-- dump date 20111121_010019 -- class Genbank::misc_feature -- table misc_feature_note -- id note 990288000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 990288000002 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288000003 Walker A motif; other site 990288000004 ATP binding site [chemical binding]; other site 990288000005 Walker B motif; other site 990288000006 arginine finger; other site 990288000007 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 990288000008 DnaA box-binding interface [nucleotide binding]; other site 990288000009 DNA polymerase III subunit beta; Validated; Region: PRK05643 990288000010 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the...; Region: beta_clamp; cd00140 990288000011 putative DNA binding surface [nucleotide binding]; other site 990288000012 dimer interface [polypeptide binding]; other site 990288000013 beta-clamp/clamp loader binding surface; other site 990288000014 beta-clamp/translesion DNA polymerase binding surface; other site 990288000015 recombination protein F; Reviewed; Region: recF; PRK00064 990288000016 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288000017 Walker A/P-loop; other site 990288000018 ATP binding site [chemical binding]; other site 990288000019 Q-loop/lid; other site 990288000020 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288000021 ABC transporter signature motif; other site 990288000022 Walker B; other site 990288000023 D-loop; other site 990288000024 H-loop/switch region; other site 990288000025 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 990288000026 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 990288000027 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 990288000028 anchoring element; other site 990288000029 dimer interface [polypeptide binding]; other site 990288000030 ATP binding site [chemical binding]; other site 990288000031 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of...; Region: TOPRIM_TopoIIA_GyrB; cd03366 990288000032 active site 990288000033 putative metal-binding site [ion binding]; other site 990288000034 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 990288000035 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 990288000036 FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-...; Region: DHOD_e_trans_like; cd06192 990288000037 FAD binding pocket [chemical binding]; other site 990288000038 FAD binding motif [chemical binding]; other site 990288000039 phosphate binding motif [ion binding]; other site 990288000040 beta-alpha-beta structure motif; other site 990288000041 NAD binding pocket [chemical binding]; other site 990288000042 Iron coordination center [ion binding]; other site 990288000043 Septum formation topological specificity factor MinE; Region: MinE; cl00538 990288000044 cell division inhibitor MinD; Provisional; Region: PRK10818 990288000045 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a...; Region: MinD; cd02036 990288000046 Switch I; other site 990288000047 Switch II; other site 990288000048 septum formation inhibitor; Reviewed; Region: minC; PRK04804 990288000049 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 990288000050 Ferredoxin [Energy production and conversion]; Region: COG1146 990288000051 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 990288000052 DNA topoisomerase I; Validated; Region: PRK06599 990288000053 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in...; Region: TOPRIM_TopoIA_TopoI; cd03363 990288000054 active site 990288000055 interdomain interaction site; other site 990288000056 putative metal-binding site [ion binding]; other site 990288000057 nucleotide binding site [chemical binding]; other site 990288000058 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded...; Region: TOP1Ac; cd00186 990288000059 domain I; other site 990288000060 DNA binding groove [nucleotide binding] 990288000061 phosphate binding site [ion binding]; other site 990288000062 domain II; other site 990288000063 domain III; other site 990288000064 nucleotide binding site [chemical binding]; other site 990288000065 catalytic site [active] 990288000066 domain IV; other site 990288000067 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 990288000068 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 990288000069 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 990288000070 Protein of unknown function (DUF494); Region: DUF494; cl01103 990288000071 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 990288000072 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 990288000073 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 990288000074 putative peptidoglycan binding site; other site 990288000075 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(...; Region: Pep_deformylase; cd00487 990288000076 active site 990288000077 catalytic residues [active] 990288000078 metal binding site [ion binding]; metal-binding site 990288000079 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 990288000080 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 990288000081 putative active site [active] 990288000082 substrate binding site [chemical binding]; other site 990288000083 putative cosubstrate binding site; other site 990288000084 catalytic site [active] 990288000085 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 990288000086 substrate binding site [chemical binding]; other site 990288000087 16S rRNA methyltransferase B; Provisional; Region: PRK10901 990288000088 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288000089 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 990288000090 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 connected by an extended linker. The...; Region: HAMP; cl01054 990288000091 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 trans-...; Region: HisKA; cl00080 990288000092 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 990288000093 ATP binding site [chemical binding]; other site 990288000094 G-X-G motif; other site 990288000095 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 990288000096 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 990288000097 active site 990288000098 phosphorylation site [posttranslational modification] 990288000099 intermolecular recognition site; other site 990288000100 dimerization interface [polypeptide binding]; other site 990288000101 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288000102 Walker A motif; other site 990288000103 ATP binding site [chemical binding]; other site 990288000104 Walker B motif; other site 990288000105 arginine finger; other site 990288000106 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea...; Region: MogA_MoaB; cd00886 990288000107 MPT binding site; other site 990288000108 trimer interface [polypeptide binding]; other site 990288000109 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288000110 Flavin-dependent tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA [Cell cycle control, cell division, chromosome partitioning]; Region: GidA; COG0445 990288000111 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288000112 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 990288000113 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 990288000114 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...; Region: ParA; cd02042 990288000115 P-loop; other site 990288000116 Magnesium ion binding site [ion binding]; other site 990288000117 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...; Region: ParA; cd02042 990288000118 Magnesium ion binding site [ion binding]; other site 990288000119 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 990288000120 ParB-like nuclease domain; Region: ParBc; cl02129 990288000121 ATP synthase A chain; Region: ATP-synt_A; cl00413 990288000122 ATP synthase subunit C; Region: ATP-synt_C; cl00466 990288000123 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 990288000124 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 990288000125 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 990288000126 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 990288000127 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 990288000128 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 990288000129 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 990288000130 beta subunit interaction interface [polypeptide binding]; other site 990288000131 Walker A motif; other site 990288000132 ATP binding site [chemical binding]; other site 990288000133 Walker B motif; other site 990288000134 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 990288000135 ATP synthase; Region: ATP-synt; cl00365 990288000136 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 990288000137 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 990288000138 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 990288000139 alpha subunit interaction interface [polypeptide binding]; other site 990288000140 Walker A motif; other site 990288000141 ATP binding site [chemical binding]; other site 990288000142 Walker B motif; other site 990288000143 inhibitor binding site; inhibition site 990288000144 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 990288000145 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 990288000146 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 990288000147 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: glmU; TIGR01173 990288000148 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 990288000149 Substrate binding site [chemical binding]; other site 990288000150 Mg++ binding site [ion binding]; other site 990288000151 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 990288000152 active site 990288000153 substrate binding site [chemical binding]; other site 990288000154 CoA binding site [chemical binding]; other site 990288000155 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 990288000156 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...; Region: GFAT; cd00714 990288000157 glutaminase active site [active] 990288000158 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 990288000159 dimer interface [polypeptide binding]; other site 990288000160 active site 990288000161 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 990288000162 dimer interface [polypeptide binding]; other site 990288000163 active site 990288000164 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288000165 Walker A motif; other site 990288000166 ATP binding site [chemical binding]; other site 990288000167 Walker B motif; other site 990288000168 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 990288000169 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 990288000170 Integrase core domain; Region: rve; cl01316 990288000171 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 990288000172 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288000173 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288000174 TM1410 hypothetical-related protein; Region: DUF297; cl00997 990288000175 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule...; Region: GT1_like_3; cd03813 990288000176 Predicted membrane protein [Function unknown]; Region: COG4267 990288000177 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288000178 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 990288000179 NAD(P) binding site [chemical binding]; other site 990288000180 active site 990288000181 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 990288000182 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288000183 metal binding site [ion binding]; metal-binding site 990288000184 active site 990288000185 I-site; other site 990288000186 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 990288000187 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of...; Region: DnaJ; cd06257 990288000188 HSP70 interaction site [polypeptide binding]; other site 990288000189 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 990288000190 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 990288000191 UvrD/REP helicase; Region: UvrD-helicase; cl14126 990288000192 UvrD/REP helicase; Region: UvrD-helicase; cl14126 990288000193 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 990288000194 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 990288000195 ATP binding site [chemical binding]; other site 990288000196 Mg2+ binding site [ion binding]; other site 990288000197 G-X-G motif; other site 990288000198 osmolarity response regulator; Provisional; Region: ompR; PRK09468 990288000199 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 990288000200 active site 990288000201 phosphorylation site [posttranslational modification] 990288000202 intermolecular recognition site; other site 990288000203 dimerization interface [polypeptide binding]; other site 990288000204 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...; Region: trans_reg_C; cd00383 990288000205 DNA binding site [nucleotide binding] 990288000206 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 990288000207 dimer interface [polypeptide binding]; other site 990288000208 Outer membrane efflux protein; Region: OEP; pfam02321 990288000209 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 990288000210 Outer membrane efflux protein; Region: OEP; pfam02321 990288000211 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 990288000212 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 990288000213 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 990288000214 RmuC family; Region: RmuC; pfam02646 990288000215 LytB protein; Region: LYTB; cl00507 990288000216 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 990288000217 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 990288000218 Inositol-monophosphatase-like domains. This family of phosphatases is dependent on bivalent metal ions such as Mg++, and many members are inhibited by Li+ (which is thought to displace a bivalent ion in the active site). Substrates include fructose-1,6-; Region: IMPase_like; cd01637 990288000219 active site 990288000220 Fructose-1,6-bisphosphatase/sedoheptulose 1,7-bisphosphatase and related proteins [Carbohydrate transport and metabolism]; Region: GlpX; COG1494 990288000221 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 990288000222 active site 990288000223 transketolase; Reviewed; Region: PRK12753 990288000224 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 990288000225 TPP-binding site [chemical binding]; other site 990288000226 dimer interface [polypeptide binding]; other site 990288000227 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 990288000228 PYR/PP interface [polypeptide binding]; other site 990288000229 dimer interface [polypeptide binding]; other site 990288000230 TPP binding site [chemical binding]; other site 990288000231 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 990288000232 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 990288000233 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 990288000234 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 990288000235 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 990288000236 substrate binding site [chemical binding]; other site 990288000237 hinge regions; other site 990288000238 ADP binding site [chemical binding]; other site 990288000239 catalytic site [active] 990288000240 pyruvate kinase; Provisional; Region: PRK05826 990288000241 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 990288000242 domain interfaces; other site 990288000243 active site 990288000244 hypothetical protein; Provisional; Region: PRK08185 990288000245 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose...; Region: TBP_aldolase_IIB; cd00947 990288000246 intersubunit interface [polypeptide binding]; other site 990288000247 active site 990288000248 zinc binding site [ion binding]; other site 990288000249 Na+ binding site [ion binding]; other site 990288000250 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative...; Region: RPE; cd00429 990288000251 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 990288000252 substrate binding site [chemical binding]; other site 990288000253 hexamer interface [polypeptide binding]; other site 990288000254 metal binding site [ion binding]; metal-binding site 990288000255 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 990288000256 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 990288000257 motif II; other site 990288000258 anthranilate synthase component I; Provisional; Region: PRK13565 990288000259 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 990288000260 chorismate binding enzyme; Region: Chorismate_bind; cl10555 990288000261 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 990288000262 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 990288000263 glutamine binding [chemical binding]; other site 990288000264 catalytic triad [active] 990288000265 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 990288000266 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 990288000267 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 990288000268 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 990288000269 active site 990288000270 ribulose/triose binding site [chemical binding]; other site 990288000271 phosphate binding site [ion binding]; other site 990288000272 substrate (anthranilate) binding pocket [chemical binding]; other site 990288000273 product (indole) binding pocket [chemical binding]; other site 990288000274 OsmC-like protein; Region: OsmC; cl00767 990288000275 Rrf2 family protein; Region: rrf2_super; TIGR00738 990288000276 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288000277 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 990288000278 diiron binding motif [ion binding]; other site 990288000279 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:; Region: TRX_Fd_family; cd02980 990288000280 dimer interface [polypeptide binding]; other site 990288000281 [2Fe-2S] cluster binding site [ion binding]; other site 990288000282 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 990288000283 nodulation ABC transporter NodI; Provisional; Region: PRK13537 990288000284 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288000285 Walker A/P-loop; other site 990288000286 ATP binding site [chemical binding]; other site 990288000287 Q-loop/lid; other site 990288000288 ABC transporter signature motif; other site 990288000289 Walker B; other site 990288000290 D-loop; other site 990288000291 H-loop/switch region; other site 990288000292 ABC-2 type transporter; Region: ABC2_membrane; cl11417 990288000293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 990288000294 Integrase core domain; Region: rve; cl01316 990288000295 Fic family protein [Function unknown]; Region: COG3177 990288000296 Fic/DOC family; Region: Fic; cl00960 990288000297 Protein of unknown function (DUF3375); Region: DUF3375; pfam11855 990288000298 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4913 990288000299 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4924 990288000300 Uncharacterized protein conserved in bacteria N-term (DUF3322); Region: DUF3322; pfam11795 990288000301 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 990288000302 Phd_YefM; Region: PhdYeFM; cl09153 990288000303 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 990288000304 ParB-like nuclease domain; Region: ParBc; cl02129 990288000305 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 990288000306 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...; Region: ParA; cd02042 990288000307 P-loop; other site 990288000308 Magnesium ion binding site [ion binding]; other site 990288000309 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 990288000310 Peptidase S26; Region: Peptidase_S26; pfam10502 990288000311 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)...; Region: Peptidase_S24_S26; cl10465 990288000312 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 990288000313 Transposase domain (DUF772); Region: DUF772; cl12084 990288000314 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288000315 DsrE/DsrF-like family; Region: DrsE; cl00672 990288000316 Predicted transcriptional regulator [Transcription]; Region: COG4190 990288000317 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 990288000318 N-acetyl-D-glucosamine binding site [chemical binding]; other site 990288000319 catalytic residue [active] 990288000320 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 990288000321 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 990288000322 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 990288000323 Ligand binding site [chemical binding]; other site 990288000324 Putative Catalytic site [active] 990288000325 DXD motif; other site 990288000326 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 990288000327 Transposase domain (DUF772); Region: DUF772; cl12084 990288000328 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288000329 Transposase domain (DUF772); Region: DUF772; cl12084 990288000330 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288000331 Transposase; Region: DEDD_Tnp_IS110; pfam01548 990288000332 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 990288000333 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 990288000334 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 990288000335 K+-transporting ATPase, A chain [Inorganic ion transport and metabolism]; Region: KdpA; cl00903 990288000336 Potassium-transporting ATPase A subunit; Region: KdpA; pfam03814 990288000337 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 990288000338 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 990288000339 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 990288000340 K+-transporting ATPase, c chain; Region: KdpC; cl00944 990288000341 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 990288000342 substrate binding site [chemical binding]; other site 990288000343 nucleotide binding site [chemical binding]; other site 990288000344 K+-transporting ATPase, A chain [Inorganic ion transport and metabolism]; Region: KdpA; cl00903 990288000345 Transposase domain (DUF772); Region: DUF772; cl12084 990288000346 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288000347 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 990288000348 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 990288000349 active site 990288000350 phosphorylation site [posttranslational modification] 990288000351 intermolecular recognition site; other site 990288000352 dimerization interface [polypeptide binding]; other site 990288000353 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...; Region: trans_reg_C; cd00383 990288000354 DNA binding site [nucleotide binding] 990288000355 Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156; Region: CsoR-like_DUF156; cd10148 990288000356 putative homotetramer interface [polypeptide binding]; other site 990288000357 putative homodimer interface [polypeptide binding]; other site 990288000358 putative allosteric switch controlling residues; other site 990288000359 putative metal binding site [ion binding]; other site 990288000360 putative homodimer-homodimer interface [polypeptide binding]; other site 990288000361 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 990288000362 active site 990288000363 DNA polymerase IV; Validated; Region: PRK02406 990288000364 DNA binding site [nucleotide binding] 990288000365 Transposase domain (DUF772); Region: DUF772; cl12084 990288000366 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288000367 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 990288000368 Coenzyme A binding pocket [chemical binding]; other site 990288000369 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 990288000370 conserved cys residue [active] 990288000371 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 990288000372 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 990288000373 classical (c) SDRs; Region: SDR_c; cd05233 990288000374 NAD(P) binding site [chemical binding]; other site 990288000375 active site 990288000376 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 990288000377 VirB8 protein; Region: VirB8; cl01500 990288000378 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 990288000379 VirB7 interaction site; other site 990288000380 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 990288000381 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 990288000382 PemK-like protein; Region: PemK; cl00995 990288000383 DNA topoisomerase III; Provisional; Region: PRK07726 990288000384 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by:...; Region: TOPRIM_TopoIA_TopoIII; cd03362 990288000385 active site 990288000386 putative interdomain interaction site [polypeptide binding]; other site 990288000387 putative metal-binding site [ion binding]; other site 990288000388 putative nucleotide binding site [chemical binding]; other site 990288000389 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded...; Region: TOP1Ac; cd00186 990288000390 domain I; other site 990288000391 DNA binding groove [nucleotide binding] 990288000392 phosphate binding site [ion binding]; other site 990288000393 domain II; other site 990288000394 domain III; other site 990288000395 nucleotide binding site [chemical binding]; other site 990288000396 catalytic site [active] 990288000397 domain IV; other site 990288000398 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases...; Region: lysozyme_like; cl00222 990288000399 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288000400 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 990288000401 Walker A motif; other site 990288000402 ATP binding site [chemical binding]; other site 990288000403 Walker B motif; other site 990288000404 Transposase domain (DUF772); Region: DUF772; cl12084 990288000405 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288000406 Transposase domain (DUF772); Region: DUF772; cl12084 990288000407 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288000408 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288000409 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 990288000410 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288000411 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 990288000412 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 990288000413 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 990288000414 Transposase domain (DUF772); Region: DUF772; cl12084 990288000415 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 990288000416 putative active site [active] 990288000417 catalytic site [active] 990288000418 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 990288000419 tetramer (dimer of dimers) interface [polypeptide binding]; other site 990288000420 Transposase domain (DUF772); Region: DUF772; cl12084 990288000421 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288000422 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 990288000423 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 990288000424 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 990288000425 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 990288000426 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 990288000427 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily...; Region: Heme_Cu_Oxidase_I; cl00275 990288000428 D-pathway; other site 990288000429 Low-spin heme binding site [chemical binding]; other site 990288000430 Putative water exit pathway; other site 990288000431 Binuclear center (active site) [active] 990288000432 K-pathway; other site 990288000433 Putative proton exit pathway; other site 990288000434 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 990288000435 Subunit I/III interface [polypeptide binding]; other site 990288000436 UbiA prenyltransferase family; Region: UbiA; cl00337 990288000437 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288000438 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288000439 PilZ domain; Region: PilZ; cl01260 990288000440 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 990288000441 PAS fold; Region: PAS_3; pfam08447 990288000442 putative active site [active] 990288000443 heme pocket [chemical binding]; other site 990288000444 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288000445 metal binding site [ion binding]; metal-binding site 990288000446 active site 990288000447 I-site; other site 990288000448 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 990288000449 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 990288000450 Response regulator receiver domain; Region: Response_reg; pfam00072 990288000451 active site 990288000452 phosphorylation site [posttranslational modification] 990288000453 intermolecular recognition site; other site 990288000454 dimerization interface [polypeptide binding]; other site 990288000455 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 990288000456 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 990288000457 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 990288000458 putative binding surface; other site 990288000459 active site 990288000460 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 990288000461 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 990288000462 ATP binding site [chemical binding]; other site 990288000463 Mg2+ binding site [ion binding]; other site 990288000464 G-X-G motif; other site 990288000465 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 990288000466 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 990288000467 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 990288000468 Fibrinogen alpha/beta chain family; Region: Fib_alpha; pfam08702 990288000469 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 990288000470 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 990288000471 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 990288000472 active site 990288000473 phosphorylation site [posttranslational modification] 990288000474 intermolecular recognition site; other site 990288000475 dimerization interface [polypeptide binding]; other site 990288000476 PAS fold; Region: PAS_4; pfam08448 990288000477 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 990288000478 putative active site [active] 990288000479 heme pocket [chemical binding]; other site 990288000480 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 990288000481 diguanylate cyclase; Provisional; Region: PRK09894 990288000482 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 990288000483 heme-binding site [chemical binding]; other site 990288000484 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 990288000485 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 990288000486 Phage integrase family; Region: Phage_integrase; pfam00589 990288000487 DNA binding site [nucleotide binding] 990288000488 Int/Topo IB signature motif; other site 990288000489 active site 990288000490 Double zinc ribbon; Region: DZR; pfam12773 990288000491 Integrase core domain; Region: rve; cl01316 990288000492 transposase; Provisional; Region: PRK06526 990288000493 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288000494 Walker A motif; other site 990288000495 ATP binding site [chemical binding]; other site 990288000496 Walker B motif; other site 990288000497 O-Antigen ligase; Region: Wzy_C; cl04850 990288000498 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 990288000499 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 990288000500 Substrate binding site [chemical binding]; other site 990288000501 Cupin domain; Region: Cupin_2; cl09118 990288000502 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 990288000503 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 990288000504 NADP-binding site; other site 990288000505 homotetramer interface [polypeptide binding]; other site 990288000506 substrate binding site [chemical binding]; other site 990288000507 homodimer interface [polypeptide binding]; other site 990288000508 active site 990288000509 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 990288000510 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 990288000511 NADP-binding site; other site 990288000512 homotetramer interface [polypeptide binding]; other site 990288000513 substrate binding site [chemical binding]; other site 990288000514 homodimer interface [polypeptide binding]; other site 990288000515 active site 990288000516 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 990288000517 This family is most closely related to the GT1 family of glycosyltransferases. wbaZ in Salmonella enterica has been shown to possess the mannosyl transferase activity. The members of this family are found in certain bacteria and Archaea; Region: GT1_wbaZ_like; cd03804 990288000518 putative ADP-binding pocket [chemical binding]; other site 990288000519 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 990288000520 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288000521 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288000522 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 990288000523 Transposase domain (DUF772); Region: DUF772; cl12084 990288000524 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288000525 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 990288000526 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 990288000527 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 990288000528 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 990288000529 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 990288000530 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 990288000531 ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides...; Region: ABC_KpsT_Wzt; cd03220 990288000532 Walker A/P-loop; other site 990288000533 ATP binding site [chemical binding]; other site 990288000534 Q-loop/lid; other site 990288000535 ABC transporter signature motif; other site 990288000536 Walker B; other site 990288000537 D-loop; other site 990288000538 H-loop/switch region; other site 990288000539 ABC-2 type transporter; Region: ABC2_membrane; cl11417 990288000540 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288000541 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 990288000542 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 990288000543 Probable Catalytic site [active] 990288000544 metal binding site [ion binding]; metal-binding site 990288000545 MatE; Region: MatE; cl10513 990288000546 MatE; Region: MatE; cl10513 990288000547 Undecaprenyl-phosphate galactose phosphotransferase, WbaP; Region: WbaP_sugtrans; TIGR03022 990288000548 Bacterial sugar transferase; Region: Bac_transf; cl00939 990288000549 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...; Region: PTS_IIA_man; cl00025 990288000550 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 990288000551 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 990288000552 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 990288000553 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 990288000554 DAK2 domain; Region: Dak2; cl03685 990288000555 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481; cl10557 990288000556 Dak1 domain; Region: Dak1; pfam02733 990288000557 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 990288000558 PAS domain S-box; Region: sensory_box; TIGR00229 990288000559 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 990288000560 putative active site [active] 990288000561 heme pocket [chemical binding]; other site 990288000562 PAS domain S-box; Region: sensory_box; TIGR00229 990288000563 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 990288000564 putative active site [active] 990288000565 heme pocket [chemical binding]; other site 990288000566 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288000567 metal binding site [ion binding]; metal-binding site 990288000568 active site 990288000569 I-site; other site 990288000570 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 990288000571 DNA repair protein RadA; Provisional; Region: PRK11823 990288000572 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 990288000573 Walker A motif/ATP binding site; other site 990288000574 ATP binding site [chemical binding]; other site 990288000575 Walker B motif; other site 990288000576 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 990288000577 alanine racemase; Reviewed; Region: alr; PRK00053 990288000578 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 990288000579 catalytic residue [active] 990288000580 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 990288000581 replicative DNA helicase; Region: DnaB; TIGR00665 990288000582 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 990288000583 Walker A motif; other site 990288000584 ATP binding site [chemical binding]; other site 990288000585 Walker B motif; other site 990288000586 DNA binding loops [nucleotide binding] 990288000587 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 990288000588 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 990288000589 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 990288000590 Predicted membrane protein (DUF2232); Region: DUF2232; cl01728 990288000591 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 990288000592 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 990288000593 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 990288000594 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 990288000595 K+ potassium transporter; Region: K_trans; cl01227 990288000596 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 990288000597 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 990288000598 TRAM domain; Region: TRAM; cl01282 990288000599 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288000600 Protein of unknown function (DUF1318); Region: DUF1318; cl01547 990288000601 cysteine synthases; Region: cysKM; TIGR01136 990288000602 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine...; Region: CBS_like; cd01561 990288000603 dimer interface [polypeptide binding]; other site 990288000604 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288000605 catalytic residue [active] 990288000606 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 990288000607 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 990288000608 putative active site [active] 990288000609 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 990288000610 SelR domain; Region: SelR; cl00369 990288000611 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 990288000612 heme-binding site [chemical binding]; other site 990288000613 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 990288000614 GAF domain; Region: GAF; cl00853 990288000615 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 990288000616 GAF domain; Region: GAF; cl00853 990288000617 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288000618 metal binding site [ion binding]; metal-binding site 990288000619 active site 990288000620 I-site; other site 990288000621 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 990288000622 exodeoxyribonuclease V, alpha subunit; Region: recD; TIGR01447 990288000623 UvrD/REP helicase; Region: UvrD-helicase; cl14126 990288000624 UvrD/REP helicase; Region: UvrD-helicase; cl14126 990288000625 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 990288000626 UvrD/REP helicase; Region: UvrD-helicase; cl14126 990288000627 UvrD/REP helicase; Region: UvrD-helicase; cl14126 990288000628 Exodeoxyribonuclease V, gamma subunit; Region: Exonuc_V_gamma; pfam04257 990288000629 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 990288000630 