/Trw family; Region: VirB; pfam08139 634504004737 VirB8 protein; Region: VirB8; pfam04335 634504004738 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 634504004739 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 634504004740 VirB7 interaction site; other site 634504004741 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 634504004742 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 634504004743 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 634504004744 Walker A motif; other site 634504004745 hexamer interface [polypeptide binding]; other site 634504004746 ATP binding site [chemical binding]; other site 634504004747 Walker B motif; other site 634504004748 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 634504004749 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 634504004750 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 634504004751 L-aspartate oxidase; Provisional; Region: PRK06175 634504004752 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 634504004753 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 634504004754 putative SdhC subunit interface [polypeptide binding]; other site 634504004755 putative proximal heme binding site [chemical binding]; other site 634504004756 putative Iron-sulfur protein interface [polypeptide binding]; other site 634504004757 putative proximal quinone binding site; other site 634504004758 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 634504004759 Iron-sulfur protein interface; other site 634504004760 proximal quinone binding site [chemical binding]; other site 634504004761 SdhD (CybS) interface [polypeptide binding]; other site 634504004762 proximal heme binding site [chemical binding]; other site 634504004763 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 634504004764 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 634504004765 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 634504004766 RimM N-terminal domain; Region: RimM; pfam01782 634504004767 PRC-barrel domain; Region: PRC; pfam05239 634504004768 SapC; Region: SapC; pfam07277 634504004769 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 634504004770 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 634504004771 active site 634504004772 DNA binding site [nucleotide binding] 634504004773 Int/Topo IB signature motif; other site 634504004774 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 634504004775 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 634504004776 HSP70 interaction site [polypeptide binding]; other site 634504004777 Cobaltochelatase CobS subunit N terminal; Region: CobS_N; pfam12556 634504004778 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 634504004779 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; cl17189 634504004780 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 634504004781 cobaltochelatase, CobT subunit; Region: CobT; TIGR01651 634504004782 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 634504004783 metal ion-dependent adhesion site (MIDAS); other site 634504004784 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 634504004785 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 634504004786 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 634504004787 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 634504004788 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 634504004789 purine monophosphate binding site [chemical binding]; other site 634504004790 dimer interface [polypeptide binding]; other site 634504004791 putative catalytic residues [active] 634504004792 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 634504004793 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 634504004794 Uncharacterized conserved small protein [Function unknown]; Region: COG5457 634504004795 Heparinase II/III-like protein; Region: Hepar_II_III; cl15421 634504004796 NusB family; Region: NusB; pfam01029 634504004797 putative RNA binding site [nucleotide binding]; other site 634504004798 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 634504004799 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 634504004800 S-adenosylmethionine binding site [chemical binding]; other site 634504004801 heat shock protein HtpX; Provisional; Region: PRK01345 634504004802 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 634504004803 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 634504004804 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 634504004805 chorismate mutase; Provisional; Region: PRK09239 634504004806 signal recognition particle protein; Provisional; Region: PRK10867 634504004807 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 634504004808 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 634504004809 P loop; other site 634504004810 GTP binding site [chemical binding]; other site 634504004811 Signal peptide binding domain; Region: SRP_SPB; pfam02978 634504004812 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_cladeB; cd00884 634504004813 active site clefts [active] 634504004814 zinc binding site [ion binding]; other site 634504004815 dimer interface [polypeptide binding]; other site 634504004816 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 634504004817 Uncharacterized protein conserved in bacteria (DUF2125); Region: DUF2125; pfam09898 634504004818 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 634504004819 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 634504004820 catalytic triad [active] 634504004821 Uncharacterized membrane-bound protein [Function unknown]; Region: COG3898 634504004822 HemY protein N-terminus; Region: HemY_N; pfam07219 634504004823 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 634504004824 TPR motif; other site 634504004825 binding surface 634504004826 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4223 634504004827 UGMP family protein; Validated; Region: PRK09604 634504004828 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 634504004829 EVE domain; Region: EVE; cl00728 634504004830 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 634504004831 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 634504004832 active site 634504004833 phosphorylation site [posttranslational modification] 634504004834 intermolecular recognition site; other site 634504004835 dimerization interface [polypeptide binding]; other site 634504004836 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 634504004837 DNA binding site [nucleotide binding] 634504004838 Methyltransferase domain; Region: Methyltransf_23; pfam13489 634504004839 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 634504004840 Domain of unknown function (DUF4175); Region: DUF4175; pfam13779 634504004841 diaminopimelate decarboxylase; Region: lysA; TIGR01048 634504004842 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 634504004843 active site 634504004844 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 634504004845 substrate binding site [chemical binding]; other site 634504004846 catalytic residues [active] 634504004847 dimer interface [polypeptide binding]; other site 634504004848 argininosuccinate