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 990288000631 Protein of unknown function (DUF692); Region: DUF692; cl01263 990288000632 response regulator GlrR; Provisional; Region: PRK15115 990288000633 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 990288000634 active site 990288000635 phosphorylation site [posttranslational modification] 990288000636 intermolecular recognition site; other site 990288000637 dimerization interface [polypeptide binding]; other site 990288000638 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288000639 Walker A motif; other site 990288000640 ATP binding site [chemical binding]; other site 990288000641 Walker B motif; other site 990288000642 arginine finger; other site 990288000643 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 connected by an extended linker. The...; Region: HAMP; cl01054 990288000644 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 trans-...; Region: HisKA; cd00082 990288000645 dimer interface [polypeptide binding]; other site 990288000646 phosphorylation site [posttranslational modification] 990288000647 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 990288000648 ATP binding site [chemical binding]; other site 990288000649 Mg2+ binding site [ion binding]; other site 990288000650 G-X-G motif; other site 990288000651 dihydroorotase; Validated; Region: pyrC; PRK09357 990288000652 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...; Region: metallo-dependent_hydrolases; cl00281 990288000653 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 990288000654 active site 990288000655 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 990288000656 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 990288000657 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288000658 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 990288000659 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 990288000660 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 990288000661 glutathione synthetase; Provisional; Region: PRK05246 990288000662 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 990288000663 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 990288000664 Glutamate-cysteine ligase; Region: GshA; pfam08886 990288000665 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 990288000666 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the...; Region: citrate_synt_like_1_1; cd06112 990288000667 citrate synthase; Provisional; Region: PRK14036 990288000668 dimer interface [polypeptide binding]; other site 990288000669 active site 990288000670 citrylCoA binding site [chemical binding]; other site 990288000671 oxalacetate/citrate binding site [chemical binding]; other site 990288000672 coenzyme A binding site [chemical binding]; other site 990288000673 catalytic triad [active] 990288000674 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 990288000675 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 990288000676 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 990288000677 G1 box; other site 990288000678 GTP/Mg2+ binding site [chemical binding]; other site 990288000679 G2 box; other site 990288000680 Switch I region; other site 990288000681 G3 box; other site 990288000682 Switch II region; other site 990288000683 G4 box; other site 990288000684 G5 box; other site 990288000685 Nucleoside recognition; Region: Gate; cl00486 990288000686 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 990288000687 Phosphate-starvation-inducible E; Region: PsiE; cl01264 990288000688 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 990288000689 E3 interaction surface; other site 990288000690 lipoyl attachment site [posttranslational modification]; other site 990288000691 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 990288000692 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 990288000693 E3 interaction surface; other site 990288000694 lipoyl attachment site [posttranslational modification]; other site 990288000695 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 990288000696 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion]; Region: Lpd; COG1249 990288000697 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288000698 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288000699 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 990288000700 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 990288000701 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 990288000702 alpha subunit interface [polypeptide binding]; other site 990288000703 TPP binding site [chemical binding]; other site 990288000704 heterodimer interface [polypeptide binding]; other site 990288000705 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 990288000706 pyruvate dehydrogenase E1 component alpha subunit; Reviewed; Region: odpA; CHL00149 990288000707 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 990288000708 tetramer interface [polypeptide binding]; other site 990288000709 TPP-binding site [chemical binding]; other site 990288000710 heterodimer interface [polypeptide binding]; other site 990288000711 phosphorylation loop region [posttranslational modification] 990288000712 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 990288000713 transmembrane helices; other site 990288000714 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 990288000715 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 990288000716 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 990288000717 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 990288000718 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 990288000719 active site 990288000720 phosphorylation site [posttranslational modification] 990288000721 intermolecular recognition site; other site 990288000722 dimerization interface [polypeptide binding]; other site 990288000723 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...; Region: trans_reg_C; cd00383 990288000724 DNA binding site [nucleotide binding] 990288000725 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 990288000726 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 990288000727 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 990288000728 Ligand Binding Site [chemical binding]; other site 990288000729 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 trans-...; Region: HisKA; cd00082 990288000730 dimer interface [polypeptide binding]; other site 990288000731 phosphorylation site [posttranslational modification] 990288000732 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 990288000733 ATP binding site [chemical binding]; other site 990288000734 Mg2+ binding site [ion binding]; other site 990288000735 G-X-G motif; other site 990288000736 K+-transporting ATPase, A chain [Inorganic ion transport and metabolism]; Region: KdpA; cl00903 990288000737 Potassium-transporting ATPase A subunit; Region: KdpA; pfam03814 990288000738 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 990288000739 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 990288000740 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 990288000741 K+-transporting ATPase, c chain; Region: KdpC; cl00944 990288000742 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 990288000743 DNA photolyase; Region: DNA_photolyase; pfam00875 990288000744 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 990288000745 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 990288000746 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 990288000747 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 990288000748 putative substrate translocation pore; other site 990288000749 EamA-like transporter family; Region: EamA; cl01037 990288000750 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 990288000751 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 990288000752 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 990288000753 DNA binding residues [nucleotide binding] 990288000754 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 990288000755 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 990288000756 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 990288000757 TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella...; Region: TypA_BipA; cd01891 990288000758 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 990288000759 G1 box; other site 990288000760 putative GEF interaction site [polypeptide binding]; other site 990288000761 GTP/Mg2+ binding site [chemical binding]; other site 990288000762 Switch I region; other site 990288000763 G2 box; other site 990288000764 G3 box; other site 990288000765 Switch II region; other site 990288000766 G4 box; other site 990288000767 G5 box; other site 990288000768 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 990288000769 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...; Region: BipA_TypA_C; cd03710 990288000770 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 990288000771 S-adenosylmethionine binding site [chemical binding]; other site 990288000772 Protein of unknown function (DUF525); Region: DUF525; cl01119 990288000773 Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]; Region: Nei; COG0266 990288000774 N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; Region: FpgNei_N; cd08773 990288000775 DNA binding site [nucleotide binding] 990288000776 H2TH interface [polypeptide binding]; other site 990288000777 putative catalytic residues [active] 990288000778 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 990288000779 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 990288000780 active site residue [active] 990288000781 potential frameshift: common BLAST hit: gi|218666065|ref|YP_002424962.1| glutamine synthetase, type I 990288000782 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 990288000783 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 990288000784 glutamine synthetase; Provisional; Region: glnA; PRK09469 990288000785 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 990288000786 Survival protein SurE; Region: SurE; cl00448 990288000787 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288000788 RNA polymerase sigma factor RpoS; Validated; Region: PRK05657 990288000789 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 990288000790 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 990288000791 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 990288000792 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 990288000793 DNA binding residues [nucleotide binding] 990288000794 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...; Region: Mth938-like; cl00182 990288000795 aspartate aminotransferase; Provisional; Region: PRK07681 990288000796 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 990288000797 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288000798 homodimer interface [polypeptide binding]; other site 990288000799 catalytic residue [active] 990288000800 homoserine dehydrogenase; Provisional; Region: PRK06349 990288000801 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288000802 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 990288000803 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 990288000804 threonine synthase; Reviewed; Region: PRK06721 990288000805 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants...; Region: Thr-synth_1; cd01563 990288000806 homodimer interface [polypeptide binding]; other site 990288000807 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288000808 catalytic residue [active] 990288000809 Sulfatase; Region: Sulfatase; cl10460 990288000810 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 990288000811 DHH family; Region: DHH; pfam01368 990288000812 peptide chain release factor 2; Validated; Region: prfB; PRK00578 990288000813 RF-1 domain; Region: RF-1; cl02875 990288000814 RF-1 domain; Region: RF-1; cl02875 990288000815 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 990288000816 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-...; Region: LysRS_N; cd04322 990288000817 dimer interface [polypeptide binding]; other site 990288000818 putative anticodon binding site; other site 990288000819 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 990288000820 motif 1; other site 990288000821 active site 990288000822 motif 2; other site 990288000823 motif 3; other site 990288000824 LolC/E family; Region: lolCE; TIGR02212 990288000825 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 990288000826 FtsX-like permease family; Region: FtsX; pfam02687 990288000827 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 990288000828 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 990288000829 Walker A/P-loop; other site 990288000830 ATP binding site [chemical binding]; other site 990288000831 Q-loop/lid; other site 990288000832 ABC transporter signature motif; other site 990288000833 Walker B; other site 990288000834 D-loop; other site 990288000835 H-loop/switch region; other site 990288000836 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 990288000837 Competence protein; Region: Competence; cl00471 990288000838 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 990288000839 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 990288000840 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 990288000841 putative acyl-acceptor binding pocket; other site 990288000842 tetraacyldisaccharide 4'-kinase; Provisional; Region: PRK01906 990288000843 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 990288000844 Trm112p-like protein; Region: Trm112p; cl01066 990288000845 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 990288000846 Ligand binding site [chemical binding]; other site 990288000847 oligomer interface [polypeptide binding]; other site 990288000848 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 990288000849 dimer interface [polypeptide binding]; other site 990288000850 substrate binding site [chemical binding]; other site 990288000851 metal binding sites [ion binding]; metal-binding site 990288000852 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 990288000853 active site residue [active] 990288000854 Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_A; cd01942 990288000855 substrate binding site [chemical binding]; other site 990288000856 ATP binding site [chemical binding]; other site 990288000857 S-adenosylmethionine synthetase; Validated; Region: PRK05250 990288000858 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 990288000859 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 990288000860 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 990288000861 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 990288000862 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288000863 oligomerization interface [polypeptide binding]; other site 990288000864 active site 990288000865 NAD+ binding site [chemical binding]; other site 990288000866 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 990288000867 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine...; Region: MTHFR; cd00537 990288000868 FAD binding site [chemical binding]; other site 990288000869 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288000870 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 990288000871 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 990288000872 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 990288000873 glycogen branching enzyme; Provisional; Region: PRK05402 990288000874 Glycogen branching enzyme N-terminus domain. Glycogen branching enzyme (AKA 1,4 alpha glucan branching enzyme) catalyzes the formation of alpha-1,6 branch points in either glycogen or starch by cleavage of the alpha-1,4 glucosidic linkage yielding a...; Region: Glycogen_branching_enzyme_N_term; cd02855 990288000875 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 990288000876 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 990288000877 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 990288000878 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 990288000879 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 990288000880 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 990288000881 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 990288000882 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 990288000883 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 990288000884 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 990288000885 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 990288000886 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 990288000887 Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]; Region: HisF; COG0107 990288000888 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-; Region: HisF; cd04731 990288000889 substrate binding site [chemical binding]; other site 990288000890 glutamase interaction surface [polypeptide binding]; other site 990288000891 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-...; Region: HisA; cd04732 990288000892 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 990288000893 catalytic residues [active] 990288000894 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 990288000895 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 990288000896 putative active site [active] 990288000897 oxyanion strand; other site 990288000898 catalytic triad [active] 990288000899 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 990288000900 putative active site pocket [active] 990288000901 4-fold oligomerization interface [polypeptide binding]; other site 990288000902 metal binding residues [ion binding]; metal-binding site 990288000903 3-fold/trimer interface [polypeptide binding]; other site 990288000904 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 990288000905 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 990288000906 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288000907 homodimer interface [polypeptide binding]; other site 990288000908 catalytic residue [active] 990288000909 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 990288000910 E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent oxidation of L-histidinol to L-...; Region: Histidinol_dh; cd06572 990288000911 NAD binding site [chemical binding]; other site 990288000912 dimerization interface [polypeptide binding]; other site 990288000913 product binding site; other site 990288000914 substrate binding site [chemical binding]; other site 990288000915 zinc binding site [ion binding]; other site 990288000916 catalytic residues [active] 990288000917 ATP phosphoribosyltransferase; Region: HisG; cl15266 990288000918 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Validated; Region: PRK09369 990288000919 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 990288000920 hinge; other site 990288000921 active site 990288000922 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 990288000923 putative GSH binding site [chemical binding]; other site 990288000924 catalytic residues [active] 990288000925 BolA-like protein; Region: BolA; cl00386 990288000926 ABC-2 type transporter; Region: ABC2_membrane; cl11417 990288000927 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 990288000928 SurA N-terminal domain; Region: SurA_N; pfam09312 990288000929 PPIC-type PPIASE domain; Region: Rotamase; cl08278 990288000930 PPIC-type PPIASE domain; Region: Rotamase; cl08278 990288000931 OstA-like protein; Region: OstA; cl00844 990288000932 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 990288000933 Organic solvent tolerance protein; Region: OstA_C; pfam04453 990288000934 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 990288000935 substrate binding site [chemical binding]; other site 990288000936 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 990288000937 Substrate binding site [chemical binding]; other site 990288000938 metal binding site [ion binding]; metal-binding site 990288000939 KpsF/GutQ family protein; Region: kpsF; TIGR00393 990288000940 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 5-...; Region: SIS_Kpsf; cd05014 990288000941 putative active site [active] 990288000942 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 990288000943 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 990288000944 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 990288000945 OstA-like protein; Region: OstA; cl00844 990288000946 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 990288000947 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 990288000948 Walker A/P-loop; other site 990288000949 ATP binding site [chemical binding]; other site 990288000950 Q-loop/lid; other site 990288000951 ABC transporter signature motif; other site 990288000952 Walker B; other site 990288000953 D-loop; other site 990288000954 H-loop/switch region; other site 990288000955 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 990288000956 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 990288000957 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 990288000958 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 990288000959 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site...; Region: RaiA; cd00552 990288000960 30S subunit binding site; other site 990288000961 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 990288000962 active site 990288000963 phosphorylation site [posttranslational modification] 990288000964 DRTGG domain; Region: DRTGG; cl12147 990288000965 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-...; Region: HprK_C; cd01918 990288000966 Hpr binding site; other site 990288000967 active site 990288000968 homohexamer subunit interaction site [polypeptide binding]; other site 990288000969 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288000970 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...; Region: PTS_IIA_man; cl00025 990288000971 active pocket/dimerization site; other site 990288000972 active site 990288000973 phosphorylation site [posttranslational modification] 990288000974 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 990288000975 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 990288000976 FIST C domain; Region: FIST_C; pfam10442 990288000977 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 990288000978 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 990288000979 minor groove reading motif; other site 990288000980 helix-hairpin-helix signature motif; other site 990288000981 substrate binding pocket [chemical binding]; other site 990288000982 active site 990288000983 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 990288000984 glycogen synthase; Provisional; Region: glgA; PRK00654 990288000985 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 990288000986 ADP-binding pocket [chemical binding]; other site 990288000987 homodimer interface [polypeptide binding]; other site 990288000988 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 990288000989 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 990288000990 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 990288000991 NAD binding site [chemical binding]; other site 990288000992 substrate binding site [chemical binding]; other site 990288000993 homodimer interface [polypeptide binding]; other site 990288000994 active site 990288000995 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 990288000996 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 990288000997 NADP binding site [chemical binding]; other site 990288000998 active site 990288000999 putative substrate binding site [chemical binding]; other site 990288001000 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 990288001001 Cupin domain; Region: Cupin_2; cl09118 990288001002 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 990288001003 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 990288001004 substrate binding site [chemical binding]; other site 990288001005 tetramer interface [polypeptide binding]; other site 990288001006 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 990288001007 active site 990288001008 tetramer interface [polypeptide binding]; other site 990288001009 Protein of unknown function (DUF502); Region: DUF502; cl01107 990288001010 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 990288001011 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 990288001012 active site 990288001013 phosphorylation site [posttranslational modification] 990288001014 intermolecular recognition site; other site 990288001015 dimerization interface [polypeptide binding]; other site 990288001016 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288001017 Walker A motif; other site 990288001018 ATP binding site [chemical binding]; other site 990288001019 Walker B motif; other site 990288001020 arginine finger; other site 990288001021 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 990288001022 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 connected by an extended linker. The...; Region: HAMP; cl01054 990288001023 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 trans-...; Region: HisKA; cl00080 990288001024 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 990288001025 ATP binding site [chemical binding]; other site 990288001026 Mg2+ binding site [ion binding]; other site 990288001027 G-X-G motif; other site 990288001028 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 990288001029 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 990288001030 Walker A/P-loop; other site 990288001031 ATP binding site [chemical binding]; other site 990288001032 Q-loop/lid; other site 990288001033 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 990288001034 ABC transporter signature motif; other site 990288001035 Walker B; other site 990288001036 D-loop; other site 990288001037 H-loop/switch region; other site 990288001038 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 990288001039 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 990288001040 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 990288001041 regulatory protein interface [polypeptide binding]; other site 990288001042 active site 990288001043 regulatory phosphorylation site [posttranslational modification]; other site 990288001044 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 990288001045 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 990288001046 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 990288001047 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 990288001048 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 990288001049 minor groove reading motif; other site 990288001050 helix-hairpin-helix signature motif; other site 990288001051 substrate binding pocket [chemical binding]; other site 990288001052 active site 990288001053 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 990288001054 DNA binding and oxoG recognition site [nucleotide binding] 990288001055 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 990288001056 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 990288001057 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 990288001058 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 990288001059 active site 990288001060 Zn binding site [ion binding]; other site 990288001061 fumarate hydratase; Reviewed; Region: fumC; PRK00485 990288001062 Class II fumarases; Region: Fumarase_classII; cd01362 990288001063 active site 990288001064 tetramer interface [polypeptide binding]; other site 990288001065 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 990288001066 NeuB family; Region: NeuB; cl00496 990288001067 Protein of unknown function (DUF805); Region: DUF805; cl01224 990288001068 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 990288001069 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 990288001070 active site 990288001071 HIGH motif; other site 990288001072 KMSKS motif; other site 990288001073 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 990288001074 tRNA binding surface [nucleotide binding]; other site 990288001075 anticodon binding site; other site 990288001076 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 990288001077 dimer interface [polypeptide binding]; other site 990288001078 putative tRNA-binding site [nucleotide binding]; other site 990288001079 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 990288001080 proline aminopeptidase P II; Provisional; Region: PRK10879 990288001081 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action...; Region: Prolidase; cd01087 990288001082 active site 990288001083 Bordetella pertussis Bvg accessory factor family; Region: Bvg_acc_factor; cl09130 990288001084 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 990288001085 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 990288001086 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 990288001087 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 990288001088 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 990288001089 putative catalytic cysteine [active] 990288001090 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 990288001091 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 990288001092 Lipopolysaccharide-assembly; Region: LptE; cl01125 990288001093 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 990288001094 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 990288001095 HIGH motif; other site 990288001096 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 990288001097 active site 990288001098 KMSKS motif; other site 990288001099 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 990288001100 tRNA binding surface [nucleotide binding]; other site 990288001101 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 990288001102 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 990288001103 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 990288001104 S-adenosylmethionine binding site [chemical binding]; other site 990288001105 integrase; Provisional; Region: int; PHA02601 990288001106 Transposase domain (DUF772); Region: DUF772; cl12084 990288001107 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288001108 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 990288001109 DNA binding site [nucleotide binding] 990288001110 Int/Topo IB signature motif; other site 990288001111 active site 990288001112 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 990288001113 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 990288001114 T5orf172 domain; Region: T5orf172; cl11176 990288001115 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 990288001116 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 990288001117 ATP binding site [chemical binding]; other site 990288001118 putative Mg++ binding site [ion binding]; other site 990288001119 FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 990288001120 putative active site [active] 990288001121 SpoVT / AbrB like domain; Region: SpoVT_AbrB; cl00877 990288001122 potential frameshift: common BLAST hit: gi|296136013|ref|YP_003643255.1| DNA methylase 990288001123 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 990288001124 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 990288001125 putative active site [active] 990288001126 homotetrameric interface [polypeptide binding]; other site 990288001127 Integrase core domain; Region: rve; cl01316 990288001128 Na+/H+ antiporter, bacterial form; Region: a_cpa1; TIGR00831 990288001129 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 990288001130 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288001131 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 990288001132 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 990288001133 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 990288001134 23S rRNA interface [nucleotide binding]; other site 990288001135 L3 interface [polypeptide binding]; other site 990288001136 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 990288001137 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 990288001138 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 990288001139 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 990288001140 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 990288001141 active site 990288001142 dimer interface [polypeptide binding]; other site 990288001143 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 990288001144 dimer interface [polypeptide binding]; other site 990288001145 active site 990288001146 Beta-lactamase; Region: Beta-lactamase; cl01009 990288001147 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 990288001148 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 990288001149 Transglycosylase; Region: Transgly; cl07896 990288001150 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 990288001151 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 990288001152 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 990288001153 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2...; Region: Biotinyl_lipoyl_domains; cl11404 990288001154 Outer membrane efflux protein; Region: OEP; pfam02321 990288001155 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 trans-...; Region: HisKA; cd00082 990288001156 dimer interface [polypeptide binding]; other site 990288001157 phosphorylation site [posttranslational modification] 990288001158 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 990288001159 Mg2+ binding site [ion binding]; other site 990288001160 G-X-G motif; other site 990288001161 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 990288001162 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 990288001163 active site 990288001164 phosphorylation site [posttranslational modification] 990288001165 intermolecular recognition site; other site 990288001166 dimerization interface [polypeptide binding]; other site 990288001167 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...; Region: trans_reg_C; cd00383 990288001168 DNA binding site [nucleotide binding] 990288001169 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 990288001170 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK04923 990288001171 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 990288001172 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 990288001173 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 990288001174 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 990288001175 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 990288001176 binding surface 990288001177 TPR motif; other site 990288001178 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 990288001179 binding surface 990288001180 TPR motif; other site 990288001181 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 990288001182 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 990288001183 binding surface 990288001184 TPR motif; other site 990288001185 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 990288001186 binding surface 990288001187 TPR motif; other site 990288001188 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 990288001189 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 990288001190 tRNA; other site 990288001191 putative tRNA binding site [nucleotide binding]; other site 990288001192 putative NADP binding site [chemical binding]; other site 990288001193 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 990288001194 peptide chain release factor 1; Validated; Region: prfA; PRK00591 990288001195 RF-1 domain; Region: RF-1; cl02875 990288001196 RF-1 domain; Region: RF-1; cl02875 990288001197 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 990288001198 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 990288001199 S-adenosylmethionine binding site [chemical binding]; other site 990288001200 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 990288001201 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 990288001202 DNA binding site [nucleotide binding] 990288001203 catalytic residue [active] 990288001204 H2TH interface [polypeptide binding]; other site 990288001205 putative catalytic residues [active] 990288001206 turnover-facilitating residue; other site 990288001207 intercalation triad [nucleotide binding]; other site 990288001208 8OG recognition residue [nucleotide binding]; other site 990288001209 putative reading head residues; other site 990288001210 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 990288001211 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 990288001212 Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs)...; Region: Era_like; cd00880 990288001213 Switch II region; other site 990288001214 G3 box; other site 990288001215 G4 box; other site 990288001216 G5 box; other site 990288001217 Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion]; Region: HdrA; COG1148 990288001218 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 990288001219 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 990288001220 active site 990288001221 (T/H)XGH motif; other site 990288001222 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 990288001223 S-adenosylmethionine binding site [chemical binding]; other site 990288001224 alpha-ketoglutarate decarboxylase; Reviewed; Region: kgd; PRK12270 990288001225 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 990288001226 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 990288001227 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 990288001228 P loop; other site 990288001229 GTP binding site [chemical binding]; other site 990288001230 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 990288001231 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288001232 Walker A/P-loop; other site 990288001233 ATP binding site [chemical binding]; other site 990288001234 Q-loop/lid; other site 990288001235 ABC transporter signature motif; other site 990288001236 Walker B; other site 990288001237 D-loop; other site 990288001238 H-loop/switch region; other site 990288001239 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 990288001240 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 990288001241 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 990288001242 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 990288001243 DsrE/DsrF-like family; Region: DrsE; cl00672 990288001244 Mechanosensitive ion channel; Region: MS_channel; pfam00924 990288001245 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 990288001246 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288001247 Walker A motif; other site 990288001248 ATP binding site [chemical binding]; other site 990288001249 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288001250 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 990288001251 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 990288001252 active site 990288001253 HslU subunit interaction site [polypeptide binding]; other site 990288001254 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 990288001255 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 990288001256 DNA binding site [nucleotide binding] 990288001257 Int/Topo IB signature motif; other site 990288001258 active site 990288001259 Protein of unknown function, DUF484; Region: DUF484; cl01228 990288001260 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 990288001261 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 990288001262 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 990288001263 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 990288001264 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed; Region: PRK12826 990288001265 classical (c) SDRs; Region: SDR_c; cd05233 990288001266 NAD(P) binding site [chemical binding]; other site 990288001267 active site 990288001268 Phosphate-selective porin O and P; Region: Porin_O_P; cl01524 990288001269 PilZ domain; Region: PilZ; cl01260 990288001270 Glycosyl hydrolases family 8; Region: Glyco_hydro_8; cl01351 990288001271 cellulose synthase regulator protein; Provisional; Region: PRK11114 990288001272 cellulose synthase regulator protein; Provisional; Region: PRK11114 990288001273 cellulose synthase catalytic subunit (UDP-forming); Region: CelA; TIGR03030 990288001274 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 990288001275 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 990288001276 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288001277 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288001278 cellulose synthase catalytic subunit (UDP-forming); Region: CelA; TIGR03030 990288001279 CESA_CelA_like are involved in the elongation of the glucan chain of cellulose; Region: CESA_CelA_like; cd06421 990288001280 DXD motif; other site 990288001281 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 990288001282 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 990288001283 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 990288001284 helicase 45; Provisional; Region: PTZ00424 990288001285 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 990288001286 ATP binding site [chemical binding]; other site 990288001287 Mg++ binding site [ion binding]; other site 990288001288 motif III; other site 990288001289 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 990288001290 nucleotide binding region [chemical binding]; other site 990288001291 ATP-binding site [chemical binding]; other site 990288001292 DbpA RNA binding domain; Region: DbpA; pfam03880 990288001293 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 990288001294 DNA-binding site [nucleotide binding]; DNA binding site 990288001295 RNA-binding motif; other site 990288001296 putative transposase OrfB; Reviewed; Region: PHA02517 990288001297 Integrase core domain; Region: rve; cl01316 990288001298 putative transposase OrfB; Reviewed; Region: PHA02517 990288001299 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288001300 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288001301 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288001302 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288001303 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various...; Region: Peptidase_C39G; cd02423 990288001304 putative active site [active] 990288001305 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 990288001306 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 990288001307 DXD motif; other site 990288001308 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 990288001309 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 990288001310 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288001311 Walker A motif; other site 990288001312 ATP binding site [chemical binding]; other site 990288001313 Walker B motif; other site 990288001314 arginine finger; other site 990288001315 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 990288001316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 990288001317 Integrase core domain; Region: rve; cl01316 990288001318 primosome assembly protein PriA; Validated; Region: PRK05580 990288001319 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 990288001320 ATP binding site [chemical binding]; other site 990288001321 putative Mg++ binding site [ion binding]; other site 990288001322 Hydrogenase expression/synthesis hypA family; Region: HypA; cl00418 990288001323 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288001324 UbiA prenyltransferase family; Region: UbiA; cl00337 990288001325 UTRA domain; Region: UTRA; cl01230 990288001326 Cation efflux family; Region: Cation_efflux; cl00316 990288001327 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288001328 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 990288001329 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 990288001330 ligand binding site [chemical binding]; other site 990288001331 oligomer interface [polypeptide binding]; other site 990288001332 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and rate-...; Region: LbH_G1P_AT_C; cd04651 990288001333 dimer interface [polypeptide binding]; other site 990288001334 N-terminal domain interface [polypeptide binding]; other site 990288001335 sulfate 1 binding site; other site 990288001336 Alpha-amylase/alpha-mannosidase [Carbohydrate transport and metabolism]; Region: COG1449 990288001337 Glycosyl hydrolase family 57; Region: Glyco_hydro_57; pfam03065 990288001338 Glycosyl hydrolases family 38 N-terminal domain; Region: Glyco_hydro_38; pfam01074 990288001339 Domain of unknown function (DUF1925); Region: DUF1925; pfam09094 990288001340 Domain of unknown function (DUF1926); Region: DUF1926; pfam09095 990288001341 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 990288001342 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 990288001343 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 990288001344 Protein of unknown function (DUF445); Region: DUF445; pfam04286 990288001345 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 990288001346 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; pfam02696 990288001347 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 990288001348 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 990288001349 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 990288001350 FeS/SAM binding site; other site 990288001351 TRAM domain; Region: TRAM; cl01282 990288001352 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 990288001353 PhoH-like protein; Region: PhoH; cl12134 990288001354 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 990288001355 FOG: CBS domain [General function prediction only]; Region: COG0517 990288001356 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 990288001357 Transporter associated domain; Region: CorC_HlyC; cl08393 990288001358 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 990288001359 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 990288001360 putative active site [active] 990288001361 catalytic triad [active] 990288001362 putative dimer interface [polypeptide binding]; other site 990288001363 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 990288001364 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 990288001365 putative active site [active] 990288001366 catalytic triad [active] 990288001367 putative dimer interface [polypeptide binding]; other site 990288001368 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288001369 disulfide isomerase/thiol-disulfide oxidase; Provisional; Region: dsbG; PRK11657 990288001370 Protein of unknown function (DUF692); Region: DUF692; cl01263 990288001371 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288001372 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288001373 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 990288001374 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 990288001375 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 990288001376 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 990288001377 DsbD alpha interface [polypeptide binding]; other site 990288001378 catalytic residues [active] 990288001379 OsmC-like protein; Region: OsmC; cl00767 990288001380 DsrE/DsrF-like family; Region: DrsE; cl00672 990288001381 Major Facilitator Superfamily; Region: MFS_1; pfam07690 990288001382 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 990288001383 putative substrate translocation pore; other site 990288001384 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 990288001385 putative substrate translocation pore; other site 990288001386 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 990288001387 dimerization interface [polypeptide binding]; other site 990288001388 putative DNA binding site [nucleotide binding]; other site 990288001389 putative Zn2+ binding site [ion binding]; other site 990288001390 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 990288001391 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288001392 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 990288001393 S-adenosylmethionine binding site [chemical binding]; other site 990288001394 Predicted membrane protein (DUF2078); Region: DUF2078; cl01373 990288001395 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 990288001396 glutaredoxin 2; Provisional; Region: PRK10387 990288001397 C-terminal domain interface [polypeptide binding]; other site 990288001398 GSH binding site (G-site) [chemical binding]; other site 990288001399 dimer interface [polypeptide binding]; other site 990288001400 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 990288001401 dimer interface [polypeptide binding]; other site 990288001402 substrate binding pocket (H-site) [chemical binding]; other site 990288001403 N-terminal domain interface [polypeptide binding]; other site 990288001404 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 990288001405 dimerization interface [polypeptide binding]; other site 990288001406 putative DNA binding site [nucleotide binding]; other site 990288001407 putative Zn2+ binding site [ion binding]; other site 990288001408 Predicted permease; Region: DUF318; cl00487 990288001409 phosphoglucomutase; Region: PLN02307 990288001410 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...; Region: PGM1; cd03085 990288001411 substrate binding site [chemical binding]; other site 990288001412 dimer interface [polypeptide binding]; other site 990288001413 active site 990288001414 metal binding site [ion binding]; metal-binding site 990288001415 Precorrin-8X methylmutase; Region: CbiC; pfam02570 990288001416 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 990288001417 signal recognition particle protein; Provisional; Region: PRK10867 990288001418 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 990288001419 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 990288001420 P loop; other site 990288001421 GTP binding site [chemical binding]; other site 990288001422 Signal peptide binding domain; Region: SRP_SPB; pfam02978 990288001423 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 990288001424 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 990288001425 RimM N-terminal domain; Region: RimM; pfam01782 990288001426 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to...; Region: PRCH; cl09959 990288001427 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 990288001428 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 990288001429 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 990288001430 DNA binding site [nucleotide binding] 990288001431 active site 990288001432 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 990288001433 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 990288001434 DNA binding site [nucleotide binding] 990288001435 Int/Topo IB signature motif; other site 990288001436 active site 990288001437 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 990288001438 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 990288001439 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 C-...; Region: PDZ_serine_protease; cd00987 990288001440 protein binding site [polypeptide binding]; other site 990288001441 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 990288001442 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 990288001443 catalytic residues [active] 990288001444 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 990288001445 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of...; Region: SHMT; cd00378 990288001446 dimer interface [polypeptide binding]; other site 990288001447 glycine-pyridoxal phosphate binding site [chemical binding]; other site 990288001448 active site 990288001449 folate binding site [chemical binding]; other site 990288001450 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 990288001451 ATP cone domain; Region: ATP-cone; pfam03477 990288001452 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 990288001453 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 990288001454 catalytic motif [active] 990288001455 Zn binding site [ion binding]; other site 990288001456 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-...; Region: DHFR; cl00161 990288001457 Lumazine binding domain; Region: Lum_binding; pfam00677 990288001458 Lumazine binding domain; Region: Lum_binding; pfam00677 990288001459 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 990288001460 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 990288001461 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cl00522 990288001462 dimerization interface [polypeptide binding]; other site 990288001463 active site 990288001464 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 990288001465 homopentamer interface [polypeptide binding]; other site 990288001466 active site 990288001467 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-...; Region: NusB_Sun; cl00223 990288001468 putative RNA binding site [nucleotide binding]; other site 990288001469 Sel1 repeat; Region: Sel1; cl02723 990288001470 Sel1 repeat; Region: Sel1; cl02723 990288001471 Sel1 repeat; Region: Sel1; cl02723 990288001472 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 990288001473 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 990288001474 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 990288001475 active site 990288001476 ATP binding site [chemical binding]; other site 990288001477 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 990288001478 ligand binding site [chemical binding]; other site 990288001479 elongation factor Tu; Reviewed; Region: PRK00049 990288001480 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 990288001481 G1 box; other site 990288001482 GEF interaction site [polypeptide binding]; other site 990288001483 GTP/Mg2+ binding site [chemical binding]; other site 990288001484 Switch I region; other site 990288001485 G2 box; other site 990288001486 G3 box; other site 990288001487 Switch II region; other site 990288001488 G4 box; other site 990288001489 G5 box; other site 990288001490 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 990288001491 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 990288001492 Antibiotic Binding Site [chemical binding]; other site 990288001493 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 990288001494 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 990288001495 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 990288001496 putative homodimer interface [polypeptide binding]; other site 990288001497 KOW motif; Region: KOW; cl00354 990288001498 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 990288001499 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 990288001500 23S rRNA interface [nucleotide binding]; other site 990288001501 L7/L12 interface [polypeptide binding]; other site 990288001502 putative thiostrepton binding site; other site 990288001503 L25 interface [polypeptide binding]; other site 990288001504 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that...; Region: Ribosomal_L1; cd00403 990288001505 mRNA/rRNA interface [nucleotide binding]; other site 990288001506 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11...; Region: Ribosomal_L10; cd05797 990288001507 23S rRNA interface [nucleotide binding]; other site 990288001508 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 990288001509 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 990288001510 core dimer interface [polypeptide binding]; other site 990288001511 peripheral dimer interface [polypeptide binding]; other site 990288001512 L10 interface [polypeptide binding]; other site 990288001513 L11 interface [polypeptide binding]; other site 990288001514 putative EF-Tu interaction site [polypeptide binding]; other site 990288001515 putative EF-G interaction site [polypeptide binding]; other site 990288001516 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 990288001517 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 990288001518 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 990288001519 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; cl04591 990288001520 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 990288001521 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 990288001522 RPB11 interaction site [polypeptide binding]; other site 990288001523 RPB12 interaction site [polypeptide binding]; other site 990288001524 Domain of unknown function (DUF1845); Region: DUF1845; cl07481 990288001525 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 990288001526 RPB3 interaction site [polypeptide binding]; other site 990288001527 RPB1 interaction site [polypeptide binding]; other site 990288001528 RPB11 interaction site [polypeptide binding]; other site 990288001529 RPB10 interaction site [polypeptide binding]; other site 990288001530 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 990288001531 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 990288001532 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 990288001533 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 990288001534 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 990288001535 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 990288001536 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 990288001537 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 990288001538 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 990288001539 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 990288001540 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 990288001541 DNA binding site [nucleotide binding] 990288001542 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 990288001543 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 990288001544 S17 interaction site [polypeptide binding]; other site 990288001545 S8 interaction site; other site 990288001546 16S rRNA interaction site [nucleotide binding]; other site 990288001547 streptomycin interaction site [chemical binding]; other site 990288001548 23S rRNA interaction site [nucleotide binding]; other site 990288001549 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 990288001550 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 990288001551 elongation factor G; Reviewed; Region: PRK00007 990288001552 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G; cd01886 990288001553 G1 box; other site 990288001554 putative GEF interaction site [polypeptide binding]; other site 990288001555 GTP/Mg2+ binding site [chemical binding]; other site 990288001556 Switch I region; other site 990288001557 G2 box; other site 990288001558 G3 box; other site 990288001559 Switch II region; other site 990288001560 G4 box; other site 990288001561 G5 box; other site 990288001562 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide...; Region: EFG_mtEFG_II; cd04088 990288001563 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor...; Region: EFG_mtEFG1_IV; cd01434 990288001564 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor...; Region: EFG_mtEFG_C; cd03713 990288001565 elongation factor Tu; Reviewed; Region: PRK00049 990288001566 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 990288001567 G1 box; other site 990288001568 GEF interaction site [polypeptide binding]; other site 990288001569 GTP/Mg2+ binding site [chemical binding]; other site 990288001570 Switch I region; other site 990288001571 G2 box; other site 990288001572 G3 box; other site 990288001573 Switch II region; other site 990288001574 G4 box; other site 990288001575 G5 box; other site 990288001576 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 990288001577 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 990288001578 Antibiotic Binding Site [chemical binding]; other site 990288001579 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 990288001580 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 990288001581 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 990288001582 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 990288001583 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 990288001584 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 990288001585 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 990288001586 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 990288001587 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 990288001588 protein-rRNA interface [nucleotide binding]; other site 990288001589 putative translocon binding site; other site 990288001590 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 990288001591 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The...; Region: 30S_S3_KH; cd02412 990288001592 G-X-X-G motif; other site 990288001593 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 990288001594 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 990288001595 23S rRNA interface [nucleotide binding]; other site 990288001596 5S rRNA interface [nucleotide binding]; other site 990288001597 putative antibiotic binding site [chemical binding]; other site 990288001598 L25 interface [polypeptide binding]; other site 990288001599 L27 interface [polypeptide binding]; other site 990288001600 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where...; Region: Ribosomal_L29_HIP; cd00427 990288001601 putative translocon interaction site; other site 990288001602 23S rRNA interface [nucleotide binding]; other site 990288001603 signal recognition particle (SRP54) interaction site; other site 990288001604 L23 interface [polypeptide binding]; other site 990288001605 trigger factor interaction site; other site 990288001606 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 990288001607 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 990288001608 KOW motif; Region: KOW; cl00354 990288001609 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 990288001610 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 990288001611 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 990288001612 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 990288001613 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 990288001614 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 990288001615 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 990288001616 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 990288001617 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 990288001618 5S rRNA interface [nucleotide binding]; other site 990288001619 23S rRNA interface [nucleotide binding]; other site 990288001620 L5 interface [polypeptide binding]; other site 990288001621 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 990288001622 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 990288001623 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 990288001624 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins...; Region: Ribosomal_L30; cd01658 990288001625 23S rRNA binding site [nucleotide binding]; other site 990288001626 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 990288001627 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 990288001628 SecY translocase; Region: SecY; pfam00344 990288001629 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 990288001630 AMP-binding site [chemical binding]; other site 990288001631 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 990288001632 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 990288001633 rRNA binding site [nucleotide binding]; other site 990288001634 predicted 30S ribosome binding site; other site 990288001635 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 990288001636 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 990288001637 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 990288001638 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 990288001639 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 990288001640 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 990288001641 RNA binding surface [nucleotide binding]; other site 990288001642 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 990288001643 alphaNTD homodimer interface [polypeptide binding]; other site 990288001644 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 990288001645 alphaNTD - beta interaction site [polypeptide binding]; other site 990288001646 alphaNTD - beta' interaction site [polypeptide binding]; other site 990288001647 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 990288001648 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 990288001649 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 990288001650 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 990288001651 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 990288001652 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 990288001653 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 990288001654 dimer interface [polypeptide binding]; other site 990288001655 ssDNA binding site [nucleotide binding]; other site 990288001656 tetramer (dimer of dimers) interface [polypeptide binding]; other site 990288001657 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 990288001658 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 990288001659 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 990288001660 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 990288001661 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 990288001662 active site 990288001663 NTP binding site [chemical binding]; other site 990288001664 metal binding triad [ion binding]; metal-binding site 990288001665 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 990288001666 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 990288001667 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 990288001668 substrate binding site [chemical binding]; other site 990288001669 ligand binding site [chemical binding]; other site 990288001670 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-...; Region: IPMI_Swivel; cd01577 990288001671 substrate binding site [chemical binding]; other site 990288001672 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 990288001673 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 990288001674 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 990288001675 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 990288001676 tetramer (dimer of dimers) interface [polypeptide binding]; other site 990288001677 active site 990288001678 dimer interface [polypeptide binding]; other site 990288001679 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 990288001680 conserved cys residue [active] 990288001681 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 990288001682 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 990288001683 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 990288001684 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 990288001685 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily...; Region: Heme_Cu_Oxidase_I; cl00275 990288001686 D-pathway; other site 990288001687 Low-spin heme binding site [chemical binding]; other site 990288001688 Putative water exit pathway; other site 990288001689 Binuclear center (active site) [active] 990288001690 K-pathway; other site 990288001691 Putative proton exit pathway; other site 990288001692 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 990288001693 Subunit I/III interface [polypeptide binding]; other site 990288001694 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 990288001695 UbiA prenyltransferase family; Region: UbiA; cl00337 990288001696 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 990288001697 Major Facilitator Superfamily; Region: MFS_1; pfam07690 990288001698 putative substrate translocation pore; other site 990288001699 Bacitracin resistance protein BacA; Region: BacA; cl00858 990288001700 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 990288001701 domain; Region: GreA_GreB_N; pfam03449 990288001702 C-term; Region: GreA_GreB; pfam01272 990288001703 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 990288001704 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 990288001705 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 990288001706 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 990288001707 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 990288001708 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 990288001709 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 990288001710 IMP binding site; other site 990288001711 dimer interface [polypeptide binding]; other site 990288001712 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 990288001713 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 990288001714 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 990288001715 catalytic site [active] 990288001716 subunit interface [polypeptide binding]; other site 990288001717 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 990288001718 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 990288001719 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 990288001720 octaprenyl diphosphate synthase; Provisional; Region: PRK10888 990288001721 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 990288001722 substrate binding pocket [chemical binding]; other site 990288001723 chain length determination region; other site 990288001724 substrate-Mg2+ binding site; other site 990288001725 catalytic residues [active] 990288001726 aspartate-rich region 1; other site 990288001727 active site lid residues [active] 990288001728 aspartate-rich region 2; other site 990288001729 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 990288001730 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 990288001731 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 990288001732 ABC transporter ATPase component; Reviewed; Region: PRK11147 990288001733 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288001734 Walker A/P-loop; other site 990288001735 ATP binding site [chemical binding]; other site 990288001736 ABC transporter signature motif; other site 990288001737 Walker B; other site 990288001738 D-loop; other site 990288001739 H-loop/switch region; other site 990288001740 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 990288001741 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3296 990288001742 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 990288001743 Fe-S cluster binding site [ion binding]; other site 990288001744 active site 990288001745 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 990288001746 UDP-glucose 4 epimerase (G4E), subgroup 3, extended (e) SDRs; Region: UDP_G4E_3_SDR_e; cd05240 990288001747 putative NAD(P) binding site [chemical binding]; other site 990288001748 active site 990288001749 putative substrate binding site [chemical binding]; other site 990288001750 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 990288001751 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 990288001752 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 990288001753 putative active site [active] 990288001754 putative substrate binding site [chemical binding]; other site 990288001755 catalytic site [active] 990288001756 dimer interface [polypeptide binding]; other site 990288001757 osmolarity response regulator; Provisional; Region: ompR; PRK09468 990288001758 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 990288001759 active site 990288001760 phosphorylation site [posttranslational modification] 990288001761 intermolecular recognition site; other site 990288001762 dimerization interface [polypeptide binding]; other site 990288001763 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...; Region: trans_reg_C; cd00383 990288001764 DNA binding site [nucleotide binding] 990288001765 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 990288001766 N-terminal plug; other site 990288001767 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 990288001768 ligand-binding site [chemical binding]; other site 990288001769 Gram-negative bacterial tonB protein; Region: TonB; cl10048 990288001770 Uncharacterized conserved protein [Function unknown]; Region: COG3391 990288001771 Sulfatase; Region: Sulfatase; cl10460 990288001772 Sulfatase; Region: Sulfatase; cl10460 990288001773 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 990288001774 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 990288001775 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16...; Region: OM_channels; cl00284 990288001776 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288001777 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288001778 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 990288001779 Outer membrane lipoprotein Slp family; Region: Slp; cl01164 990288001780 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 990288001781 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 990288001782 putative peptidoglycan binding site; other site 990288001783 Protein of unknown function (DUF3568); Region: DUF3568; pfam12092 990288001784 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 990288001785 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...; Region: DHOD_2_like; cd04738 990288001786 quinone interaction residues [chemical binding]; other site 990288001787 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 990288001788 active site 990288001789 catalytic residues [active] 990288001790 FMN binding site [chemical binding]; other site 990288001791 substrate binding site [chemical binding]; other site 990288001792 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 990288001793 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 990288001794 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 990288001795 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 990288001796 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 990288001797 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 990288001798 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 990288001799 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 5-aminoimidazole-4-carboxamide-; Region: IMPCH; cd01421 990288001800 purine monophosphate binding site [chemical binding]; other site 990288001801 dimer interface [polypeptide binding]; other site 990288001802 putative catalytic residues [active] 990288001803 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 990288001804 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 990288001805 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 990288001806 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 990288001807 dimer interface [polypeptide binding]; other site 990288001808 active site 990288001809 metal binding site [ion binding]; metal-binding site 990288001810 GTP-binding protein YchF; Reviewed; Region: PRK09601 990288001811 YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated...; Region: YchF; cd01900 990288001812 G1 box; other site 990288001813 GTP/Mg2+ binding site [chemical binding]; other site 990288001814 Switch I region; other site 990288001815 G2 box; other site 990288001816 Switch II region; other site 990288001817 G3 box; other site 990288001818 G4 box; other site 990288001819 G5 box; other site 990288001820 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 990288001821 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 990288001822 putative active site [active] 990288001823 catalytic residue [active] 990288001824 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 990288001825 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 990288001826 5S rRNA interface [nucleotide binding]; other site 990288001827 CTC domain interface [polypeptide binding]; other site 990288001828 L16 interface [polypeptide binding]; other site 990288001829 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 990288001830 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 990288001831 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 990288001832 Cell division protein ZapA; Region: ZapA; cl01146 990288001833 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 990288001834 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 990288001835 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 990288001836 putative active site [active] 990288001837 metal binding site [ion binding]; metal-binding site 990288001838 homodimer binding site [polypeptide binding]; other site 990288001839 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 990288001840 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 990288001841 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them...; Region: YcaC_related; cd01012 990288001842 catalytic triad [active] 990288001843 conserved cis-peptide bond; other site 990288001844 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 990288001845 S-adenosylmethionine binding site [chemical binding]; other site 990288001846 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 990288001847 mce related protein; Region: MCE; pfam02470 990288001848 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 990288001849 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 990288001850 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 990288001851 Outer membrane efflux protein; Region: OEP; pfam02321 990288001852 Outer membrane efflux protein; Region: OEP; pfam02321 990288001853 SpoVT / AbrB like domain; Region: SpoVT_AbrB; cl00877 990288001854 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 990288001855 Ligand Binding Site [chemical binding]; other site 990288001856 prolyl-tRNA synthetase; Provisional; Region: PRK09194 990288001857 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation...; Region: ProRS_core_prok; cd00779 990288001858 dimer interface [polypeptide binding]; other site 990288001859 motif 1; other site 990288001860 active site 990288001861 motif 2; other site 990288001862 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and single-...; Region: ProRS-INS; cd04334 990288001863 putative deacylase active site [active] 990288001864 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 990288001865 active site 990288001866 motif 3; other site 990288001867 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-...; Region: ProRS_anticodon_short; cd00861 990288001868 anticodon binding site; other site 990288001869 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 990288001870 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 990288001871 Putative transmembrane protein (Alph_Pro_TM); Region: Alph_Pro_TM; cl09826 990288001872 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 990288001873 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 990288001874 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 990288001875 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 990288001876 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 990288001877 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-...; Region: QPRTase; cd01572 990288001878 dimerization interface [polypeptide binding]; other site 990288001879 active site 990288001880 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 990288001881 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 990288001882 active site 990288001883 HIGH motif; other site 990288001884 nucleotide binding site [chemical binding]; other site 990288001885 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 990288001886 active site 990288001887 KMSKS motif; other site 990288001888 