lyase; Provisional; Region: PRK00855 634504004849 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 634504004850 active sites [active] 634504004851 tetramer interface [polypeptide binding]; other site 634504004852 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 634504004853 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 634504004854 catalytic residues [active] 634504004855 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 634504004856 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 634504004857 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 634504004858 prephenate dehydrogenase; Validated; Region: PRK08507 634504004859 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 634504004860 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 634504004861 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 634504004862 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 634504004863 Walker A/P-loop; other site 634504004864 ATP binding site [chemical binding]; other site 634504004865 Q-loop/lid; other site 634504004866 ABC transporter signature motif; other site 634504004867 Walker B; other site 634504004868 D-loop; other site 634504004869 H-loop/switch region; other site 634504004870 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 634504004871 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 634504004872 TM-ABC transporter signature motif; other site 634504004873 Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_uncharacterized_transporter; cd06325 634504004874 zinc binding site [ion binding]; other site 634504004875 putative ligand binding site [chemical binding]; other site 634504004876 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 634504004877 dimer interface [polypeptide binding]; other site 634504004878 substrate binding site [chemical binding]; other site 634504004879 ATP binding site [chemical binding]; other site 634504004880 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 634504004881 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 634504004882 putative acyl-acceptor binding pocket; other site 634504004883 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 634504004884 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 634504004885 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 634504004886 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 634504004887 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 634504004888 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 634504004889 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 634504004890 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 634504004891 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 634504004892 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 634504004893 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 634504004894 active site 634504004895 DNA binding site [nucleotide binding] 634504004896 Int/Topo IB signature motif; other site 634504004897 shikimate kinase; Provisional; Region: PRK13946 634504004898 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 634504004899 ADP binding site [chemical binding]; other site 634504004900 magnesium binding site [ion binding]; other site 634504004901 putative shikimate binding site; other site 634504004902 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 634504004903 active site 634504004904 dimer interface [polypeptide binding]; other site 634504004905 metal binding site [ion binding]; metal-binding site 634504004906 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 634504004907 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 634504004908 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12671 634504004909 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK06161 634504004910 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK08965 634504004911 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 634504004912 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 634504004913 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK09094 634504004914 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 634504004915 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 634504004916 Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]; Region: MnhB; COG2111 634504004917 monovalent cation:proton antiporter; Region: 2a6301s02; TIGR00943 634504004918 BA14K-like protein; Region: BA14K; pfam07886 634504004919 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 634504004920 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 634504004921 dimer interface [polypeptide binding]; other site 634504004922 active site 634504004923 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 634504004924 catalytic residues [active] 634504004925 substrate binding site [chemical binding]; other site 634504004926 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 634504004927 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 634504004928 NAD(P) binding pocket [chemical binding]; other site 634504004929 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 634504004930 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 634504004931 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 634504004932 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 634504004933 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 634504004934 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 634504004935 E3 interaction surface; other site 634504004936 lipoyl attachment site [posttranslational modification]; other site 634504004937 e3 binding domain; Region: E3_binding; pfam02817 634504004938 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 634504004939 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 634504004940 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 634504004941 TPP-binding site [chemical binding]; other site 634504004942 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 634504004943 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 634504004944 CoA binding domain; Region: CoA_binding; smart00881 634504004945 CoA-ligase; Region: Ligase_CoA; pfam00549 634504004946 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 634504004947 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 634504004948 CoA-ligase; Region: Ligase_CoA; pfam00549 634504004949 malate dehydrogenase; Reviewed; Region: PRK06223 634504004950 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 634504004951 NAD(P) binding site [chemical binding]; other site 634504004952 dimer interface [polypeptide binding]; other site 634504004953 tetramer (dimer of dimers) interface [polypeptide binding]; other site 634504004954 substrate binding site [chemical binding]; other site 634504004955 Predicted ATPase [General function prediction only]; Region: COG1485 634504004956 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 634504004957 Walker A/P-loop; other site 634504004958 ATP binding site [chemical binding]; other site 634504004959 Q-loop/lid; other site 634504004960 ABC transporter signature motif; other site 634504004961 Walker B; other site 634504004962 D-loop; other site 