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 990288001889 tRNA binding surface [nucleotide binding]; other site 990288001890 anticodon binding site; other site 990288001891 autotransport protein MisL; Provisional; Region: PRK15313 990288001892 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 990288001893 multifunctional aminopeptidase A; Provisional; Region: PRK00913 990288001894 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein...; Region: Peptidase_M17; cd00433 990288001895 interface (dimer of trimers) [polypeptide binding]; other site 990288001896 Substrate-binding/catalytic site; other site 990288001897 Zn-binding sites [ion binding]; other site 990288001898 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 990288001899 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 990288001900 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 990288001901 Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs)...; Region: Era_like; cd00880 990288001902 Switch II region; other site 990288001903 G3 box; other site 990288001904 G4 box; other site 990288001905 G5 box; other site 990288001906 EVE domain; Region: EVE; cl00728 990288001907 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in...; Region: Frataxin; cl00238 990288001908 putative iron binding site [ion binding]; other site 990288001909 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 990288001910 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 990288001911 ATP binding site [chemical binding]; other site 990288001912 putative Mg++ binding site [ion binding]; other site 990288001913 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 990288001914 nucleotide binding region [chemical binding]; other site 990288001915 ATP-binding site [chemical binding]; other site 990288001916 RQC domain; Region: RQC; cl09632 990288001917 HRDC domain; Region: HRDC; cl02578 990288001918 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 990288001919 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 990288001920 active site 990288001921 metal binding site [ion binding]; metal-binding site 990288001922 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cl00251 990288001923 SecA binding site; other site 990288001924 Preprotein binding site; other site 990288001925 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 990288001926 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288001927 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 990288001928 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 990288001929 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 990288001930 ATP binding site [chemical binding]; other site 990288001931 Mg2+ binding site [ion binding]; other site 990288001932 G-X-G motif; other site 990288001933 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 990288001934 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 990288001935 active site 990288001936 phosphorylation site [posttranslational modification] 990288001937 intermolecular recognition site; other site 990288001938 dimerization interface [polypeptide binding]; other site 990288001939 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288001940 Walker A motif; other site 990288001941 ATP binding site [chemical binding]; other site 990288001942 Walker B motif; other site 990288001943 arginine finger; other site 990288001944 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 990288001945 Phage integrase family; Region: Phage_integrase; pfam00589 990288001946 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 990288001947 DNA binding site [nucleotide binding] 990288001948 Int/Topo IB signature motif; other site 990288001949 active site 990288001950 DNA polymerase type B, organellar and viral; Region: DNA_pol_B_2; pfam03175 990288001951 Fic family protein [Function unknown]; Region: COG3177 990288001952 Fic/DOC family; Region: Fic; cl00960 990288001953 HipA N-terminal domain; Region: couple_hipA; TIGR03071 990288001954 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 990288001955 HipA-like N-terminal domain; Region: HipA_N; pfam07805 990288001956 HipA-like C-terminal domain; Region: HipA_C; pfam07804 990288001957 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 990288001958 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cl00559 990288001959 putative transposase OrfB; Reviewed; Region: PHA02517 990288001960 Integrase core domain; Region: rve; cl01316 990288001961 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 990288001962 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 990288001963 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288001964 Walker A motif; other site 990288001965 ATP binding site [chemical binding]; other site 990288001966 Walker B motif; other site 990288001967 arginine finger; other site 990288001968 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 990288001969 trimerization site [polypeptide binding]; other site 990288001970 active site 990288001971 HipA-like N-terminal domain; Region: HipA_N; pfam07805 990288001972 HipA-like C-terminal domain; Region: HipA_C; pfam07804 990288001973 PilZ domain; Region: PilZ; cl01260 990288001974 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288001975 MatE; Region: MatE; cl10513 990288001976 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 990288001977 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_d; cd04196 990288001978 Probable Catalytic site [active] 990288001979 ABC-2 type transporter; Region: ABC2_membrane; cl11417 990288001980 Transposase domain (DUF772); Region: DUF772; cl12084 990288001981 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288001982 Transposase domain (DUF772); Region: DUF772; cl12084 990288001983 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288001984 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 990288001985 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 990288001986 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288001987 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288001988 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288001989 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 990288001990 Myxococcus xanthus RfbC like proteins are required for O-antigen biosynthesis; Region: GT2_RfbC_Mx_like; cd04184 990288001991 Probable Catalytic site [active] 990288001992 metal binding site [ion binding]; metal-binding site 990288001993 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 990288001994 Probable Catalytic site [active] 990288001995 metal binding site [ion binding]; metal-binding site 990288001996 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 990288001997 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 990288001998 active site 990288001999 dimer interface [polypeptide binding]; other site 990288002000 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes...; Region: Asn_Synthase_B_C; cd01991 990288002001 Ligand Binding Site [chemical binding]; other site 990288002002 Molecular Tunnel; other site 990288002003 Transposase domain (DUF772); Region: DUF772; cl12084 990288002004 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288002005 Undecaprenyl-phosphate galactose phosphotransferase, WbaP; Region: WbaP_sugtrans; TIGR03022 990288002006 Bacterial sugar transferase; Region: Bac_transf; cl00939 990288002007 O-Antigen ligase; Region: Wzy_C; cl04850 990288002008 PAS domain S-box; Region: sensory_box; TIGR00229 990288002009 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 990288002010 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 990288002011 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288002012 Walker A motif; other site 990288002013 ATP binding site [chemical binding]; other site 990288002014 Walker B motif; other site 990288002015 arginine finger; other site 990288002016 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 990288002017 Transposase domain (DUF772); Region: DUF772; cl12084 990288002018 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288002019 potential frameshift: common BLAST hit: gi|220934912|ref|YP_002513811.1| acriflavin resistance protein 990288002020 Protein export membrane protein; Region: SecD_SecF; cl14618 990288002021 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 990288002022 Protein export membrane protein; Region: SecD_SecF; cl14618 990288002023 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 990288002024 active site 990288002025 dimer interface [polypeptide binding]; other site 990288002026 motif 2; other site 990288002027 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 990288002028 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 990288002029 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 990288002030 Beta-Casp domain; Region: Beta-Casp; cl12567 990288002031 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 990288002032 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 990288002033 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 990288002034 UvrD/REP helicase; Region: UvrD-helicase; cl14126 990288002035 UvrD/REP helicase; Region: UvrD-helicase; cl14126 990288002036 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 990288002037 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; cl01113 990288002038 agmatine deiminase; Region: agmatine_aguA; TIGR03380 990288002039 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 990288002040 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 990288002041 active site 990288002042 uracil binding [chemical binding]; other site 990288002043 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X...; Region: Nudix_Hydrolase_2; cd03675 990288002044 nudix motif; other site 990288002045 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...; Region: Ap4A_hydrolase_plant_like; cd03671 990288002046 putative active site [active] 990288002047 Ap4A binding site [chemical binding]; other site 990288002048 nudix motif; other site 990288002049 putative metal binding site [ion binding]; other site 990288002050 psiF repeat; Region: PsiF_repeat; pfam07769 990288002051 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 990288002052 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 990288002053 putative substrate translocation pore; other site 990288002054 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 990288002055 catalytic residues [active] 990288002056 transcription termination factor Rho; Provisional; Region: rho; PRK09376 990288002057 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 990288002058 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...; Region: Rho_CSD; cd04459 990288002059 RNA binding site [nucleotide binding]; other site 990288002060 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...; Region: rho_factor; cd01128 990288002061 multimer interface [polypeptide binding]; other site 990288002062 Walker A motif; other site 990288002063 ATP binding site [chemical binding]; other site 990288002064 Walker B motif; other site 990288002065 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 990288002066 Malic enzyme, N-terminal domain; Region: malic; pfam00390 990288002067 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288002068 NAD(P) binding pocket [chemical binding]; other site 990288002069 Dehydratase family; Region: ILVD_EDD; cl00340 990288002070 dihydroxy-acid dehydratase; Region: ilvD; TIGR00110 990288002071 LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback...; Region: LabA_like; cd06167 990288002072 putative metal binding site [ion binding]; other site 990288002073 N-acetylglutamate synthase; Validated; Region: PRK05279 990288002074 AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an N-...; Region: AAK_NAGS-ABP; cd04237 990288002075 putative feedback inhibition sensing region; other site 990288002076 putative nucleotide binding site [chemical binding]; other site 990288002077 putative substrate binding site [chemical binding]; other site 990288002078 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 990288002079 BolA-like protein; Region: BolA; cl00386 990288002080 YCII-related domain; Region: YCII; cl00999 990288002081 Intracellular septation protein A; Region: IspA; cl01098 990288002082 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288002083 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 990288002084 Walker A motif; other site 990288002085 ATP binding site [chemical binding]; other site 990288002086 Walker B motif; other site 990288002087 arginine finger; other site 990288002088 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 990288002089 active site 990288002090 dimerization interface [polypeptide binding]; other site 990288002091 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 990288002092 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 990288002093 serine O-acetyltransferase; Region: cysE; TIGR01172 990288002094 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of L-...; Region: LbH_SAT; cd03354 990288002095 trimer interface [polypeptide binding]; other site 990288002096 active site 990288002097 substrate binding site [chemical binding]; other site 990288002098 CoA binding site [chemical binding]; other site 990288002099 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288002100 Rrf2 family protein; Region: rrf2_super; TIGR00738 990288002101 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 990288002102 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 990288002103 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 990288002104 catalytic residue [active] 990288002105 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 990288002106 trimerization site [polypeptide binding]; other site 990288002107 active site 990288002108 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 990288002109 co-chaperone HscB; Provisional; Region: hscB; PRK03578 990288002110 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 990288002111 chaperone protein HscA; Provisional; Region: hscA; PRK05183 990288002112 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 990288002113 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 990288002114 catalytic loop [active] 990288002115 iron binding site [ion binding]; other site 990288002116 Protein of unknown function (DUF528); Region: DUF528; cl01123 990288002117 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 990288002118 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 990288002119 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 990288002120 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 990288002121 active site 990288002122 phosphorylation site [posttranslational modification] 990288002123 intermolecular recognition site; other site 990288002124 dimerization interface [polypeptide binding]; other site 990288002125 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...; Region: trans_reg_C; cd00383 990288002126 DNA binding site [nucleotide binding] 990288002127 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 990288002128 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 990288002129 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 990288002130 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 trans-...; Region: HisKA; cd00082 990288002131 dimer interface [polypeptide binding]; other site 990288002132 phosphorylation site [posttranslational modification] 990288002133 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 990288002134 ATP binding site [chemical binding]; other site 990288002135 Mg2+ binding site [ion binding]; other site 990288002136 G-X-G motif; other site 990288002137 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 990288002138 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 990288002139 Walker A/P-loop; other site 990288002140 ATP binding site [chemical binding]; other site 990288002141 Q-loop/lid; other site 990288002142 ABC transporter signature motif; other site 990288002143 Walker B; other site 990288002144 D-loop; other site 990288002145 H-loop/switch region; other site 990288002146 transcriptional regulator PhoU; Provisional; Region: PRK11115 990288002147 PhoU domain; Region: PhoU; pfam01895 990288002148 PhoU domain; Region: PhoU; pfam01895 990288002149 exopolyphosphatase; Provisional; Region: PRK10854 990288002150 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 990288002151 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 990288002152 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 990288002153 rRNA interaction site [nucleotide binding]; other site 990288002154 S8 interaction site; other site 990288002155 putative laminin-1 binding site; other site 990288002156 elongation factor Ts; Provisional; Region: tsf; PRK09377 990288002157 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 990288002158 Elongation factor TS; Region: EF_TS; pfam00889 990288002159 Elongation factor TS; Region: EF_TS; pfam00889 990288002160 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control...; Region: AAK_UMPK-PyrH-Ec; cd04254 990288002161 putative nucleotide binding site [chemical binding]; other site 990288002162 uridine monophosphate binding site [chemical binding]; other site 990288002163 homohexameric interface [polypeptide binding]; other site 990288002164 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 990288002165 hinge region; other site 990288002166 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 990288002167 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 990288002168 catalytic residue [active] 990288002169 putative FPP diphosphate binding site; other site 990288002170 putative FPP binding hydrophobic cleft; other site 990288002171 dimer interface [polypeptide binding]; other site 990288002172 putative IPP diphosphate binding site; other site 990288002173 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 990288002174 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 990288002175 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 990288002176 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 990288002177 zinc metallopeptidase RseP; Provisional; Region: PRK10779 990288002178 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 990288002179 active site 990288002180 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...; Region: PDZ_metalloprotease; cd00989 990288002181 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...; Region: PDZ_metalloprotease; cd00989 990288002182 protein binding site [polypeptide binding]; other site 990288002183 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 990288002184 putative substrate binding region [chemical binding]; other site 990288002185 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 990288002186 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 990288002187 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 990288002188 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 990288002189 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 990288002190 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 990288002191 Surface antigen; Region: Bac_surface_Ag; cl03097 990288002192 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 990288002193 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 990288002194 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 990288002195 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-2,3-...; Region: LbH_LpxD; cd03352 990288002196 trimer interface [polypeptide binding]; other site 990288002197 active site 990288002198 UDP-GlcNAc binding site [chemical binding]; other site 990288002199 lipid binding site [chemical binding]; lipid-binding site 990288002200 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 990288002201 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 990288002202 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...; Region: LbH_UDP-GlcNAc_AT; cd03351 990288002203 active site 990288002204 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 990288002205 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288002206 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 990288002207 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 990288002208 inhibitor-cofactor binding pocket; inhibition site 990288002209 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288002210 catalytic residue [active] 990288002211 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 990288002212 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 990288002213 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 990288002214 RNA/DNA hybrid binding site [nucleotide binding]; other site 990288002215 active site 990288002216 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 990288002217 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 990288002218 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 990288002219 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...; Region: DnaE_OBF; cd04485 990288002220 generic binding surface II; other site 990288002221 generic binding surface I; other site 990288002222 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 990288002223 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 990288002224 Ligand Binding Site [chemical binding]; other site 990288002225 B3/4 domain; Region: B3_4; cl11458 990288002226 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 990288002227 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as...; Region: OYE_like_FMN_family; cd02803 990288002228 active site 990288002229 FMN binding site [chemical binding]; other site 990288002230 substrate binding site [chemical binding]; other site 990288002231 putative catalytic residue [active] 990288002232 GH3 auxin-responsive promoter; Region: GH3; cl04006 990288002233 Penicillin amidase; Region: Penicil_amidase; pfam01804 990288002234 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-...; Region: Ntn_hydrolase; cl00467 990288002235 active site 990288002236 Sel1 repeat; Region: Sel1; cl02723 990288002237 Sel1 repeat; Region: Sel1; cl02723 990288002238 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 990288002239 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 990288002240 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002241 Walker A/P-loop; other site 990288002242 ATP binding site [chemical binding]; other site 990288002243 Q-loop/lid; other site 990288002244 ABC transporter signature motif; other site 990288002245 Walker B; other site 990288002246 D-loop; other site 990288002247 H-loop/switch region; other site 990288002248 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 990288002249 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288002250 NAD(P) binding site [chemical binding]; other site 990288002251 active site 990288002252 Protein of unknown function (DUF3501); Region: DUF3501; pfam12007 990288002253 sn-glycerol-3-phosphate dehydrogenase subunit C; Provisional; Region: glpC; PRK11168 990288002254 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 990288002255 Ferritin-like domain; Region: Ferritin; pfam00210 990288002256 binuclear metal center [ion binding]; other site 990288002257 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 990288002258 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 single-strand-...; Region: ExoVII_LU_OBF; cd04489 990288002259 generic binding surface II; other site 990288002260 generic binding surface I; other site 990288002261 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 990288002262 catalytic residues [active] 990288002263 Protein of unknown function (DUF3429); Region: DUF3429; pfam11911 990288002264 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 990288002265 Gram-negative bacterial tonB protein; Region: TonB; cl10048 990288002266 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 990288002267 lytic murein transglycosylase; Provisional; Region: PRK11619 990288002268 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 990288002269 N-acetyl-D-glucosamine binding site [chemical binding]; other site 990288002270 catalytic residue [active] 990288002271 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cl00462 990288002272 putative PBP binding regions; other site 990288002273 ABC-ATPase subunit interface; other site 990288002274 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 990288002275 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002276 Walker A/P-loop; other site 990288002277 ATP binding site [chemical binding]; other site 990288002278 Q-loop/lid; other site 990288002279 ABC transporter signature motif; other site 990288002280 Walker B; other site 990288002281 D-loop; other site 990288002282 H-loop/switch region; other site 990288002283 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 990288002284 Major Facilitator Superfamily; Region: MFS_1; pfam07690 990288002285 putative substrate translocation pore; other site 990288002286 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 990288002287 ManB is a bacterial phosphomannomutase (PMM) that catalyzes the conversion of mannose 6-phosphate to mannose-1-phosphate in the second of three steps in the GDP-mannose pathway, in which GDP-D-mannose is synthesized from fructose-6-phosphate. In...; Region: ManB; cd03088 990288002288 active site 990288002289 substrate binding site [chemical binding]; other site 990288002290 metal binding site [ion binding]; metal-binding site 990288002291 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 990288002292 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 990288002293 putative substrate translocation pore; other site 990288002294 Phd_YefM; Region: PhdYeFM; cl09153 990288002295 PIN domain of the VapC-like Sll0205 protein and homologs; Region: PIN_Sll0205; cd09872 990288002296 putative active site [active] 990288002297 MerC mercury resistance protein; Region: MerC; cl03934 990288002298 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 990288002299 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288002300 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288002301 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288002302 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288002303 DsrE/DsrF-like family; Region: DrsE; cl00672 990288002304 Transposase domain (DUF772); Region: DUF772; cl12084 990288002305 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288002306 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 990288002307 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 990288002308 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 990288002309 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 990288002310 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 990288002311 tandem repeat interface [polypeptide binding]; other site 990288002312 oligomer interface [polypeptide binding]; other site 990288002313 active site residues [active] 990288002314 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 990288002315 MoaE interaction surface [polypeptide binding]; other site 990288002316 MoeB interaction surface [polypeptide binding]; other site 990288002317 thiocarboxylated glycine; other site 990288002318 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 990288002319 MoaE homodimer interface [polypeptide binding]; other site 990288002320 MoaD interaction [polypeptide binding]; other site 990288002321 active site residues [active] 990288002322 Protein of unknown function (DUF520); Region: DUF520; cl00723 990288002323 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 990288002324 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 990288002325 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 990288002326 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 990288002327 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 990288002328 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 L-...; Region: GCS_H; cd06848 990288002329 lipoyl attachment site [posttranslational modification]; other site 990288002330 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 990288002331 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 990288002332 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 990288002333 catalytic residue [active] 990288002334 Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG1003 990288002335 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 990288002336 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 990288002337 catalytic residue [active] 990288002338 MoxR-like ATPases [General function prediction only]; Region: COG0714 990288002339 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288002340 Walker A motif; other site 990288002341 ATP binding site [chemical binding]; other site 990288002342 Walker B motif; other site 990288002343 arginine finger; other site 990288002344 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 990288002345 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 990288002346 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 990288002347 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 990288002348 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002349 Walker A/P-loop; other site 990288002350 ATP binding site [chemical binding]; other site 990288002351 Q-loop/lid; other site 990288002352 ABC transporter signature motif; other site 990288002353 Walker B; other site 990288002354 D-loop; other site 990288002355 H-loop/switch region; other site 990288002356 Ferredoxin [Energy production and conversion]; Region: COG1146 990288002357 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 990288002358 DsrE/DsrF-like family; Region: DrsE; cl00672 990288002359 peroxidase; Provisional; Region: PRK15000 990288002360 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic...; Region: PRX_Typ2cys; cd03015 990288002361 dimer interface [polypeptide binding]; other site 990288002362 decamer (pentamer of dimers) interface [polypeptide binding]; other site 990288002363 catalytic triad [active] 990288002364 peroxidatic and resolving cysteines [active] 990288002365 Domain of unknown function DUF; Region: DUF202; cl09954 990288002366 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...; Region: DUS_like_FMN; cd02801 990288002367 tRNA dihydrouridine synthase A; Region: yjbN; TIGR00742 990288002368 FMN binding site [chemical binding]; other site 990288002369 active site 990288002370 catalytic residues [active] 990288002371 substrate binding site [chemical binding]; other site 990288002372 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 990288002373 Transcriptional regulator [Transcription]; Region: LysR; COG0583 990288002374 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288002375 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 990288002376 putative dimerization interface [polypeptide binding]; other site 990288002377 ribulose bisophosphate carboxylase; Reviewed; Region: rbcL; PRK04208 990288002378 Ribulose bisphosphate carboxylase large chain; Region: RuBisCO_large; cl08232 990288002379 dimer interface [polypeptide binding]; other site 990288002380 catalytic residue [active] 990288002381 metal binding site [ion binding]; metal-binding site 990288002382 Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco...; Region: RuBisCO_small; cd03527 990288002383 multimerization interface [polypeptide binding]; other site 990288002384 Carboxysome shell peptide mid-region; Region: CsoS2_M; pfam12288 990288002385 Carboxysome Shell Carbonic Anhydrase; Region: CsoSCA; cl07510 990288002386 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cd01614 990288002387 Hexamer/Pentamer interface [polypeptide binding]; other site 990288002388 central pore; other site 990288002389 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cd01614 990288002390 Hexamer/Pentamer interface [polypeptide binding]; other site 990288002391 central pore; other site 990288002392 Carboxysome Shell 1 (CsoS1); Bacterial Micro-Compartment (BCM) domain; Region: BMC_CsoS1; cd07058 990288002393 Hexamer interface [polypeptide binding]; other site 990288002394 Hexagonal pore residue; other site 990288002395 Hexagonal pore; other site 990288002396 Carboxysome Shell 1 (CsoS1); Bacterial Micro-Compartment (BCM) domain; Region: BMC_CsoS1; cd07058 990288002397 Hexamer interface [polypeptide binding]; other site 990288002398 Hexagonal pore residue; other site 990288002399 Hexagonal pore; other site 990288002400 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 990288002401 Ferritin-like domain; Region: Ferritin; pfam00210 990288002402 dinuclear metal binding motif [ion binding]; other site 990288002403 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH; cl00942 990288002404 DCoH dimer interaction site [polypeptide binding]; other site 990288002405 aromatic arch; other site 990288002406 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 990288002407 DCoH tetramer interaction site [polypeptide binding]; other site 990288002408 substrate binding site [chemical binding]; other site 990288002409 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...; Region: ParA; cd02042 990288002410 ParA-like protein; Provisional; Region: PHA02518 990288002411 P-loop; other site 990288002412 Magnesium ion binding site [ion binding]; other site 990288002413 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 990288002414 metal ion-dependent adhesion site (MIDAS); other site 990288002415 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 990288002416 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 990288002417 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 990288002418 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 990288002419 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl00412 990288002420 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 990288002421 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 990288002422 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a...; Region: Nudix_Hydrolase_1; cd03674 990288002423 nudix motif; other site 990288002424 Bacterial Micro-Compartment (BMC)-like domain 1 repeat 1; Region: BMC_like_1_repeat1; cd07051 990288002425 putative hexamer interface [polypeptide binding]; other site 990288002426 putative hexagonal pore; other site 990288002427 Bacterial Micro-Compartment (BMC)-like domain 1 repeat 2; Region: BMC_like_1_repeat2; cd07052 990288002428 putative hexamer interface [polypeptide binding]; other site 990288002429 putative hexagonal pore; other site 990288002430 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...; Region: TlpA_like_family; cd02966 990288002431 catalytic residues [active] 990288002432 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 990288002433 Proline dehydrogenase; Region: Pro_dh; cl03282 990288002434 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 990288002435 Glutamate binding site [chemical binding]; other site 990288002436 NAD binding site [chemical binding]; other site 990288002437 catalytic residues [active] 990288002438 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant...; Region: GltS_FMN; cd02808 990288002439 active site 990288002440 FMN binding site [chemical binding]; other site 990288002441 substrate binding site [chemical binding]; other site 990288002442 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 990288002443 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 990288002444 ATP binding site [chemical binding]; other site 990288002445 Mg2+ binding site [ion binding]; other site 990288002446 G-X-G motif; other site 990288002447 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 990288002448 dimerization interface [polypeptide binding]; other site 990288002449 putative DNA binding site [nucleotide binding]; other site 990288002450 putative Zn2+ binding site [ion binding]; other site 990288002451 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 990288002452 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 990288002453 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 990288002454 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288002455 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK12490 990288002456 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 990288002457 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 990288002458 hypothetical protein; Validated; Region: PRK07682 990288002459 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 990288002460 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288002461 homodimer interface [polypeptide binding]; other site 990288002462 catalytic residue [active] 990288002463 Domain of unknown function (DUF74); Region: DUF74; cl00426 990288002464 Domain of unknown function (DUF74); Region: DUF74; cl00426 990288002465 Domain of unknown function (DUF74); Region: DUF74; cl00426 990288002466 phage shock protein PspA; Provisional; Region: PRK10698 990288002467 phage shock protein A; Region: phageshock_pspA; TIGR02977 990288002468 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 990288002469 ligand binding site [chemical binding]; other site 990288002470 flexible hinge region; other site 990288002471 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 990288002472 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 990288002473 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; cl15259 990288002474 HemN C-terminal region; Region: HemN_C; pfam06969 990288002475 Uncharacterized conserved protein [Function unknown]; Region: COG3461 990288002476 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 990288002477 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 990288002478 Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this...; Region: PseudoU_synth_RsuA_like; cd02870 990288002479 active site 990288002480 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 990288002481 Major Facilitator Superfamily; Region: MFS_1; pfam07690 990288002482 putative substrate translocation pore; other site 990288002483 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 990288002484 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 990288002485 Beta-lactamase; Region: Beta-lactamase; cl01009 990288002486 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 990288002487 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 990288002488 S-adenosylmethionine binding site [chemical binding]; other site 990288002489 Protein of unknown function DUF45; Region: DUF45; cl00636 990288002490 Dihydroorotase [Nucleotide transport and metabolism]; Region: PyrC; COG0418 990288002491 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 990288002492 active site 990288002493 substrate binding pocket [chemical binding]; other site 990288002494 dimer interface [polypeptide binding]; other site 990288002495 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_20; cd07254 990288002496 putative metal binding site [ion binding]; other site 990288002497 Low molecular weight phosphatase family; Region: LMWPc; cd00115 990288002498 Active site [active] 990288002499 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 990288002500 dimerization interface [polypeptide binding]; other site 990288002501 putative DNA binding site [nucleotide binding]; other site 990288002502 putative Zn2+ binding site [ion binding]; other site 990288002503 arsenical pump membrane protein; Provisional; Region: PRK15445 990288002504 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 990288002505 transmembrane helices; other site 990288002506 EamA-like transporter family; Region: EamA; cl01037 990288002507 EamA-like transporter family; Region: EamA; cl01037 990288002508 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 990288002509 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 990288002510 active site 990288002511 FMN binding site [chemical binding]; other site 990288002512 substrate binding site [chemical binding]; other site 990288002513 homotetramer interface [polypeptide binding]; other site 990288002514 catalytic residue [active] 990288002515 Dienelactone hydrolase family; Region: DLH; pfam01738 990288002516 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 990288002517 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 990288002518 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 990288002519 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 990288002520 hydrophobic ligand binding site; other site 990288002521 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is...; Region: Trunc_globin; cd00454 990288002522 apolar tunnel; other site 990288002523 heme binding site [chemical binding]; other site 990288002524 dimerization interface [polypeptide binding]; other site 990288002525 This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH...; Region: NfsA_FRP; cd02146 990288002526 dimer interface [polypeptide binding]; other site 990288002527 FMN binding site [chemical binding]; other site 990288002528 NADPH bind site [chemical binding]; other site 990288002529 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 990288002530 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 990288002531 active site 990288002532 substrate binding site [chemical binding]; other site 990288002533 catalytic site [active] 990288002534 nucleotide excision repair endonuclease; Provisional; Region: PRK10545 990288002535 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 990288002536 GIY-YIG motif/motif A; other site 990288002537 active site 990288002538 catalytic site [active] 990288002539 putative DNA binding site [nucleotide binding]; other site 990288002540 metal binding site [ion binding]; metal-binding site 990288002541 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; cl01467 990288002542 Translocon-associated protein, delta subunit precursor (TRAP-delta); Region: TRAP-delta; pfam05404 990288002543 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288002544 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288002545 Uncharacterized conserved protein [Function unknown]; Region: HdeD; cl01277 990288002546 polynucleotide kinase; Provisional; Region: pseT; PHA02530 990288002547 ribonuclease R; Region: RNase_R; TIGR02063 990288002548 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 990288002549 RNB domain; Region: RNB; pfam00773 990288002550 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an...; Region: S1_RNase_R; cd04471 990288002551 RNA binding site [nucleotide binding]; other site 990288002552 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002553 Active site [active] 990288002554 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 990288002555 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288002556 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 990288002557 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 990288002558 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 990288002559 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 990288002560 putative MPT binding site; other site 990288002561 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 990288002562 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 990288002563 active site 990288002564 substrate binding site [chemical binding]; other site 990288002565 cosubstrate binding site; other site 990288002566 catalytic site [active] 990288002567 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 990288002568 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...; Region: PurM; cd02196 990288002569 dimerization interface [polypeptide binding]; other site 990288002570 putative ATP binding site [chemical binding]; other site 990288002571 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 990288002572 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 990288002573 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002574 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 990288002575 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 990288002576 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 990288002577 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 990288002578 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 990288002579 dimer interface [polypeptide binding]; other site 990288002580 active site 990288002581 CoA binding pocket [chemical binding]; other site 990288002582 Acyl transferase domain; Region: Acyl_transf_1; cl08282 990288002583 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 990288002584 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 990288002585 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288002586 NAD(P) binding site [chemical binding]; other site 990288002587 active site 990288002588 Phosphopantetheine attachment site; Region: PP-binding; cl09936 990288002589 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 990288002590 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 990288002591 dimer interface [polypeptide binding]; other site 990288002592 active site 990288002593 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 990288002594 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288002595 catalytic residue [active] 990288002596 YceG-like family; Region: YceG; pfam02618 990288002597 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 990288002598 dimerization interface [polypeptide binding]; other site 990288002599 thymidylate kinase; Validated; Region: tmk; PRK00698 990288002600 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting...; Region: TMPK; cd01672 990288002601 TMP-binding site; other site 990288002602 ATP-binding site [chemical binding]; other site 990288002603 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 990288002604 PilZ domain; Region: PilZ; cl01260 990288002605 Rci recombinase, C-terminal catalytic domain. Rci enzymes are found in IncI1 incompatibility group plasmids such as R64. These recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic...; Region: INT_Rci; cd00796 990288002606 Phage integrase family; Region: Phage_integrase; pfam00589 990288002607 Int/Topo IB signature motif; other site 990288002608 catalytic residues [active] 990288002609 Transposase, Mutator family; Region: Transposase_mut; pfam00872 990288002610 MULE transposase domain; Region: MULE; pfam10551 990288002611 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002612 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 990288002613 Walker A motif; other site 990288002614 ATP binding site [chemical binding]; other site 990288002615 Walker B motif; other site 990288002616 TrwC relaxase; Region: TrwC; cl08490 990288002617 conjugative transfer relaxase protein TraI; Region: TraI_TIGR; TIGR02760 990288002618 conjugative transfer relaxase protein TraI; Region: TraI_TIGR; TIGR02760 990288002619 Domain of unknown function DUF87; Region: DUF87; pfam01935 990288002620 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288002621 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288002622 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288002623 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288002624 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 990288002625 DNA binding site [nucleotide binding] 990288002626 Int/Topo IB signature motif; other site 990288002627 active site 990288002628 Transposase domain (DUF772); Region: DUF772; cl12084 990288002629 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288002630 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 990288002631 putative dimerization interface [polypeptide binding]; other site 990288002632 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 990288002633 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 990288002634 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 990288002635 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3002 990288002636 Dehydratase family; Region: ILVD_EDD; cl00340 990288002637 dihydroxy-acid dehydratase; Region: ilvD; TIGR00110 990288002638 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 990288002639 SUA5 domain; Region: SUA5; pfam03481 990288002640 Y-family of DNA polymerases; Region: PolY; cl12025 990288002641 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 990288002642 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 990288002643 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 990288002644 Protein of unknown function (DUF962); Region: DUF962; cl01879 990288002645 Transposase domain (DUF772); Region: DUF772; cl12084 990288002646 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288002647 AMMECR1; Region: AMMECR1; cl00911 990288002648 Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility; Region: MEMO_like; cd07361 990288002649 putative ligand binding pocket/active site [active] 990288002650 putative metal binding site [ion binding]; other site 990288002651 Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]; Region: PflA; COG1180 990288002652 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 990288002653 FeS/SAM binding site; other site 990288002654 Glycoside hydrolase family 15, N-terminal domain; Region: GH15_N; cd07430 990288002655 Domain interface; other site 990288002656 glucan 1,4-alpha-glucosidase; Region: glucan_glucosid; TIGR01535 990288002657 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 990288002658 Alkylmercury lyase; Region: MerB; pfam03243 990288002659 putative mercuric reductase; Provisional; Region: PRK13748 990288002660 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 990288002661 metal-binding site [ion binding] 990288002662 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288002663 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 990288002664 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 990288002665 metal-binding site [ion binding] 990288002666 MerT mercuric transport protein; Region: MerT; cl03578 990288002667 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 990288002668 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 990288002669 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 990288002670 transposase; Provisional; Region: PRK06526 990288002671 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288002672 Walker A motif; other site 990288002673 ATP binding site [chemical binding]; other site 990288002674 Walker B motif; other site 990288002675 Integrase core domain; Region: rve; cl01316 990288002676 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 990288002677 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 990288002678 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 990288002679 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288002680 DsrE/DsrF-like family; Region: DrsE; cl00672 990288002681 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 990288002682 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 990288002683 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 990288002684 Protein of unknown function (DUF692); Region: DUF692; cl01263 990288002685 hypothetical protein; Provisional; Region: PRK05409 990288002686 Predicted integral membrane protein (DUF2282); Region: DUF2282; cl02366 990288002687 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288002688 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288002689 DoxX; Region: DoxX; cl00976 990288002690 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 990288002691 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 990288002692 ABC-2 type transporter; Region: ABC2_membrane; cl11417 990288002693 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 990288002694 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 990288002695 ABC-2 type transporter; Region: ABC2_membrane; cl11417 990288002696 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 990288002697 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002698 Walker A/P-loop; other site 990288002699 ATP binding site [chemical binding]; other site 990288002700 Q-loop/lid; other site 990288002701 ABC transporter signature motif; other site 990288002702 Walker B; other site 990288002703 D-loop; other site 990288002704 H-loop/switch region; other site 990288002705 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 990288002706 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 990288002707 Walker A/P-loop; other site 990288002708 ATP binding site [chemical binding]; other site 990288002709 Q-loop/lid; other site 990288002710 ABC transporter signature motif; other site 990288002711 Walker B; other site 990288002712 D-loop; other site 990288002713 H-loop/switch region; other site 990288002714 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 990288002715 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 990288002716 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 990288002717 Outer membrane efflux protein; Region: OEP; pfam02321 990288002718 Outer membrane efflux protein; Region: OEP; pfam02321 990288002719 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 990288002720 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 990288002721 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288002722 Transposase, Mutator family; Region: Transposase_mut; pfam00872 990288002723 MULE transposase domain; Region: MULE; pfam10551 990288002724 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 990288002725 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288002726 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 990288002727 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3002 990288002728 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 990288002729 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 990288002730 Transcriptional regulator [Transcription]; Region: LysR; COG0583 990288002731 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288002732 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 990288002733 dimerization interface [polypeptide binding]; other site 990288002734 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 990288002735 PAS domain S-box; Region: sensory_box; TIGR00229 990288002736 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 990288002737 putative active site [active] 990288002738 heme pocket [chemical binding]; other site 990288002739 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288002740 metal binding site [ion binding]; metal-binding site 990288002741 active site 990288002742 I-site; other site 990288002743 YceI-like domain; Region: YceI; cl01001 990288002744 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 990288002745 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288002746 Protein of unknown function (DUF511); Region: DUF511; cl01114 990288002747 Protein of unknown function (DUF511); Region: DUF511; cl01114 990288002748 Transposase domain (DUF772); Region: DUF772; cl12084 990288002749 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288002750 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 990288002751 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288002752 Walker A motif; other site 990288002753 ATP binding site [chemical binding]; other site 990288002754 Walker B motif; other site 990288002755 arginine finger; other site 990288002756 putative transposase OrfB; Reviewed; Region: PHA02517 990288002757 Integrase core domain; Region: rve; cl01316 990288002758 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 990288002759 outer membrane porin, OprD family; Region: OprD; pfam03573 990288002760 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 990288002761 Fic family protein [Function unknown]; Region: COG3177 990288002762 Fic/DOC family; Region: Fic; cl00960 990288002763 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288002764 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288002765 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cl01287 990288002766 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 990288002767 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 990288002768 ATP binding site [chemical binding]; other site 990288002769 putative Mg++ binding site [ion binding]; other site 990288002770 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002771 voltage-gated potassium channel; Provisional; Region: PRK10537 990288002772 Ion channel; Region: Ion_trans_2; cl11596 990288002773 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288002774 RecD/TraA family; Region: recD_rel; TIGR01448 990288002775 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002776 Putative ATPase (DUF699); Region: DUF699; pfam05127 990288002777 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 990288002778 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 990288002779 active site 990288002780 phosphorylation site [posttranslational modification] 990288002781 intermolecular recognition site; other site 990288002782 dimerization interface [polypeptide binding]; other site 990288002783 ANTAR domain; Region: ANTAR; cl04297 990288002784 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 990288002785 NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored...; Region: MopB_Nitrate-R-NapA-like; cd02754 990288002786 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 990288002787 [4Fe-4S] binding site [ion binding]; other site 990288002788 molybdopterin cofactor binding site; other site 990288002789 NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 990288002790 molybdopterin cofactor binding site; other site 990288002791 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 990288002792 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 990288002793 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1)...; Region: Rieske; cl00938 990288002794 iron-sulfur cluster [ion binding]; other site 990288002795 [2Fe-2S] cluster binding site [ion binding]; other site 990288002796 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 990288002797 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288002798 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 990288002799 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 990288002800 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 990288002801 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 990288002802 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 990288002803 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 990288002804 Transposase domain (DUF772); Region: DUF772; cl12084 990288002805 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288002806 Plasmid pRiA4b ORF-3-like protein; Region: PRiA4_ORF3; pfam07929 990288002807 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 990288002808 HsdM N-terminal domain; Region: HsdM_N; pfam12161 990288002809 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288002810 T5orf172 domain; Region: T5orf172; cl11176 990288002811 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 990288002812 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 990288002813 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288002814 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288002815 Integrase core domain; Region: rve; cl01316 990288002816 transposase; Provisional; Region: PRK06526 990288002817 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288002818 Walker A motif; other site 990288002819 ATP binding site [chemical binding]; other site 990288002820 Walker B motif; other site 990288002821 Phd_YefM; Region: PhdYeFM; cl09153 990288002822 putative zinc finger/helix-turn-helix protein, YgiT family; Region: CxxCG_CxxCG_HTH; TIGR03830 990288002823 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 990288002824 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 990288002825 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 990288002826 ATP binding site [chemical binding]; other site 990288002827 putative Mg++ binding site [ion binding]; other site 990288002828 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 990288002829 putative active site [active] 990288002830 catalytic site [active] 990288002831 Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; Region: PLDc_unchar1_2; cd09128 990288002832 putative active site [active] 990288002833 putative catalytic site [active] 990288002834 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 990288002835 Microscilla MS158 and related proteins, metallophosphatase domain; Region: MPP_MS158; cd07404 990288002836 putative active site [active] 990288002837 putative metal binding site [ion binding]; other site 990288002838 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 990288002839 dimer interface [polypeptide binding]; other site 990288002840 ssDNA binding site [nucleotide binding]; other site 990288002841 tetramer (dimer of dimers) interface [polypeptide binding]; other site 990288002842 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 990288002843 Fe-S cluster binding site [ion binding]; other site 990288002844 active site 990288002845 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 990288002846 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 990288002847 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 990288002848 active site 990288002849 metal binding site [ion binding]; metal-binding site 990288002850 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 990288002851 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 990288002852 S-adenosylmethionine binding site [chemical binding]; other site 990288002853 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 990288002854 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 990288002855 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 990288002856 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 990288002857 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...; Region: VirB11-like_ATPase; cd01130 990288002858 ATP binding site [chemical binding]; other site 990288002859 Walker A motif; other site 990288002860 hexamer interface [polypeptide binding]; other site 990288002861 Walker B motif; other site 990288002862 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 990288002863 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 990288002864 N-acetyl-D-glucosamine binding site [chemical binding]; other site 990288002865 catalytic residue [active] 990288002866 type IVB pilus formation outer membrane protein, R64 PilN family; Region: pilus_B_mal_scr; TIGR02520 990288002867 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 990288002868 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 990288002869 Type II/IV secretion system protein; Region: GSPII_E; pfam00437 990288002870 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002871 Walker A motif; other site 990288002872 ATP binding site [chemical binding]; other site 990288002873 Walker B motif; other site 990288002874 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 990288002875 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 990288002876 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002877 Walker A motif; other site 990288002878 ATP binding site [chemical binding]; other site 990288002879 Walker B motif; other site 990288002880 Bacterial shufflon protein, N-terminal constant region; Region: Shufflon_N; pfam04917 990288002881 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 990288002882 HicB family; Region: HicB; pfam05534 990288002883 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 990288002884 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 990288002885 VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 990288002886 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a...; Region: Hint; cl12032 990288002887 Hom_end-associated Hint; Region: Hom_end_hint; pfam05203 990288002888 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 990288002889 YcfA-like protein; Region: YcfA; cl00752 990288002890 Uncharacterised protein family (UPF0150); Region: UPF0150; cl00691 990288002891 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314; cl02193 990288002892 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 990288002893 Restriction endonuclease [Defense mechanisms]; Region: COG3587 990288002894 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002895 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002896 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 990288002897 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288002898 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288002899 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288002900 Predicted ATPase [General function prediction only]; Region: COG5293 990288002901 Uncharacterized protein conserved in bacteria (DUF2326); Region: DUF2326; pfam10088 990288002902 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 990288002903 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 990288002904 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 990288002905 VirB8 protein; Region: VirB8; cl01500 990288002906 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 990288002907 VirB7 interaction site; other site 990288002908 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 990288002909 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 990288002910 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...; Region: ParA; cd02042 990288002911 P-loop; other site 990288002912 Magnesium ion binding site [ion binding]; other site 990288002913 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...; Region: ParA; cd02042 990288002914 Magnesium ion binding site [ion binding]; other site 990288002915 ParB-like nuclease domain; Region: ParBc; cl02129 990288002916 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 990288002917 AntA/AntB antirepressor; Region: AntA; cl01430 990288002918 AntA/AntB antirepressor; Region: AntA; cl01430 990288002919 T5orf172 domain; Region: T5orf172; cl11176 990288002920 conjugal transfer coupling protein TraG; Provisional; Region: PRK13880 990288002921 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002922 Walker A motif; other site 990288002923 ATP binding site [chemical binding]; other site 990288002924 Walker B motif; other site 990288002925 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the...; Region: beta_clamp; cl02940 990288002926 putative DNA binding surface [nucleotide binding]; other site 990288002927 DNA polymerase III subunit beta; Validated; Region: PRK05643 990288002928 dimer interface [polypeptide binding]; other site 990288002929 beta-clamp/clamp loader binding surface; other site 990288002930 beta-clamp/translesion DNA polymerase binding surface; other site 990288002931 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases...; Region: lysozyme_like; cl00222 990288002932 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 990288002933 nucleotide binding region [chemical binding]; other site 990288002934 CRISPR/Cas system-associated RAMP superfamily protein Csf2; Region: Csf2_U; cl11864 990288002935 CRISPR/Cas system-associated RAMP superfamily protein Cas6e; Region: Cas6_I-E; cl08497 990288002936 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 990288002937 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002938 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288002939 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288002940 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 990288002941 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 990288002942 active site 990288002943 catalytic triad [active] 990288002944 oxyanion hole [active] 990288002945 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 990288002946 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288002947 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288002948 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288002949 metal binding site 2 [ion binding]; metal-binding site 990288002950 metal binding site 1 [ion binding]; metal-binding site 990288002951 structural Zn2+ binding site [ion binding]; other site 990288002952 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288002953 Helicase associated domain; Region: HA; pfam03457 990288002954 MT-A70; Region: MT-A70; cl01947 990288002955 Peptidase S26; Region: Peptidase_S26; pfam10502 990288002956 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)...; Region: Peptidase_S24_S26; cl10465 990288002957 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 990288002958 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 990288002959 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 990288002960 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288002961 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 990288002962 cofactor binding site; other site 990288002963 DNA binding site [nucleotide binding] 990288002964 substrate interaction site [chemical binding]; other site 990288002965 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288002966 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 990288002967 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288002968 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288002969 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 990288002970 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 990288002971 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 990288002972 DNA topoisomerase III; Provisional; Region: PRK07726 990288002973 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by:...; Region: TOPRIM_TopoIA_TopoIII; cd03362 990288002974 active site 990288002975 putative interdomain interaction site [polypeptide binding]; other site 990288002976 putative metal-binding site [ion binding]; other site 990288002977 putative nucleotide binding site [chemical binding]; other site 990288002978 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded...; Region: TOP1Ac; cd00186 990288002979 domain I; other site 990288002980 DNA binding groove [nucleotide binding] 990288002981 phosphate binding site [ion binding]; other site 990288002982 domain II; other site 990288002983 domain III; other site 990288002984 nucleotide binding site [chemical binding]; other site 990288002985 catalytic site [active] 990288002986 domain IV; other site 990288002987 T5-5'nuclease, and homologs; Region: PIN_T4-like; cd09860 990288002988 5'-3' exonuclease; Region: 53EXOc; smart00475 990288002989 active site 990288002990 metal binding site 1 [ion binding]; metal-binding site 990288002991 5' ssDNA interaction site; other site 990288002992 3' ssDNA interaction site; other site 990288002993 metal binding site 2 [ion binding]; metal-binding site 990288002994 T5-5' nucleases, and homologs; Region: H3TH_T4-like; cd09899 990288002995 DNA binding site [nucleotide binding] 990288002996 metal binding site [ion binding]; metal-binding site 990288002997 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 990288002998 IHF dimer interface [polypeptide binding]; other site 990288002999 IHF - DNA interface [nucleotide binding]; other site 990288003000 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 990288003001 N-acetyl-D-glucosamine binding site [chemical binding]; other site 990288003002 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: Arch_glmU; TIGR03992 990288003003 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 990288003004 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 990288003005 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 990288003006 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 990288003007 Endodeoxyribonuclease RusA; Region: RusA; cl01885 990288003008 Loader and inhibitor of phage G40P; Region: Inhibitor_G39P; pfam11417 990288003009 ParB-like nuclease domain; Region: ParBc; cl02129 990288003010 DNA N-6-adenine-methyltransferase (Dam); Region: Dam; cl05442 990288003011 Bacteriophage CII protein; Region: Phage_CII; pfam05269 990288003012 RecT family; Region: RecT; cl04285 990288003013 Phage-related protein, predicted endonuclease [DNA replication, recombination, and repair]; Region: COG5377 990288003014 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 990288003015 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 990288003016 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 990288003017 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 990288003018 DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial and phage integrases, including those similar to phage P22-like integrases, DLP12 and APSE-1; Region: INT_P22_C; cd01192 990288003019 Phage integrase family; Region: Phage_integrase; pfam00589 990288003020 Int/Topo IB signature motif; other site 990288003021 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 990288003022 metal binding site 2 [ion binding]; metal-binding site 990288003023 putative DNA binding helix; other site 990288003024 metal binding site 1 [ion binding]; metal-binding site 990288003025 structural Zn2+ binding site [ion binding]; other site 990288003026 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 990288003027 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16...; Region: OM_channels; cl00284 990288003028 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 990288003029 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 990288003030 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 990288003031 Family of unknown function (DUF490); Region: DUF490; pfam04357 990288003032 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 990288003033 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 990288003034 Surface antigen; Region: Bac_surface_Ag; cl03097 990288003035 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 990288003036 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288003037 Walker A motif; other site 990288003038 ATP binding site [chemical binding]; other site 990288003039 Walker B motif; other site 990288003040 arginine finger; other site 990288003041 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 990288003042 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 990288003043 recombination protein RecR; Reviewed; Region: recR; PRK00076 990288003044 RecR protein; Region: RecR; pfam02132 990288003045 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 990288003046 putative active site [active] 990288003047 putative metal-binding site [ion binding]; other site 990288003048 tetramer interface [polypeptide binding]; other site 990288003049 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 990288003050 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 990288003051 putative substrate binding site [chemical binding]; other site 990288003052 putative ATP binding site [chemical binding]; other site 990288003053 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06916 990288003054 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 990288003055 inhibitor-cofactor binding pocket; inhibition site 990288003056 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288003057 catalytic residue [active] 990288003058 FOG: CBS domain [General function prediction only]; Region: COG0517 990288003059 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl09141 990288003060 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 990288003061 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 990288003062 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 990288003063 ATP binding site [chemical binding]; other site 990288003064 Mg2+ binding site [ion binding]; other site 990288003065 G-X-G motif; other site 990288003066 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 990288003067 ATP binding site [chemical binding]; other site 990288003068 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 990288003069 IPP transferase; Region: IPPT; cl00403 990288003070 Heme NO binding; Region: HNOB; cl15268 990288003071 Domain of unknown function (DUF74); Region: DUF74; cl00426 990288003072 Protein of unknown function (DUF3311); Region: DUF3311; pfam11755 990288003073 Sodium:solute symporter family; Region: SSF; cl00456 990288003074 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 990288003075 heme-binding site [chemical binding]; other site 990288003076 threonine dehydratase; Reviewed; Region: PRK09224 990288003077 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 990288003078 tetramer interface [polypeptide binding]; other site 990288003079 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288003080 catalytic residue [active] 990288003081 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 990288003082 putative Ile/Val binding site [chemical binding]; other site 990288003083 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 990288003084 putative Ile/Val binding site [chemical binding]; other site 990288003085 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288003086 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 990288003087 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 990288003088 MG2 domain; Region: A2M_N; pfam01835 990288003089 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 990288003090 Alpha-2-macroglobulin family; Region: A2M; pfam00207 990288003091 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 990288003092 surface patch; other site 990288003093 thioester region; other site 990288003094 specificity defining residues; other site 990288003095 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 990288003096 Transglycosylase; Region: Transgly; cl07896 990288003097 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 990288003098 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 990288003099 Acetokinase family; Region: Acetate_kinase; cl01029 990288003100 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 990288003101 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 990288003102 E3 interaction surface; other site 990288003103 lipoyl attachment site [posttranslational modification]; other site 990288003104 e3 binding domain; Region: E3_binding; pfam02817 990288003105 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 990288003106 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 990288003107 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 990288003108 alpha subunit interface [polypeptide binding]; other site 990288003109 TPP binding site [chemical binding]; other site 990288003110 heterodimer interface [polypeptide binding]; other site 990288003111 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 990288003112 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 990288003113 tetramer interface [polypeptide binding]; other site 990288003114 TPP-binding site [chemical binding]; other site 990288003115 heterodimer interface [polypeptide binding]; other site 990288003116 phosphorylation loop region [posttranslational modification] 990288003117 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 990288003118 Sulfatase; Region: Sulfatase; cl10460 990288003119 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 990288003120 phosphoenolpyruvate synthase; Validated; Region: PRK06464 990288003121 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 990288003122 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 990288003123 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 990288003124 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 990288003125 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 990288003126 Sporulation related domain; Region: SPOR; cl10051 990288003127 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 990288003128 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 990288003129 metal binding site [ion binding]; metal-binding site 990288003130 