634504004963 H-loop/switch region; other site 634504004964 Protease inhibitor Inh; Region: Inh; pfam02974 634504004965 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 634504004966 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 634504004967 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 634504004968 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 634504004969 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 634504004970 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 634504004971 FeS/SAM binding site; other site 634504004972 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 634504004973 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 634504004974 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 634504004975 P loop; other site 634504004976 GTP binding site [chemical binding]; other site 634504004977 intracellular septation protein A; Reviewed; Region: PRK00259 634504004978 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 634504004979 ParB-like nuclease domain; Region: ParBc; pfam02195 634504004980 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 634504004981 KorB domain; Region: KorB; pfam08535 634504004982 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 634504004983 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 634504004984 P-loop; other site 634504004985 Magnesium ion binding site [ion binding]; other site 634504004986 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 634504004987 Magnesium ion binding site [ion binding]; other site 634504004988 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 634504004989 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 634504004990 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 634504004991 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 634504004992 L-aspartate oxidase; Provisional; Region: PRK06175 634504004993 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 634504004994 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 634504004995 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 634504004996 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 634504004997 trmE is a tRNA modification GTPase; Region: trmE; cd04164 634504004998 G1 box; other site 634504004999 GTP/Mg2+ binding site [chemical binding]; other site 634504005000 Switch I region; other site 634504005001 G2 box; other site 634504005002 Switch II region; other site 634504005003 G3 box; other site 634504005004 G4 box; other site 634504005005 G5 box; other site 634504005006 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 634504005007 transcription termination factor Rho; Provisional; Region: rho; PRK09376 634504005008 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 634504005009 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 634504005010 RNA binding site [nucleotide binding]; other site 634504005011 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 634504005012 multimer interface [polypeptide binding]; other site 634504005013 Walker A motif; other site 634504005014 ATP binding site [chemical binding]; other site 634504005015 Walker B motif; other site 634504005016 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 634504005017 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 634504005018 putative active site [active] 634504005019 multiple promoter invertase; Provisional; Region: mpi; PRK13413 634504005020 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 634504005021 catalytic residues [active] 634504005022 catalytic nucleophile [active] 634504005023 Presynaptic Site I dimer interface [polypeptide binding]; other site 634504005024 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 634504005025 Synaptic Flat tetramer interface [polypeptide binding]; other site 634504005026 Synaptic Site I dimer interface [polypeptide binding]; other site 634504005027 DNA binding site [nucleotide binding] 634504005028 Predicted nucleotide-binding protein containing TIR-like domain; Region: TIR-like; cl17861 634504005029 Replication protein C N-terminal domain; Region: RP-C; pfam03428 634504005030 Replication protein C C-terminal region; Region: RP-C_C; pfam11800 634504005031 TrbC/VIRB2 family; Region: TrbC; pfam04956 634504005032 Type IV secretory pathway, VirB3 components [Intracellular trafficking and secretion]; Region: VirB3; COG3702 634504005033 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 634504005034 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 634504005035 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 634504005036 Walker A motif; other site 634504005037 ATP binding site [chemical binding]; other site 634504005038 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 634504005039 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 634504005040 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 634504005041 VirB7 interaction site; other site 634504005042 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 634504005043 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 634504005044 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 634504005045 Walker A motif; other site 634504005046 hexamer interface [polypeptide binding]; other site 634504005047 ATP binding site [chemical binding]; other site 634504005048 Walker B motif; other site 634504005049 RelB antitoxin; Region: RelB; cl01171 634504005050 Fic/DOC family; Region: Fic; cl00960 634504005051 VbhA antitoxin and related proteins; Region: VbhA_like; cd11586 634504005052 FIC domain binding interface [polypeptide binding]; other site 634504005053 Ti-type conjugative transfer relaxase TraA; Region: TraA_Ti; TIGR02768 634504005054 MobA/MobL family; Region: MobA_MobL; pfam03389 634504005055 AAA domain; Region: AAA_30; pfam13604 634504005056 Family description; Region: UvrD_C_2; pfam13538 634504005057 Conjugal transfer protein TraD; Region: TraD; pfam06412 634504005058 conjugal transfer coupling protein TraG; Provisional; Region: PRK13822 634504005059 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 634504005060 Walker A motif; other site 634504005061 ATP binding site [chemical binding]; other site 634504005062 Walker B motif; other site 634504005063 Plasmid maintenance system killer protein; Region: Plasmid_killer; pfam05015 634504005064 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 634504005065 non-specific DNA binding site [nucleotide binding]; other site 634504005066 salt bridge; other site 634504005067 sequence-specific DNA binding site [nucleotide binding]; other site 634504005068 UDP-3-O-[3-hydroxymyristoyl]; Region: LpxD; COG1044 634504005069 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 634504005070 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 634504005071 non-specific DNA binding site [nucleotide binding]; other site 634504005072 salt bridge; other site 634504005073 sequence-specific DNA binding site [nucleotide binding]; other site 634504005074 ParA-like protein; Provisional; Region: PHA02518 634504005075 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 634504005076 P-loop; other site 634504005077 Magnesium ion binding site [ion binding]; other site