dimer interface [polypeptide binding]; other site 990288003131 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 990288003132 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 990288003133 trimer interface [polypeptide binding]; other site 990288003134 active site 990288003135 substrate binding site [chemical binding]; other site 990288003136 CoA binding site [chemical binding]; other site 990288003137 aspartate aminotransferase; Provisional; Region: PRK07681 990288003138 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 990288003139 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288003140 homodimer interface [polypeptide binding]; other site 990288003141 catalytic residue [active] 990288003142 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 990288003143 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 990288003144 S-adenosylmethionine binding site [chemical binding]; other site 990288003145 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 990288003146 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 990288003147 active site 990288003148 putative substrate binding pocket [chemical binding]; other site 990288003149 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases...; Region: lysozyme_like; cl00222 990288003150 NlpC/P60 family; Region: NLPC_P60; cl11438 990288003151 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 990288003152 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 990288003153 Pirin-related protein [General function prediction only]; Region: COG1741 990288003154 Cupin domain; Region: Cupin_2; cl09118 990288003155 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 990288003156 Transposase domain (DUF772); Region: DUF772; cl12084 990288003157 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288003158 Uncharacterized conserved protein [Function unknown]; Region: COG2326 990288003159 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 990288003160 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 990288003161 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16...; Region: OM_channels; cl00284 990288003162 Uncharacterized conserved protein [Function unknown]; Region: COG3391 990288003163 Sulfatase; Region: Sulfatase; cl10460 990288003164 benzoate transport; Region: 2A0115; TIGR00895 990288003165 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 990288003166 putative substrate translocation pore; other site 990288003167 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 990288003168 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule...; Region: GT1_like_2; cd03814 990288003169 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 990288003170 putative active site [active] 990288003171 putative metal binding site [ion binding]; other site 990288003172 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 990288003173 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...; Region: trans_reg_C; cd00383 990288003174 DNA binding site [nucleotide binding] 990288003175 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 990288003176 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 990288003177 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 990288003178 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16...; Region: OM_channels; cl00284 990288003179 Gram-negative bacterial tonB protein; Region: TonB; cl10048 990288003180 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 990288003181 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 990288003182 dimer interface [polypeptide binding]; other site 990288003183 conserved gate region; other site 990288003184 putative PBP binding loops; other site 990288003185 ABC-ATPase subunit interface; other site 990288003186 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 990288003187 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 990288003188 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 990288003189 Walker A/P-loop; other site 990288003190 ATP binding site [chemical binding]; other site 990288003191 Q-loop/lid; other site 990288003192 ABC transporter signature motif; other site 990288003193 Walker B; other site 990288003194 D-loop; other site 990288003195 H-loop/switch region; other site 990288003196 Predicted membrane protein [Function unknown]; Region: COG4280 990288003197 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf...; Region: RNase_T2; cl00208 990288003198 CAS motifs; other site 990288003199 active site 990288003200 NodT family; Region: outer_NodT; TIGR01845 990288003201 Outer membrane efflux protein; Region: OEP; pfam02321 990288003202 Outer membrane efflux protein; Region: OEP; pfam02321 990288003203 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 990288003204 multicopper oxidase; Provisional; Region: PRK10965 990288003205 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 990288003206 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 990288003207 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 990288003208 active site 990288003209 multimer interface [polypeptide binding]; other site 990288003210 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 990288003211 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 990288003212 FeS/SAM binding site; other site 990288003213 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 990288003214 binding surface 990288003215 TPR motif; other site 990288003216 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 990288003217 cytoskeletal protein RodZ; Provisional; Region: PRK10856 990288003218 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 990288003219 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; Region: ispG_gcpE; TIGR00612 990288003220 histidyl-tRNA synthetase; Region: hisS; TIGR00442 990288003221 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 990288003222 dimer interface [polypeptide binding]; other site 990288003223 motif 1; other site 990288003224 active site 990288003225 motif 2; other site 990288003226 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 990288003227 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 990288003228 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 990288003229 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 990288003230 GTP-binding protein Der; Reviewed; Region: PRK00093 990288003231 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA1; cd01894 990288003232 G1 box; other site 990288003233 GTP/Mg2+ binding site [chemical binding]; other site 990288003234 Switch I region; other site 990288003235 G2 box; other site 990288003236 Switch II region; other site 990288003237 G3 box; other site 990288003238 G4 box; other site 990288003239 G5 box; other site 990288003240 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA2; cd01895 990288003241 G1 box; other site 990288003242 GTP/Mg2+ binding site [chemical binding]; other site 990288003243 Switch I region; other site 990288003244 G2 box; other site 990288003245 G3 box; other site 990288003246 Switch II region; other site 990288003247 G4 box; other site 990288003248 G5 box; other site 990288003249 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 990288003250 catalytic core [active] 990288003251 DsrE/DsrF-like family; Region: DrsE; cl00672 990288003252 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 990288003253 Moco binding site; other site 990288003254 metal coordination site [ion binding]; other site 990288003255 Transposase domain (DUF772); Region: DUF772; cl12084 990288003256 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288003257 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 990288003258 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 990288003259 dimer interface [polypeptide binding]; other site 990288003260 conserved gate region; other site 990288003261 putative PBP binding loops; other site 990288003262 ABC-ATPase subunit interface; other site 990288003263 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 990288003264 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 990288003265 dimer interface [polypeptide binding]; other site 990288003266 conserved gate region; other site 990288003267 putative PBP binding loops; other site 990288003268 ABC-ATPase subunit interface; other site 990288003269 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 990288003270 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 990288003271 S-adenosylmethionine binding site [chemical binding]; other site 990288003272 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 990288003273 Initiation factor 2 subunit family; Region: IF-2B; pfam01008 990288003274 Uncharacterized conserved protein [Function unknown]; Region: COG3391 990288003275 Uncharacterized conserved protein [Function unknown]; Region: COG3391 990288003276 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 990288003277 Sulfatase; Region: Sulfatase; cl10460 990288003278 DNA gyrase subunit A; Validated; Region: PRK05560 990288003279 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in...; Region: TOP4c; cd00187 990288003280 CAP-like domain; other site 990288003281 Active site [active] 990288003282 primary dimer interface [polypeptide binding]; other site 990288003283 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 990288003284 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 990288003285 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 990288003286 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 990288003287 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 990288003288 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 990288003289 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active...; Region: PSAT_like; cd00611 990288003290 homodimer interface [polypeptide binding]; other site 990288003291 substrate-cofactor binding pocket; other site 990288003292 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288003293 catalytic residue [active] 990288003294 Chorismate mutase type II; Region: CM_2; cl00693 990288003295 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 990288003296 Prephenate dehydratase; Region: PDT; pfam00800 990288003297 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 990288003298 putative L-Phe binding site [chemical binding]; other site 990288003299 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 990288003300 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 990288003301 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288003302 homodimer interface [polypeptide binding]; other site 990288003303 catalytic residue [active] 990288003304 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 990288003305 NeuB family; Region: NeuB; cl00496 990288003306 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288003307 Prephenate dehydrogenase; Region: PDH; pfam02153 990288003308 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 990288003309 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 5-enolpyruvylshkimate-3-...; Region: EPSP_synthase; cd01556 990288003310 hinge; other site 990288003311 active site 990288003312 cytidylate kinase; Provisional; Region: cmk; PRK00023 990288003313 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 990288003314 CMP-binding site; other site 990288003315 The sites determining sugar specificity; other site 990288003316 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 990288003317 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 990288003318 RNA binding site [nucleotide binding]; other site 990288003319 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 990288003320 RNA binding site [nucleotide binding]; other site 990288003321 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 990288003322 RNA binding site [nucleotide binding]; other site 990288003323 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec4; cd05689 990288003324 RNA binding site [nucleotide binding]; other site 990288003325 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec5; cd05690 990288003326 RNA binding site [nucleotide binding]; other site 990288003327 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 990288003328 RNA binding site [nucleotide binding]; other site 990288003329 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 990288003330 IHF - DNA interface [nucleotide binding]; other site 990288003331 IHF dimer interface [polypeptide binding]; other site 990288003332 tetratricopeptide repeat protein; Provisional; Region: PRK11788 990288003333 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 990288003334 active site 990288003335 dimer interface [polypeptide binding]; other site 990288003336 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 990288003337 trigger factor; Provisional; Region: tig; PRK01490 990288003338 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 990288003339 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 990288003340 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 990288003341 oligomer interface [polypeptide binding]; other site 990288003342 active site residues [active] 990288003343 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 990288003344 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 990288003345 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288003346 Walker A motif; other site 990288003347 ATP binding site [chemical binding]; other site 990288003348 Walker B motif; other site 990288003349 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 990288003350 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 990288003351 Found in ATP-dependent protease La (LON); Region: LON; smart00464 990288003352 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288003353 Walker A motif; other site 990288003354 ATP binding site [chemical binding]; other site 990288003355 Walker B motif; other site 990288003356 arginine finger; other site 990288003357 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 990288003358 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 990288003359 IHF dimer interface [polypeptide binding]; other site 990288003360 IHF - DNA interface [nucleotide binding]; other site 990288003361 SurA N-terminal domain; Region: SurA_N; pfam09312 990288003362 PilZ domain; Region: PilZ; cl01260 990288003363 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 990288003364 PAS domain S-box; Region: sensory_box; TIGR00229 990288003365 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 990288003366 putative active site [active] 990288003367 heme pocket [chemical binding]; other site 990288003368 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288003369 metal binding site [ion binding]; metal-binding site 990288003370 active site 990288003371 I-site; other site 990288003372 Sel1 repeat; Region: Sel1; cl02723 990288003373 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 990288003374 GAF domain; Region: GAF; cl00853 990288003375 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 990288003376 PAS fold; Region: PAS_3; pfam08447 990288003377 putative active site [active] 990288003378 heme pocket [chemical binding]; other site 990288003379 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288003380 metal binding site [ion binding]; metal-binding site 990288003381 active site 990288003382 I-site; other site 990288003383 PilZ domain; Region: PilZ; cl01260 990288003384 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 990288003385 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 990288003386 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 990288003387 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 990288003388 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 990288003389 Uncharacterized conserved protein (DUF2173); Region: DUF2173; cl01994 990288003390 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 990288003391 dimer interface [polypeptide binding]; other site 990288003392 catalytic triad [active] 990288003393 peroxidatic and resolving cysteines [active] 990288003394 Transglycosylase; Region: Transgly; cl07896 990288003395 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 990288003396 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 990288003397 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 990288003398 active site 990288003399 HIGH motif; other site 990288003400 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 990288003401 active site 990288003402 KMSKS motif; other site 990288003403 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 990288003404 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 990288003405 active site 990288003406 HIGH motif; other site 990288003407 nucleotide binding site [chemical binding]; other site 990288003408 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 990288003409 KMSKS motif; other site 990288003410 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 990288003411 tRNA binding surface [nucleotide binding]; other site 990288003412 anticodon binding site; other site 990288003413 ribonuclease E; Reviewed; Region: rne; PRK10811 990288003414 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 990288003415 homodimer interface [polypeptide binding]; other site 990288003416 oligonucleotide binding site [chemical binding]; other site 990288003417 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 990288003418 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 990288003419 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 990288003420 active site 990288003421 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 990288003422 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 990288003423 motif II; other site 990288003424 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 990288003425 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288003426 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 990288003427 Walker A/P-loop; other site 990288003428 ATP binding site [chemical binding]; other site 990288003429 Q-loop/lid; other site 990288003430 ABC transporter signature motif; other site 990288003431 Walker B; other site 990288003432 D-loop; other site 990288003433 H-loop/switch region; other site 990288003434 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288003435 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288003436 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 990288003437 Glycoside hydrolase family 15, N-terminal domain; Region: GH15_N; cd07430 990288003438 Domain interface; other site 990288003439 glucan 1,4-alpha-glucosidase; Region: glucan_glucosid; TIGR01535 990288003440 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 990288003441 glucose-1-dehydrogenase; Provisional; Region: PRK08936 990288003442 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288003443 NAD(P) binding site [chemical binding]; other site 990288003444 active site 990288003445 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 990288003446 tandem repeat interface [polypeptide binding]; other site 990288003447 oligomer interface [polypeptide binding]; other site 990288003448 active site residues [active] 990288003449 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 990288003450 tandem repeat interface [polypeptide binding]; other site 990288003451 oligomer interface [polypeptide binding]; other site 990288003452 active site residues [active] 990288003453 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and...; Region: Aldo_ket_red; cd06660 990288003454 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 990288003455 active site 990288003456 catalytic tetrad [active] 990288003457 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 990288003458 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 990288003459 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 990288003460 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 990288003461 active site 990288003462 phosphorylation site [posttranslational modification] 990288003463 intermolecular recognition site; other site 990288003464 dimerization interface [polypeptide binding]; other site 990288003465 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 990288003466 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 990288003467 putative binding surface; other site 990288003468 active site 990288003469 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 990288003470 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 990288003471 ATP binding site [chemical binding]; other site 990288003472 Mg2+ binding site [ion binding]; other site 990288003473 G-X-G motif; other site 990288003474 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 990288003475 Response regulator receiver domain; Region: Response_reg; pfam00072 990288003476 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 990288003477 active site 990288003478 phosphorylation site [posttranslational modification] 990288003479 intermolecular recognition site; other site 990288003480 dimerization interface [polypeptide binding]; other site 990288003481 Sporulation related domain; Region: SPOR; cl10051 990288003482 flagellar motor protein MotD; Reviewed; Region: PRK09038 990288003483 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 990288003484 ligand binding site [chemical binding]; other site 990288003485 PilZ domain; Region: PilZ; cl01260 990288003486 FliW protein; Region: FliW; cl00740 990288003487 Global regulator protein family; Region: CsrA; cl00670 990288003488 FlgN protein; Region: FlgN; cl09176 990288003489 SAF domain; Region: SAF; cl00555 990288003490 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 990288003491 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 990288003492 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 990288003493 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 990288003494 Flagellar hook capping protein; Region: FlgD; cl04347 990288003495 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 990288003496 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 990288003497 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 990288003498 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 990288003499 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 990288003500 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 990288003501 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 990288003502 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 990288003503 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 990288003504 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 990288003505 Flagellar L-ring protein; Region: FlgH; cl00905 990288003506 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 990288003507 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 990288003508 Rod binding protein; Region: Rod-binding; cl01626 990288003509 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 990288003510 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl00743 990288003511 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 990288003512 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 990288003513 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 990288003514 S-adenosylmethionine binding site [chemical binding]; other site 990288003515 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 990288003516 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288003517 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288003518 Rhamnan synthesis protein F; Region: RgpF; cl01529 990288003519 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 990288003520 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 990288003521 Probable Catalytic site [active] 990288003522 metal binding site [ion binding]; metal-binding site 990288003523 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 990288003524 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 990288003525 flagellin; Reviewed; Region: PRK08869 990288003526 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 990288003527 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 990288003528 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 990288003529 Flagellar protein FliS; Region: FliS; cl00654 990288003530 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288003531 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 990288003532 Walker A motif; other site 990288003533 ATP binding site [chemical binding]; other site 990288003534 Walker B motif; other site 990288003535 arginine finger; other site 990288003536 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 990288003537 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 990288003538 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 990288003539 ATP binding site [chemical binding]; other site 990288003540 Mg2+ binding site [ion binding]; other site 990288003541 G-X-G motif; other site 990288003542 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 990288003543 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 990288003544 active site 990288003545 phosphorylation site [posttranslational modification] 990288003546 intermolecular recognition site; other site 990288003547 dimerization interface [polypeptide binding]; other site 990288003548 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288003549 Walker A motif; other site 990288003550 ATP binding site [chemical binding]; other site 990288003551 Walker B motif; other site 990288003552 arginine finger; other site 990288003553 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 990288003554 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 990288003555 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 990288003556 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 990288003557 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 990288003558 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 990288003559 MgtE intracellular N domain; Region: MgtE_N; cl15244 990288003560 FliG C-terminal domain; Region: FliG_C; pfam01706 990288003561 flagellar assembly protein H; Validated; Region: fliH; PRK05687 990288003562 Flagellar assembly protein FliH; Region: FliH; pfam02108 990288003563 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 990288003564 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 990288003565 Walker A motif/ATP binding site; other site 990288003566 Walker B motif; other site 990288003567 Flagellar FliJ protein; Region: FliJ; cl09161 990288003568 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 990288003569 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 990288003570 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 990288003571 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 990288003572 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 990288003573 FliP family; Region: FliP; cl00593 990288003574 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 990288003575 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 990288003576 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 990288003577 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 990288003578 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 990288003579 Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhA; cl07980 990288003580 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 990288003581 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 990288003582 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 990288003583 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 990288003584 P-loop; other site 990288003585 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 990288003586 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 990288003587 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 990288003588 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 990288003589 DNA binding residues [nucleotide binding] 990288003590 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 990288003591 flagellar motor protein MotA; Validated; Region: PRK08124 990288003592 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 990288003593 MutS domain I; Region: MutS_I; pfam01624 990288003594 MutS domain II; Region: MutS_II; pfam05188 990288003595 MutS family domain IV; Region: MutS_IV; pfam05190 990288003596 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 990288003597 Walker A/P-loop; other site 990288003598 ATP binding site [chemical binding]; other site 990288003599 Q-loop/lid; other site 990288003600 ABC transporter signature motif; other site 990288003601 Walker B; other site 990288003602 D-loop; other site 990288003603 H-loop/switch region; other site 990288003604 YccA-like proteins; Region: YccA_like; cd10433 990288003605 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 990288003606 exodeoxyribonuclease X; Provisional; Region: PRK07983 990288003607 active site 990288003608 substrate binding site [chemical binding]; other site 990288003609 catalytic site [active] 990288003610 Protein of unknown function (DUF3820); Region: DUF3820; cl01411 990288003611 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II)...; Region: Aldolase_II; cl00214 990288003612 Smr domain; Region: Smr; cl02619 990288003613 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 990288003614 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 990288003615 FAD binding domain; Region: FAD_binding_4; pfam01565 990288003616 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 990288003617 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 990288003618 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 990288003619 Pantoate-beta-alanine ligase; Region: PanC; cd00560 990288003620 pantoate--beta-alanine ligase; Region: panC; TIGR00018 990288003621 active site 990288003622 ATP-binding site [chemical binding]; other site 990288003623 pantoate-binding site; other site 990288003624 HXXH motif; other site 990288003625 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 990288003626 active site 990288003627 oligomerization interface [polypeptide binding]; other site 990288003628 metal binding site [ion binding]; metal-binding site 990288003629 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 990288003630 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7...; Region: dNK; cd01673 990288003631 Substrate-binding site [chemical binding]; other site 990288003632 Substrate specificity [chemical binding]; other site 990288003633 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 990288003634 catalytic center binding site [active] 990288003635 ATP binding site [chemical binding]; other site 990288003636 poly(A) polymerase; Region: pcnB; TIGR01942 990288003637 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 990288003638 active site 990288003639 NTP binding site [chemical binding]; other site 990288003640 metal binding triad [ion binding]; metal-binding site 990288003641 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 990288003642 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 990288003643 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 990288003644 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 990288003645 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 990288003646 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the...; Region: IMPDH; cd00381 990288003647 active site 990288003648 GMP synthase; Reviewed; Region: guaA; PRK00074 990288003649 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 990288003650 AMP/PPi binding site [chemical binding]; other site 990288003651 candidate oxyanion hole; other site 990288003652 catalytic triad [active] 990288003653 potential glutamine specificity residues [chemical binding]; other site 990288003654 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 990288003655 ATP Binding subdomain [chemical binding]; other site 990288003656 Ligand Binding sites [chemical binding]; other site 990288003657 Dimerization subdomain; other site 990288003658 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 990288003659 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 990288003660 ligand binding site [chemical binding]; other site 990288003661 flexible hinge region; other site 990288003662 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 990288003663 putative switch regulator; other site 990288003664 non-specific DNA interactions [nucleotide binding]; other site 990288003665 DNA binding site [nucleotide binding] 990288003666 sequence specific DNA binding site [nucleotide binding]; other site 990288003667 putative cAMP binding site [chemical binding]; other site 990288003668 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 990288003669 heme-binding site [chemical binding]; other site 990288003670 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 990288003671 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 990288003672 catalytic loop [active] 990288003673 iron binding site [ion binding]; other site 990288003674 The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S]...; Region: O2ase_reductase_like; cd06187 990288003675 FAD binding pocket [chemical binding]; other site 990288003676 FAD binding motif [chemical binding]; other site 990288003677 phosphate binding motif [ion binding]; other site 990288003678 beta-alpha-beta structure motif; other site 990288003679 NAD binding pocket [chemical binding]; other site 990288003680 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 990288003681 minor groove reading motif; other site 990288003682 helix-hairpin-helix signature motif; other site 990288003683 substrate binding pocket [chemical binding]; other site 990288003684 active site 990288003685 Protein of unknown function, DUF488; Region: DUF488; cl01246 990288003686 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 990288003687 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 990288003688 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 990288003689 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 990288003690 Cl- selectivity filter; other site 990288003691 Cl- binding residues [ion binding]; other site 990288003692 pore gating glutamate residue; other site 990288003693 dimer interface [polypeptide binding]; other site 990288003694 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 990288003695 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 990288003696 Cl- selectivity filter; other site 990288003697 Cl- binding residues [ion binding]; other site 990288003698 pore gating glutamate residue; other site 990288003699 dimer interface [polypeptide binding]; other site 990288003700 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 990288003701 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 990288003702 dimerization interface [polypeptide binding]; other site 990288003703 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288003704 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288003705 acetyl-CoA synthetase; Provisional; Region: PRK00174 990288003706 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 990288003707 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 990288003708 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 990288003709 alpha-glucan phosphorylases; Region: more_P_ylases; TIGR02094 990288003710 pyruvate kinase; Provisional; Region: PRK05826 990288003711 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 990288003712 domain interfaces; other site 990288003713 active site 990288003714 DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes [Carbohydrate transport and metabolism]; Region: FbaB; COG1830 990288003715 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs); Region: DhnA; cd00958 990288003716 putative active site; other site 990288003717 catalytic residue [active] 990288003718 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 990288003719 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288003720 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288003721 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 990288003722 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 990288003723 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 990288003724 putative substrate binding site [chemical binding]; other site 990288003725 putative ATP binding site [chemical binding]; other site 990288003726 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 990288003727 potential frameshift: common BLAST hit: gi|198282301|ref|YP_002218622.1| carbohydrate-selective porin OprB 990288003728 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 990288003729 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 990288003730 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 990288003731 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 990288003732 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 990288003733 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 990288003734 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 990288003735 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 990288003736 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 990288003737 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 990288003738 Natural resistance-associated macrophage protein; Region: Nramp; cl00836 990288003739 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 990288003740 MgtC family; Region: MgtC; cl12207 990288003741 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 990288003742 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 990288003743 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 990288003744 putative active site [active] 990288003745 catalytic site [active] 990288003746 Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; Region: PLDc_unchar1_2; cd09128 990288003747 putative active site [active] 990288003748 putative catalytic site [active] 990288003749 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 990288003750 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288003751 metal binding site [ion binding]; metal-binding site 990288003752 active site 990288003753 I-site; other site 990288003754 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288003755 I-site; other site 990288003756 active site 990288003757 metal binding site [ion binding]; metal-binding site 990288003758 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288003759 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288003760 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 990288003761 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 990288003762 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 990288003763 flagellar motor protein MotB; Validated; Region: motB; PRK09041 990288003764 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 990288003765 ligand binding site [chemical binding]; other site 990288003766 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288003767 metal binding site [ion binding]; metal-binding site 990288003768 active site 990288003769 I-site; other site 990288003770 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 990288003771 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 990288003772 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 990288003773 putative active site [active] 990288003774 heme pocket [chemical binding]; other site 990288003775 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 990288003776 putative active site [active] 990288003777 heme pocket [chemical binding]; other site 990288003778 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288003779 metal binding site [ion binding]; metal-binding site 990288003780 active site 990288003781 I-site; other site 990288003782 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 990288003783 active site 990288003784 catalytic triad [active] 990288003785 oxyanion hole [active] 990288003786 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 990288003787 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288003788 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288003789 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 990288003790 active site 990288003791 catalytic triad [active] 990288003792 oxyanion hole [active] 990288003793 transposase; Provisional; Region: PRK06526 990288003794 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288003795 Walker A motif; other site 990288003796 ATP binding site [chemical binding]; other site 990288003797 Walker B motif; other site 990288003798 Integrase core domain; Region: rve; cl01316 990288003799 Transposase domain (DUF772); Region: DUF772; cl12084 990288003800 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288003801 Transposase domain (DUF772); Region: DUF772; cl12084 990288003802 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288003803 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288003804 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288003805 Integrase core domain; Region: rve; cl01316 990288003806 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 990288003807 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 990288003808 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 990288003809 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288003810 Walker A motif; other site 990288003811 ATP binding site [chemical binding]; other site 990288003812 Walker B motif; other site 990288003813 outer membrane porin, OprD family; Region: OprD; pfam03573 990288003814 Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes sulfite sensitivity protein (sulfite efflux pump; SSU1); Region: TDT_SSU1; cd09318 990288003815 C4-dicarboxylate transporter/malic acid transport protein; Region: C4dic_mal_tran; pfam03595 990288003816 gating phenylalanine in ion channel; other site 990288003817 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 990288003818 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 990288003819 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 990288003820 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 990288003821 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 990288003822 ligand binding site [chemical binding]; other site 990288003823 flexible hinge region; other site 990288003824 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 990288003825 putative switch regulator; other site 990288003826 non-specific DNA interactions [nucleotide binding]; other site 990288003827 DNA binding site [nucleotide binding] 990288003828 sequence specific DNA binding site [nucleotide binding]; other site 990288003829 putative cAMP binding site [chemical binding]; other site 990288003830 phosphate:H+ symporter; Region: 2A0109; TIGR00887 990288003831 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 990288003832 putative substrate translocation pore; other site 990288003833 Transposase domain (DUF772); Region: DUF772; cl12084 990288003834 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288003835 multidrug efflux protein; Reviewed; Region: PRK09579 990288003836 Protein export membrane protein; Region: SecD_SecF; cl14618 990288003837 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 990288003838 NodT family; Region: outer_NodT; TIGR01845 990288003839 Outer membrane efflux protein; Region: OEP; pfam02321 990288003840 Outer membrane efflux protein; Region: OEP; pfam02321 990288003841 MULE transposase domain; Region: MULE; pfam10551 990288003842 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 990288003843 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 990288003844 active site 990288003845 phosphorylation site [posttranslational modification] 990288003846 intermolecular recognition site; other site 990288003847 dimerization interface [polypeptide binding]; other site 990288003848 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...; Region: trans_reg_C; cd00383 990288003849 DNA binding site [nucleotide binding] 990288003850 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 connected by an extended linker. The...; Region: HAMP; cl01054 990288003851 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 990288003852 ATP binding site [chemical binding]; other site 990288003853 Mg2+ binding site [ion binding]; other site 990288003854 G-X-G motif; other site 990288003855 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 990288003856 Trp docking motif; other site 990288003857 FOG: WD40-like repeat [Function unknown]; Region: COG1520 990288003858 'Velcro' closure; other site 990288003859 DoxX; Region: DoxX; cl00976 990288003860 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 990288003861 Integrase core domain; Region: rve; cl01316 990288003862 Sel1 repeat; Region: Sel1; cl02723 990288003863 Sel1 repeat; Region: Sel1; cl02723 990288003864 Transposase domain (DUF772); Region: DUF772; cl12084 990288003865 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288003866 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 990288003867 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 990288003868 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 990288003869 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 990288003870 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 990288003871 Domain of unknown function DUF; Region: DUF202; cl09954 990288003872 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 990288003873 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 990288003874 molybdopterin cofactor binding site; other site 990288003875 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 990288003876 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD...; Region: MopB_CT_2; cd02783 990288003877 putative molybdopterin cofactor binding site; other site 990288003878 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 990288003879 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl04869 990288003880 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288003881 NAD(P) binding site [chemical binding]; other site 990288003882 active site 990288003883 Domain of unknown function DUF; Region: DUF202; cl09954 990288003884 molybdenum cofactor biosynthesis protein A, bacterial; Region: moaA; TIGR02666 990288003885 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 990288003886 FeS/SAM binding site; other site 990288003887 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 990288003888 Baculoviral E56 protein, specific to ODV envelope; Region: Baculo_E56; pfam04639 990288003889 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288003890 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 990288003891 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 990288003892 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 990288003893 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 990288003894 dimerization interface [polypeptide binding]; other site 990288003895 putative transposase OrfB; Reviewed; Region: PHA02517 990288003896 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 990288003897 Integrase core domain; Region: rve; cl01316 990288003898 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 990288003899 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 990288003900 Transposase domain (DUF772); Region: DUF772; cl12084 990288003901 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288003902 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 990288003903 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 990288003904 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 990288003905 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 990288003906 Outer membrane efflux protein; Region: OEP; pfam02321 990288003907 Outer membrane efflux protein; Region: OEP; pfam02321 990288003908 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 990288003909 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 990288003910 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 990288003911 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl15297 990288003912 siderophore transporter, RhtX/FptX family; Region: sider_RhtX_FptX; TIGR02718 990288003913 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; cl11420 990288003914 Cytochrome c; Region: Cytochrom_C; cl11414 990288003915 The Delta12 Fatty Acid Desaturase (Delta12-FADS)-like CD includes the integral-membrane enzymes, delta-12 acyl-lipid desaturases, oleate 12-hydroxylases, omega3 and omega6 fatty acid desaturases, and other related proteins, found in a wide range of...; Region: Delta12-FADS-like; cd03507 990288003916 Fatty acid desaturase; Region: FA_desaturase; pfam00487 990288003917 putative di-iron ligands [ion binding]; other site 990288003918 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 990288003919 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 990288003920 putative NAD(P) binding site [chemical binding]; other site 990288003921 active site 990288003922 putative substrate binding site [chemical binding]; other site 990288003923 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 990288003924 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 990288003925 NADP binding site [chemical binding]; other site 990288003926 homopentamer interface [polypeptide binding]; other site 990288003927 substrate binding site [chemical binding]; other site 990288003928 active site 990288003929 putative cation:proton antiport protein; Provisional; Region: PRK10669 990288003930 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 990288003931 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 990288003932 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288003933 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 990288003934 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 990288003935 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 990288003936 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 990288003937 putative molybdopterin cofactor binding site [chemical binding]; other site 990288003938 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT)...; Region: MopB_CT_ydeP; cd02787 990288003939 putative molybdopterin cofactor binding site; other site 990288003940 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 990288003941 arginine decarboxylase; Provisional; Region: PRK05354 990288003942 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 990288003943 dimer interface [polypeptide binding]; other site 990288003944 active site 990288003945 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 990288003946 catalytic residues [active] 990288003947 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 990288003948 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 990288003949 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 990288003950 putative active site [active] 990288003951 PhoH-like protein; Region: PhoH; cl12134 990288003952 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...; Region: PRX_BCP; cd03017 990288003953 catalytic triad [active] 990288003954 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 990288003955 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 990288003956 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 990288003957 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 990288003958 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB2; cd01048 990288003959 diiron binding motif [ion binding]; other site 990288003960 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288003961 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 990288003962 Transposase; Region: DEDD_Tnp_IS110; pfam01548 990288003963 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 990288003964 ribulose bisphosphate carboxylase; Provisional; Region: PRK13475 990288003965 Ribulose bisphosphate carboxylase large chain, Form II; Region: RuBisCO_large_II; cd08211 990288003966 dimer interface [polypeptide binding]; other site 990288003967 active site 990288003968 catalytic residue [active] 990288003969 metal binding site [ion binding]; metal-binding site 990288003970 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 990288003971 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 990288003972 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 990288003973 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 990288003974 sequence-specific DNA binding site [nucleotide binding]; other site 990288003975 salt bridge; other site 990288003976 Cupin domain; Region: Cupin_2; cl09118 990288003977 hydrogenase 4 subunit B; Validated; Region: PRK06521 990288003978 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 990288003979 NADH dehydrogenase; Region: NADHdh; cl00469 990288003980 Hydrogenase 4 membrane component (E) [Energy production and conversion]; Region: HyfE; cl12087 990288003981 hydrogenase 4 subunit F; Validated; Region: PRK06458 990288003982 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 990288003983 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 990288003984 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 990288003985 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 990288003986 DNA-binding transcriptional regulator DsdC; Provisional; Region: PRK10086 990288003987 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 990288003988 putative dimerization interface [polypeptide binding]; other site 990288003989 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 990288003990 DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and...; Region: DOPA_deC_like; cd06450 990288003991 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288003992 catalytic residue [active] 990288003993 aromatic acid decarboxylase; Validated; Region: PRK05920 990288003994 Flavoprotein; Region: Flavoprotein; cl08021 990288003995 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 990288003996 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 990288003997 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 990288003998 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 990288003999 ThiS interaction site; other site 990288004000 putative active site [active] 990288004001 tetramer interface [polypeptide binding]; other site 990288004002 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 990288004003 thiS-thiF/thiG interaction site; other site 990288004004 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 990288004005 dinuclear metal binding motif [ion binding]; other site 990288004006 Anti-sigma-K factor rskA; Region: RskA; cl02208 990288004007 RNA polymerase sigma factor; Provisional; Region: PRK12514 990288004008 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 990288004009 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 990288004010 DNA binding residues [nucleotide binding] 990288004011 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 990288004012 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation...; Region: AlaRS_core; cd00673 990288004013 motif 1; other site 990288004014 active site 990288004015 motif 2; other site 990288004016 motif 3; other site 990288004017 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 990288004018 DHHA1 domain; Region: DHHA1; pfam02272 990288004019 RecX family; Region: RecX; cl00936 990288004020 recombinase A; Provisional; Region: recA; PRK09354 990288004021 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 990288004022 hexamer interface [polypeptide binding]; other site 990288004023 Walker A motif; other site 990288004024 ATP binding site [chemical binding]; other site 990288004025 Walker B motif; other site 990288004026 Competence-damaged protein; Region: CinA; cl00666 990288004027 thiamine monophosphate kinase; Provisional; Region: PRK05731 990288004028 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 990288004029 ATP binding site [chemical binding]; other site 990288004030 dimerization interface [polypeptide binding]; other site 990288004031 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 990288004032 active site 990288004033 HIGH motif; other site 990288004034 nucleotide binding site [chemical binding]; other site 990288004035 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 990288004036 KMSKS motif; other site 990288004037 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 990288004038 Sugar fermentation stimulation protein; Region: SfsA; cl00647 990288004039 methionine aminopeptidase; Reviewed; Region: PRK07281 990288004040 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 990288004041 active site 990288004042 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 990288004043 UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: GlnD; COG2844 990288004044 metal binding triad; other site 990288004045 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 990288004046 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_UUR-like_1; cd04900 990288004047 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_ACR-UUR-like_2; cd04899 990288004048 Protein of unknown function (DUF489); Region: DUF489; cl01097 990288004049 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 990288004050 Mechanosensitive ion channel; Region: MS_channel; pfam00924 990288004051 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 990288004052 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 990288004053 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 990288004054 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 990288004055 nucleotide binding pocket [chemical binding]; other site 990288004056 K-X-D-G motif; other site 990288004057 catalytic site [active] 990288004058 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 990288004059 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 990288004060 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 990288004061 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 990288004062 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 990288004063 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 990288004064 Walker A/P-loop; other site 990288004065 ATP binding site [chemical binding]; other site 990288004066 Q-loop/lid; other site 990288004067 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 990288004068 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 990288004069 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 990288004070 ABC transporter signature motif; other site 990288004071 Walker B; other site 990288004072 D-loop; other site 990288004073 H-loop/switch region; other site 990288004074 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 990288004075 potential frameshift: common BLAST hit: gi|218665880|ref|YP_002425208.1| FAD-dependent oxidoreductase 990288004076 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 990288004077 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 990288004078 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]; Region: COG2231 990288004079 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 990288004080 minor groove reading motif; other site 990288004081 helix-hairpin-helix signature motif; other site 990288004082 substrate binding pocket [chemical binding]; other site 990288004083 active site 990288004084 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 990288004085 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 990288004086 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 990288004087 probable active site [active] 990288004088 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 990288004089 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 990288004090 ScpA/B protein; Region: ScpA_ScpB; cl00598 990288004091 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 990288004092 active site 990288004093 HIGH motif; other site 990288004094 dimer interface [polypeptide binding]; other site 990288004095 KMSKS motif; other site 990288004096 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 990288004097 active site 990288004098 putative substrate binding region [chemical binding]; other site 990288004099 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 990288004100 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 990288004101 Ligand Binding Site [chemical binding]; other site 990288004102 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 990288004103 dinuclear metal binding motif [ion binding]; other site 990288004104 Mechanosensitive ion channel; Region: MS_channel; pfam00924 990288004105 gamma-glutamyl kinase; Provisional; Region: PRK05429 990288004106 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 990288004107 nucleotide binding site [chemical binding]; other site 990288004108 homotetrameric interface [polypeptide binding]; other site 990288004109 putative phosphate binding site [ion binding]; other site 990288004110 putative allosteric binding site; other site 990288004111 PUA domain; Region: PUA; cl00607 990288004112 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 990288004113 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 990288004114 Response regulator receiver domain; Region: Response_reg; pfam00072 990288004115 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 990288004116 active site 990288004117 phosphorylation site [posttranslational modification] 990288004118 intermolecular recognition site; other site 990288004119 dimerization interface [polypeptide binding]; other site 990288004120 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 990288004121 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 990288004122 GAF domain; Region: GAF; cl00853 990288004123 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 990288004124 PAS fold; Region: PAS_4; pfam08448 990288004125 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 990288004126 PAS fold; Region: PAS_3; pfam08447 990288004127 putative active site [active] 990288004128 heme pocket [chemical binding]; other site 990288004129 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 990288004130 GAF domain; Region: GAF; cl00853 990288004131 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 trans-...; Region: HisKA; cd00082 990288004132 dimer interface [polypeptide binding]; other site 990288004133 phosphorylation site [posttranslational modification] 990288004134 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 990288004135 ATP binding site [chemical binding]; other site 990288004136 Mg2+ binding site [ion binding]; other site 990288004137 G-X-G motif; other site 990288004138 Response regulator receiver domain; Region: Response_reg; pfam00072 990288004139 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 990288004140 active site 990288004141 phosphorylation site [posttranslational modification] 990288004142 intermolecular recognition site; other site 990288004143 dimerization interface [polypeptide binding]; other site 990288004144 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 990288004145 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 990288004146 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 990288004147 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...; Region: DnaE_OBF; cd04485 990288004148 generic binding surface I; other site 990288004149 generic binding surface II; other site 990288004150 Y-family of DNA polymerases; Region: PolY; cl12025 990288004151 active site 990288004152 DNA binding site [nucleotide binding] 990288004153 Cell division inhibitor SulA; Region: SulA; cl01880 990288004154 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288004155 LexA repressor; Validated; Region: PRK00215 990288004156 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 (...; Region: S24_LexA-like; cd06529 990288004157 Catalytic site [active] 990288004158 Protein required for attachment to host cells; Region: Host_attach; cl02398 990288004159 Predicted membrane protein [Function unknown]; Region: COG2860 990288004160 UPF0126 domain; Region: UPF0126; pfam03458 990288004161 UPF0126 domain; Region: UPF0126; pfam03458 990288004162 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 990288004163 putative mercuric reductase; Provisional; Region: PRK13748 990288004164 metal-binding site [ion binding] 990288004165 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288004166 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 990288004167 sucrose synthase; Region: sucr_synth; TIGR02470 990288004168 This family is most closely related to the GT1 family of glycosyltransferases. The sucrose-phosphate synthases in this family may be unique to plants and photosynthetic bacteria. This enzyme catalyzes the synthesis of sucrose 6-phosphate from fructose...; Region: GT1_Sucrose_synthase; cd03800 990288004169 putative ADP-binding pocket [chemical binding]; other site 990288004170 sucrose-phosphate synthase, putative, glycosyltransferase domain; Region: sucr_P_syn_N; TIGR02472 990288004171 This family is most closely related to the GT1 family of glycosyltransferases. The sucrose-phosphate synthases in this family may be unique to plants and photosynthetic bacteria. This enzyme catalyzes the synthesis of sucrose 6-phosphate from fructose...; Region: GT1_Sucrose_synthase; cd03800 990288004172 putative ADP-binding pocket [chemical binding]; other site 990288004173 sucrose phosphate synthase, sucrose phosphatase-like domain, bacterial; Region: sucr_syn_bact_C; TIGR02471 990288004174 pfkB family carbohydrate kinase; Region: PfkB; pfam00294 990288004175 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 990288004176 putative substrate binding site [chemical binding]; other site 990288004177 putative ATP binding site [chemical binding]; other site 990288004178 Mechanosensitive ion channel; Region: MS_channel; pfam00924 990288004179 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 990288004180 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 990288004181 dimer interface [polypeptide binding]; other site 990288004182 conserved gate region; other site 990288004183 putative PBP binding loops; other site 990288004184 ABC-ATPase subunit interface; other site 990288004185 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 990288004186 dimer interface [polypeptide binding]; other site 990288004187 conserved gate region; other site 990288004188 putative PBP binding loops; other site 990288004189 ABC-ATPase subunit interface; other site 990288004190 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 990288004191 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 990288004192 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 990288004193 active site 990288004194 Riboflavin kinase; Region: Flavokinase; cl03312 990288004195 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 990288004196 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 990288004197 active site 990288004198 HIGH motif; other site 990288004199 nucleotide binding site [chemical binding]; other site 990288004200 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 990288004201 active site 990288004202 KMSKS motif; other site 990288004203 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 990288004204 tRNA binding surface [nucleotide binding]; other site 990288004205 anticodon binding site; other site 990288004206 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 990288004207 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 990288004208 bacteriophage N4 adsorption protein B; Provisional; Region: nfrB; PRK11234 990288004209 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 990288004210 putative catalytic residue [active] 990288004211 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 990288004212 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 990288004213 Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed...; Region: ABCD_peroxisomal_ALDP; cd03223 990288004214 DsrE/DsrF-like family; Region: DrsE; cl00672 990288004215 Predicted amidohydrolase [General function prediction only]; Region: COG0388 990288004216 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 990288004217 putative active site [active] 990288004218 catalytic triad [active] 990288004219 dimer interface [polypeptide binding]; other site 990288004220 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 990288004221 active site 990288004222 metal binding site [ion binding]; metal-binding site 990288004223 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 990288004224 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 990288004225 catalytic residues [active] 990288004226 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 990288004227 GSH binding site [chemical binding]; other site 990288004228 catalytic residues [active] 990288004229 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 990288004230 active site residue [active] 990288004231 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 990288004232 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 990288004233 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 990288004234 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 990288004235 Outer membrane efflux protein; Region: OEP; pfam02321 990288004236 Outer membrane efflux protein; Region: OEP; pfam02321 990288004237 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 990288004238 dimerization interface [polypeptide binding]; other site 990288004239 putative DNA binding site [nucleotide binding]; other site 990288004240 putative Zn2+ binding site [ion binding]; other site 990288004241 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 990288004242 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 990288004243 SCP-2 sterol transfer family; Region: SCP2; cl01225 990288004244 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 990288004245 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-...; Region: YgdL_like; cd00755 990288004246 putative ATP binding site [chemical binding]; other site 990288004247 putative substrate interface [chemical binding]; other site 990288004248 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 990288004249 active site 990288004250 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288004251 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 990288004252 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 990288004253 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288004254 Membrane fusogenic activity; Region: BMFP; cl01115 990288004255 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 990288004256 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288004257 Domain of unknown function DUF; Region: DUF202; cl09954 990288004258 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 990288004259 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 990288004260 ketol-acid reductoisomerase; Provisional; Region: PRK05479 990288004261 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288004262 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 990288004263 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 990288004264 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 990288004265 putative valine binding site [chemical binding]; other site 990288004266 dimer interface [polypeptide binding]; other site 990288004267 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 990288004268 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 990288004269 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 990288004270 PYR/PP interface [polypeptide binding]; other site 990288004271 dimer interface [polypeptide binding]; other site 990288004272 TPP binding site [chemical binding]; other site 990288004273 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 990288004274 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 990288004275 TPP-binding site [chemical binding]; other site 990288004276 dimer interface [polypeptide binding]; other site 990288004277 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 990288004278 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288004279 Walker A/P-loop; other site 990288004280 ATP binding site [chemical binding]; other site 990288004281 Q-loop/lid; other site 990288004282 ABC transporter signature motif; other site 990288004283 Walker B; other site 990288004284 D-loop; other site 990288004285 H-loop/switch region; other site 990288004286 Uncharacterised protein family UPF0047; Region: UPF0047; cl00439 990288004287 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 990288004288 nucleoside/Zn binding site; other site 990288004289 dimer interface [polypeptide binding]; other site 990288004290 catalytic motif [active] 990288004291 Competence protein A; Region: Competence_A; pfam11104 990288004292 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 990288004293 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 990288004294 Pilus assembly protein, PilO; Region: PilO; cl01234 990288004295 Pilus assembly protein, PilP; Region: PilP; cl01235 990288004296 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 990288004297 Secretin and TonB N terminus short domain; Region: STN; cl06624 990288004298 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 990288004299 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 990288004300 shikimate kinase; Reviewed; Region: aroK; PRK00131 990288004301 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...; Region: SK; cd00464 990288004302 ADP binding site [chemical binding]; other site 990288004303 magnesium binding site [ion binding]; other site 990288004304 putative shikimate binding site; other site 990288004305 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 990288004306 active site 990288004307 dimer interface [polypeptide binding]; other site 990288004308 metal binding site [ion binding]; metal-binding site 990288004309 Thymidylate synthase complementing protein; Region: Thy1; cl03630 990288004310 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 990288004311 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 990288004312 Zn2+ binding site [ion binding]; other site 990288004313 Mg2+ binding site [ion binding]; other site 990288004314 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 990288004315 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 990288004316 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The N-...; Region: GltS; cd00713 990288004317 active site 990288004318 dimer interface [polypeptide binding]; other site 990288004319 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 990288004320 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant...; Region: GltS_FMN; cd02808 990288004321 active site 990288004322 FMN binding site [chemical binding]; other site 990288004323 substrate binding site [chemical binding]; other site 990288004324 3Fe-4S cluster binding site [ion binding]; other site 990288004325 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 990288004326 domain interface; other site 990288004327 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 990288004328 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288004329 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 990288004330 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This...; Region: URO-D; cd00717 990288004331 substrate binding site [chemical binding]; other site 990288004332 active site 990288004333 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 990288004334 putative acyl-acceptor binding pocket; other site 990288004335 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 990288004336 adenylosuccinate synthetase; Provisional; Region: PRK01117 990288004337 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 r-...; Region: AdSS; cd03108 990288004338 GDP-binding site [chemical binding]; other site 990288004339 ACT binding site; other site 990288004340 IMP binding site; other site 990288004341 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 990288004342 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 990288004343 dimer interface [polypeptide binding]; other site 990288004344 motif 1; other site 990288004345 active site 990288004346 motif 2; other site 990288004347 motif 3; other site 990288004348 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 990288004349 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 990288004350 HflK protein; Region: hflK; TIGR01933 990288004351 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 990288004352 HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual...; Region: HflX; cd01878 990288004353 G1 box; other site 990288004354 GTP/Mg2+ binding site [chemical binding]; other site 990288004355 Switch I region; other site 990288004356 G2 box; other site 990288004357 G3 box; other site 990288004358 Switch II region; other site 990288004359 G4 box; other site 990288004360 G5 box; other site 990288004361 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 990288004362 Sm1 motif; other site 990288004363 intra - hexamer interaction site; other site 990288004364 inter - hexamer interaction site [polypeptide binding]; other site 990288004365 nucleotide binding pocket [chemical binding]; other site 990288004366 Sm2 motif; other site 990288004367 Phosphoenolpyruvate carboxylase [Carbohydrate transport and metabolism; Energy production and conversion]; Region: COG1892; cl14656 990288004368 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 990288004369 Maf-like protein; Region: Maf; pfam02545 990288004370 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 990288004371 active site 990288004372 dimer interface [polypeptide binding]; other site 990288004373 Integrase core domain; Region: rve; cl01316 990288004374 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 990288004375 Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]; Region: COG4705 990288004376 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 990288004377 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 990288004378 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 990288004379 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004380 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004381 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 990288004382 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 990288004383 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 990288004384 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 990288004385 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288004386 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 990288004387 dimerization interface [polypeptide binding]; other site 990288004388 putative DNA binding site [nucleotide binding]; other site 990288004389 putative Zn2+ binding site [ion binding]; other site 990288004390 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004391 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004392 transposase; Provisional; Region: PRK06526 990288004393 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288004394 Walker A motif; other site 990288004395 ATP binding site [chemical binding]; other site 990288004396 Walker B motif; other site 990288004397 Integrase core domain; Region: rve; cl01316 990288004398 Transposase domain (DUF772); Region: DUF772; cl12084 990288004399 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288004400 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 990288004401 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 990288004402 DNA binding site [nucleotide binding] 990288004403 Int/Topo IB signature motif; other site 990288004404 active site 990288004405 TspO/MBR family; Region: TspO_MBR; cl01379 990288004406 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 990288004407 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 990288004408 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 990288004409 GIY-YIG motif/motif A; other site 990288004410 active site 990288004411 catalytic site [active] 990288004412 putative DNA binding site [nucleotide binding]; other site 990288004413 metal binding site [ion binding]; metal-binding site 990288004414 UvrB/uvrC motif; Region: UVR; pfam02151 990288004415 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 990288004416 Protein of unknown function (DUF971); Region: DUF971; cl01414 990288004417 translation elongation factor P; Region: efp; TIGR00038 990288004418 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 990288004419 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-...; Region: S1_EF-P_repeat_1; cd04470 990288004420 RNA binding site [nucleotide binding]; other site 990288004421 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-...; Region: S1_EF-P_repeat_2; cd05794 990288004422 RNA binding site [nucleotide binding]; other site 990288004423 hypothetical protein; Provisional; Region: PRK11770 990288004424 Domain of unknown function (DUF307); Region: DUF307; pfam03733 990288004425 Septum formation initiator; Region: DivIC; cl11433 990288004426 enolase; Provisional; Region: eno; PRK00077 990288004427 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 990288004428 dimer interface [polypeptide binding]; other site 990288004429 metal binding site [ion binding]; metal-binding site 990288004430 substrate binding pocket [chemical binding]; other site 990288004431 NeuB family; Region: NeuB; cl00496 990288004432 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 990288004433 CTP synthetase; Validated; Region: pyrG; PRK05380 990288004434 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer...; Region: CTGs; cd03113 990288004435 UTP binding site [chemical binding]; other site 990288004436 Active site [active] 990288004437 Catalytic site [active] 990288004438 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 990288004439 active site 990288004440 putative oxyanion hole; other site 990288004441 catalytic triad [active] 990288004442 excinuclease ABC subunit B; Provisional; Region: PRK05298 990288004443 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 990288004444 ATP binding site [chemical binding]; other site 990288004445 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 990288004446 nucleotide binding region [chemical binding]; other site 990288004447 ATP-binding site [chemical binding]; other site 990288004448 Ultra-violet resistance protein B; Region: UvrB; pfam12344 990288004449 UvrB/uvrC motif; Region: UVR; pfam02151 990288004450 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 990288004451 Integrase core domain; Region: rve; cl01316 990288004452 Domain of unknown function (DUF1818); Region: DUF1818; pfam08848 990288004453 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288004454 Walker A motif; other site 990288004455 ATP binding site [chemical binding]; other site 990288004456 Walker B motif; other site 990288004457 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004458 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004459 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 990288004460 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 990288004461 Phage integrase family; Region: Phage_integrase; pfam00589 990288004462 DNA binding site [nucleotide binding] 990288004463 Int/Topo IB signature motif; other site 990288004464 active site 990288004465 Protein of unknown function (DUF2614); Region: DUF2614; cl07936 990288004466 Double zinc ribbon; Region: DZR; pfam12773 990288004467 Double zinc ribbon; Region: DZR; pfam12773 990288004468 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004469 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004470 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 990288004471 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 990288004472 ATP binding site [chemical binding]; other site 990288004473 Mg++ binding site [ion binding]; other site 990288004474 motif III; other site 990288004475 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 990288004476 nucleotide binding region [chemical binding]; other site 990288004477 ATP-binding site [chemical binding]; other site 990288004478 High potential iron-sulfur protein; Region: HIPIP; pfam01355 990288004479 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 990288004480 catalytic triad [active] 990288004481 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 990288004482 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl00412 990288004483 glutamine synthetase; Provisional; Region: glnA; PRK09469 990288004484 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 990288004485 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 990288004486 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 990288004487 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 990288004488 active site 990288004489 phosphorylation site [posttranslational modification] 990288004490 intermolecular recognition site; other site 990288004491 dimerization interface [polypeptide binding]; other site 990288004492 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288004493 Walker A motif; other site 990288004494 ATP binding site [chemical binding]; other site 990288004495 Walker B motif; other site 990288004496 arginine finger; other site 990288004497 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 990288004498 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 990288004499 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 990288004500 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 trans-...; Region: HisKA; cd00082 990288004501 dimer interface [polypeptide binding]; other site 990288004502 phosphorylation site [posttranslational modification] 990288004503 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 990288004504 ATP binding site [chemical binding]; other site 990288004505 Mg2+ binding site [ion binding]; other site 990288004506 G-X-G motif; other site 990288004507 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 990288004508 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-...; Region: Ntn_hydrolase; cl00467 990288004509 active site 990288004510 RNA polymerase factor sigma-70; Validated; Region: PRK09047 990288004511 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 990288004512 DNA binding residues [nucleotide binding] 990288004513 Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156; Region: CsoR-like_DUF156; cd10148 990288004514 putative homotetramer interface [polypeptide binding]; other site 990288004515 putative homodimer interface [polypeptide binding]; other site 990288004516 putative allosteric switch controlling residues; other site 990288004517 putative metal binding site [ion binding]; other site 990288004518 putative homodimer-homodimer interface [polypeptide binding]; other site 990288004519 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 990288004520 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 990288004521 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 990288004522 Outer membrane efflux protein; Region: OEP; pfam02321 990288004523 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 990288004524 metal-binding site [ion binding] 990288004525 Domain of unknown function DUF302; Region: DUF302; cl01364 990288004526 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 990288004527 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 990288004528 metal-binding site [ion binding] 990288004529 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 990288004530 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 990288004531 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 990288004532 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 990288004533 Predicted permease; Region: DUF318; cl00487 990288004534 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 990288004535 dimerization interface [polypeptide binding]; other site 990288004536 putative DNA binding site [nucleotide binding]; other site 990288004537 putative Zn2+ binding site [ion binding]; other site 990288004538 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 990288004539 glutaredoxin 2; Provisional; Region: PRK10387 990288004540 C-terminal domain interface [polypeptide binding]; other site 990288004541 GSH binding site (G-site) [chemical binding]; other site 990288004542 dimer interface [polypeptide binding]; other site 990288004543 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 990288004544 dimer interface [polypeptide binding]; other site 990288004545 substrate binding pocket (H-site) [chemical binding]; other site 990288004546 N-terminal domain interface [polypeptide binding]; other site 990288004547 Predicted membrane protein (DUF2078); Region: DUF2078; cl01373 990288004548 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 990288004549 S-adenosylmethionine binding site [chemical binding]; other site 990288004550 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288004551 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 990288004552 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 990288004553 dimerization interface [polypeptide binding]; other site 990288004554 putative DNA binding site [nucleotide binding]; other site 990288004555 putative Zn2+ binding site [ion binding]; other site 990288004556 Major Facilitator Superfamily; Region: MFS_1; pfam07690 990288004557 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 990288004558 putative substrate translocation pore; other site 990288004559 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 990288004560 putative substrate translocation pore; other site 990288004561 DsrE/DsrF-like family; Region: DrsE; cl00672 990288004562 OsmC-like protein; Region: OsmC; cl00767 990288004563 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 990288004564 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 990288004565 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 990288004566 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 990288004567 DsbD alpha interface [polypeptide binding]; other site 990288004568 catalytic residues [active] 990288004569 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288004570 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288004571 Protein of unknown function (DUF692); Region: DUF692; cl01263 990288004572 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288004573 disulfide isomerase/thiol-disulfide oxidase; Provisional; Region: dsbG; PRK11657 990288004574 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 990288004575 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 990288004576 putative active site [active] 990288004577 catalytic triad [active] 990288004578 putative dimer interface [polypeptide binding]; other site 990288004579 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 990288004580 active site 990288004581 DNA polymerase IV; Validated; Region: PRK02406 990288004582 DNA binding site [nucleotide binding] 990288004583 potential frameshift: common BLAST hit: gi|218668077|ref|YP_002425766.1| ISAfe2, transposase 990288004584 Transposase, Mutator family; Region: Transposase_mut; pfam00872 990288004585 MULE transposase domain; Region: MULE; pfam10551 990288004586 Transposase, Mutator family; Region: Transposase_mut; pfam00872 990288004587 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 990288004588 Transposase; Region: DEDD_Tnp_IS110; pfam01548 990288004589 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 990288004590 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 990288004591 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 990288004592 ligand binding site [chemical binding]; other site 990288004593 flexible hinge region; other site 990288004594 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 990288004595 putative switch regulator; other site 990288004596 non-specific DNA interactions [nucleotide binding]; other site 990288004597 DNA binding site [nucleotide binding] 990288004598 sequence specific DNA binding site [nucleotide binding]; other site 990288004599 putative cAMP binding site [chemical binding]; other site 990288004600 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 990288004601 heme-binding site [chemical binding]; other site 990288004602 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 990288004603 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 990288004604 catalytic loop [active] 990288004605 iron binding site [ion binding]; other site 990288004606 The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S]...; Region: O2ase_reductase_like; cd06187 990288004607 FAD binding pocket [chemical binding]; other site 990288004608 FAD binding motif [chemical binding]; other site 990288004609 phosphate binding motif [ion binding]; other site 990288004610 beta-alpha-beta structure motif; other site 990288004611 NAD binding pocket [chemical binding]; other site 990288004612 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288004613 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 L-...; Region: GCS_H; cd06848 990288004614 lipoyl attachment site [posttranslational modification]; other site 990288004615 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 990288004616 endonuclease III; Region: ENDO3c; smart00478 990288004617 minor groove reading motif; other site 990288004618 helix-hairpin-helix signature motif; other site 990288004619 substrate binding pocket [chemical binding]; other site 990288004620 active site 990288004621 The Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_like_1; cd09319 990288004622 C4-dicarboxylate transporter/malic acid transport protein; Region: C4dic_mal_tran; pfam03595 990288004623 gating phenylalanine in ion channel; other site 990288004624 GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing...; Region: GST_N_GTT2_like; cd03051 990288004625 putative C-terminal domain interface [polypeptide binding]; other site 990288004626 putative dimer interface [polypeptide binding]; other site 990288004627 putative GSH binding site (G-site) [chemical binding]; other site 990288004628 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 990288004629 N-terminal domain interface [polypeptide binding]; other site 990288004630 dimer interface [polypeptide binding]; other site 990288004631 substrate binding pocket (H-site) [chemical binding]; other site 990288004632 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004633 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004634 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 990288004635 Uncharacterized conserved protein [Function unknown]; Region: COG3945 990288004636 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 990288004637 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate...; Region: MopB_Nitrate-R-NarG-like; cd02750 990288004638 [4Fe-4S] binding site [ion binding]; other site 990288004639 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 990288004640 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 990288004641 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 990288004642 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 990288004643 molybdopterin cofactor binding site; other site 990288004644 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 990288004645 4Fe-4S binding domain; Region: Fer4; cl02805 990288004646 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 990288004647 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 990288004648 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 990288004649 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 990288004650 putative substrate translocation pore; other site 990288004651 Protein of unknown function, DUF488; Region: DUF488; cl01246 990288004652 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 990288004653 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 990288004654 Uncharacterized protein conserved in archaea (DUF2114); Region: DUF2114; cl01680 990288004655 Integrase core domain; Region: rve; cl01316 990288004656 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004657 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004658 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288004659 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 990288004660 Walker A motif; other site 990288004661 ATP binding site [chemical binding]; other site 990288004662 Walker B motif; other site 990288004663 NodT family; Region: outer_NodT; TIGR01845 990288004664 Outer membrane efflux protein; Region: OEP; pfam02321 990288004665 Outer membrane efflux protein; Region: OEP; pfam02321 990288004666 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 990288004667 putative substrate translocation pore; other site 990288004668 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 990288004669 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288004670 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 990288004671 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 990288004672 dimerization interface [polypeptide binding]; other site 990288004673 Transposase domain (DUF772); Region: DUF772; cl12084 990288004674 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288004675 putative transposase OrfB; Reviewed; Region: PHA02517 990288004676 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 990288004677 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 990288004678 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 990288004679 active site 990288004680 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 990288004681 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 990288004682 Domain of unknown function DUF20; Region: UPF0118; cl00465 990288004683 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 990288004684 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 990288004685 Domain of unknown function DUF20; Region: UPF0118; cl00465 990288004686 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288004687 protoporphyrinogen oxidase; Region: proto_IX_ox; TIGR00562 990288004688 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 990288004689 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 990288004690 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 990288004691 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 990288004692 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 four-...; Region: RecG_wedge_OBF; cd04488 990288004693 ssDNA binding site; other site 990288004694 generic binding surface II; other site 990288004695 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 990288004696 ATP binding site [chemical binding]; other site 990288004697 putative Mg++ binding site [ion binding]; other site 990288004698 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 990288004699 nucleotide binding region [chemical binding]; other site 990288004700 ATP-binding site [chemical binding]; other site 990288004701 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 990288004702 YjgF, YER057c, and UK114 belong to a large family of 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 similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 990288004703 homotrimer interaction site [polypeptide binding]; other site 990288004704 putative active site [active] 990288004705 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 990288004706 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 990288004707 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 990288004708 synthetase active site [active] 990288004709 NTP binding site [chemical binding]; other site 990288004710 metal binding site [ion binding]; metal-binding site 990288004711 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named...; Region: TGS_RelA_SpoT; cd01668 990288004712 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 990288004713 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 990288004714 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and...; Region: GMPK; cd00071 990288004715 catalytic site [active] 990288004716 G-X2-G-X-G-K; other site 990288004717 hypothetical protein; Provisional; Region: PRK11820 990288004718 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 990288004719 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 990288004720 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 990288004721 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 990288004722 metal binding triad; other site 990288004723 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 990288004724 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 990288004725 metal binding triad; other site 990288004726 branched-chain amino acid aminotransferase; Provisional; Region: PRK12479 990288004727 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 alpha-...; Region: BCAT_beta_family; cd01557 990288004728 homodimer interface [polypeptide binding]; other site 990288004729 substrate-cofactor binding pocket; other site 990288004730 catalytic residue [active] 990288004731 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 990288004732 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 990288004733 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 990288004734 DsbD alpha interface [polypeptide binding]; other site 990288004735 catalytic residues [active] 990288004736 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 990288004737 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288004738 metal binding site [ion binding]; metal-binding site 990288004739 active site 990288004740 I-site; other site 990288004741 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is...; Region: Trunc_globin; cd00454 990288004742 apolar tunnel; other site 990288004743 heme binding site [chemical binding]; other site 990288004744 dimerization interface [polypeptide binding]; other site 990288004745 Protein of unknown function (DUF3034); Region: DUF3034; pfam11231 990288004746 CrcB-like protein; Region: CRCB; cl09114 990288004747 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 990288004748 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 990288004749 Phage integrase family; Region: Phage_integrase; pfam00589 990288004750 DNA binding site [nucleotide binding] 990288004751 Int/Topo IB signature motif; other site 990288004752 active site 990288004753 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 990288004754 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 990288004755 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 990288004756 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 990288004757 active site 990288004758 metal binding site [ion binding]; metal-binding site 990288004759 D5 N terminal like; Region: D5_N; cl07360 990288004760 C-terminal domain; Region: primase_Cterm; TIGR01613 990288004761 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 990288004762 generic binding surface I; other site 990288004763 generic binding surface II; other site 990288004764 Restriction endonuclease; Region: Mrr_cat; cl00747 990288004765 integrase; Provisional; Region: PRK09692 990288004766 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 990288004767 DNA binding site [nucleotide binding] 990288004768 Int/Topo IB signature motif; other site 990288004769 active site 990288004770 potential frameshift: common BLAST hit: gi|218667415|ref|YP_002425496.1| HNH endonuclease domain protein 990288004771 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins...; Region: HNHc; cd00085 990288004772 active site 990288004773 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288004774 4-hydroxyphenylacetate catabolism regulatory protein HpaA; Region: HpaA; TIGR02297 990288004775 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004776 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004777 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 990288004778 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 four-...; Region: RecG_wedge_OBF; cd04488 990288004779 generic binding surface II; other site 990288004780 ssDNA binding site; other site 990288004781 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 990288004782 putative Mg++ binding site [ion binding]; other site 990288004783 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 990288004784 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 990288004785 nucleotide binding region [chemical binding]; other site 990288004786 ATP-binding site [chemical binding]; other site 990288004787 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 990288004788 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 990288004789 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288004790 PRTRC system protein D; Region: PRTRC_D; TIGR03739 990288004791 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 990288004792 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 990288004793 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl14888 990288004794 AntA/AntB antirepressor; Region: AntA; cl01430 990288004795 MT-A70; Region: MT-A70; cl01947 990288004796 Type II/IV secretion system protein; Region: GSPII_E; pfam00437 990288004797 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...; Region: VirB11-like_ATPase; cd01130 990288004798 Walker A motif; other site 990288004799 hexamer interface [polypeptide binding]; other site 990288004800 ATP binding site [chemical binding]; other site 990288004801 Walker B motif; other site 990288004802 Peptidase family M48; Region: Peptidase_M48; cl12018 990288004803 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 990288004804 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 990288004805 VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 990288004806 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004807 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004808 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314; cl02193 990288004809 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004810 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004811 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 990288004812 VirB8 protein; Region: VirB8; cl01500 990288004813 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 990288004814 VirB7 interaction site; other site 990288004815 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 990288004816 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 990288004817 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 990288004818 Type II/IV secretion system protein; Region: GSPII_E; pfam00437 990288004819 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288004820 Walker A motif; other site 990288004821 ATP binding site [chemical binding]; other site 990288004822 Walker B motif; other site 990288004823 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 990288004824 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 990288004825 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 990288004826 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 990288004827 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288004828 Walker A motif; other site 990288004829 ATP binding site [chemical binding]; other site 990288004830 Walker B motif; other site 990288004831 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004832 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004833 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases...; Region: lysozyme_like; cl00222 990288004834 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 990288004835 N-acetyl-D-glucosamine binding site [chemical binding]; other site 990288004836 catalytic residue [active] 990288004837 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 990288004838 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004839 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004840 ParB-like nuclease domain; Region: ParBc; cl02129 990288004841 RelB antitoxin; Region: RelB; cl01171 990288004842 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 990288004843 Transposase; Region: DEDD_Tnp_IS110; pfam01548 990288004844 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 990288004845 Primase C terminal 1 (PriCT-1); Region: PriCT_1; cl07362 990288004846 SET domain; Region: SET; cl02566 990288004847 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 990288004848 catalytic triad [active] 990288004849 conserved cis-peptide bond; other site 990288004850 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288004851 Transposase, Mutator family; Region: Transposase_mut; pfam00872 990288004852 MULE transposase domain; Region: MULE; pfam10551 990288004853 BsuBI/PstI restriction endonuclease C-terminus; Region: BsuBI_PstI_RE; pfam06616 990288004854 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 990288004855 transposase; Provisional; Region: PRK06526 990288004856 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288004857 Walker A motif; other site 990288004858 ATP binding site [chemical binding]; other site 990288004859 Walker B motif; other site 990288004860 Integrase core domain; Region: rve; cl01316 990288004861 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 990288004862 UvrD/REP helicase; Region: UvrD-helicase; cl14126 990288004863 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 990288004864 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 990288004865 N-acetyl-D-glucosamine binding site [chemical binding]; other site 990288004866 catalytic residue [active] 990288004867 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 990288004868 putative active site [active] 990288004869 catalytic site [active] 990288004870 Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins; Region: PLDc_unchar1_2; cd09128 990288004871 putative active site [active] 990288004872 putative catalytic site [active] 990288004873 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 990288004874 dimer interface [polypeptide binding]; other site 990288004875 ssDNA binding site [nucleotide binding]; other site 990288004876 tetramer (dimer of dimers) interface [polypeptide binding]; other site 990288004877 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004878 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004879 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004880 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004881 Predicted membrane protein [Function unknown]; Region: COG5373 990288004882 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 990288004883 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 990288004884 Integrase core domain; Region: rve; cl01316 990288004885 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 990288004886 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288004887 Walker A motif; other site 990288004888 ATP binding site [chemical binding]; other site 990288004889 Walker B motif; other site 990288004890 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 990288004891 active site 990288004892 metal binding site [ion binding]; metal-binding site 990288004893 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the...; Region: beta_clamp; cl02940 990288004894 putative DNA binding surface [nucleotide binding]; other site 990288004895 dimer interface [polypeptide binding]; other site 990288004896 beta-clamp/translesion DNA polymerase binding surface; other site 990288004897 beta-clamp/clamp loader binding surface; other site 990288004898 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 990288004899 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288004900 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288004901 Walker A/P-loop; other site 990288004902 Walker A/P-loop; other site 990288004903 ATP binding site [chemical binding]; other site 990288004904 ATP binding site [chemical binding]; other site 990288004905 Q-loop/lid; other site 990288004906 ABC transporter signature motif; other site 990288004907 Walker B; other site 990288004908 D-loop; other site 990288004909 H-loop/switch region; other site 990288004910 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288004911 ABC transporter signature motif; other site 990288004912 Walker B; other site 990288004913 D-loop; other site 990288004914 H-loop/switch region; other site 990288004915 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004916 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004917 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 990288004918 dimer interface [polypeptide binding]; other site 990288004919 putative radical transfer pathway; other site 990288004920 diiron center [ion binding]; other site 990288004921 tyrosyl radical; other site 990288004922 ParB-like nuclease domain; Region: ParBc; cl02129 990288004923 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 990288004924 PRTRC system protein E; Region: PRTRC_E; TIGR03741 990288004925 PRTRC system protein C; Region: PRTRC_C; TIGR03738 990288004926 PRTRC system protein F; Region: PRTRC_F; TIGR03742 990288004927 PRTRC system protein B; Region: PRTRC_B; TIGR03737 990288004928 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cd01483 990288004929 PRTRC system ThiF family protein; Region: PRTRC_ThiF; TIGR03736 990288004930 ATP binding site [chemical binding]; other site 990288004931 substrate interface [chemical binding]; other site 990288004932 DEAD-like helicases superfamily; Region: DEXDc; smart00487 990288004933 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 990288004934 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 990288004935 nucleotide binding region [chemical binding]; other site 990288004936 ATP-binding site [chemical binding]; other site 990288004937 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288004938 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288004939 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 990288004940 ParB-like nuclease domain; Region: ParBc; cl02129 990288004941 Zinc-binding domain of primase-helicase; Region: Prim_Zn_Ribbon; cl07038 990288004942 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 990288004943 TPR motif; other site 990288004944 binding surface 990288004945 NodT family; Region: outer_NodT; TIGR01845 990288004946 Outer membrane efflux protein; Region: OEP; pfam02321 990288004947 Outer membrane efflux protein; Region: OEP; pfam02321 990288004948 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 990288004949 multidrug efflux protein; Reviewed; Region: PRK09579 990288004950 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 990288004951 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 990288004952 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 990288004953 homodimer interface [polypeptide binding]; other site 990288004954 NADP binding site [chemical binding]; other site 990288004955 substrate binding site [chemical binding]; other site 990288004956 Polyphosphate kinase; Region: PP_kinase; pfam02503 990288004957 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 990288004958 putative domain interface [polypeptide binding]; other site 990288004959 putative active site [active] 990288004960 catalytic site [active] 990288004961 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 990288004962 putative domain interface [polypeptide binding]; other site 990288004963 putative active site [active] 990288004964 catalytic site [active] 990288004965 ParA-like protein; Provisional; Region: PHA02518 990288004966 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 990288004967 Uncharacterized conserved protein [Function unknown]; Region: COG3025 990288004968 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 990288004969 putative active site [active] 990288004970 putative metal binding residues [ion binding]; other site 990288004971 signature motif; other site 990288004972 putative triphosphate binding site [ion binding]; other site 990288004973 CHAD domain; Region: CHAD; cl10506 990288004974 aminopeptidase N; Provisional; Region: pepN; PRK14015 990288004975 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 990288004976 Zn binding site [ion binding]; other site 990288004977 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide...; Region: DsbA_DsbC_DsbG; cd03020 990288004978 dimerization domain [polypeptide binding]; other site 990288004979 dimer interface [polypeptide binding]; other site 990288004980 catalytic residues [active] 990288004981 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 990288004982 Clp amino terminal domain; Region: Clp_N; pfam02861 990288004983 Clp amino terminal domain; Region: Clp_N; pfam02861 990288004984 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288004985 Walker A motif; other site 990288004986 ATP binding site [chemical binding]; other site 990288004987 Walker B motif; other site 990288004988 arginine finger; other site 990288004989 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288004990 Walker A motif; other site 990288004991 ATP binding site [chemical binding]; other site 990288004992 Walker B motif; other site 990288004993 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 990288004994 MFS_1 like family; Region: MFS_1_like; pfam12832 990288004995 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 990288004996 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 990288004997 Tetramer interface [polypeptide binding]; other site 990288004998 Active site [active] 990288004999 FMN-binding site [chemical binding]; other site 990288005000 Uncharacterized ACR, COG1469; Region: DUF198; cl00642 990288005001 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 990288005002 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 with important pharmaceutical activity. DXS...; Region: TPP_DXS; cd02007 990288005003 TPP-binding site; other site 990288005004 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 990288005005 PYR/PP interface [polypeptide binding]; other site 990288005006 dimer interface [polypeptide binding]; other site 990288005007 TPP binding site [chemical binding]; other site 990288005008 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 990288005009 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 990288005010 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 990288005011 substrate binding pocket [chemical binding]; other site 990288005012 chain length determination region; other site 990288005013 substrate-Mg2+ binding site; other site 990288005014 catalytic residues [active] 990288005015 aspartate-rich region 1; other site 990288005016 active site lid residues [active] 990288005017 aspartate-rich region 2; other site 990288005018 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 990288005019 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 990288005020 Protein export membrane protein; Region: SecD_SecF; cl14618 990288005021 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 990288005022 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 990288005023 Protein export membrane protein; Region: SecD_SecF; cl14618 990288005024 Preprotein translocase subunit; Region: YajC; cl00806 990288005025 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 990288005026 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 990288005027 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 990288005028 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 990288005029 Domain of unknown function DUF21; Region: DUF21; pfam01595 990288005030 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 990288005031 Transporter associated domain; Region: CorC_HlyC; cl08393 990288005032 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl09141 990288005033 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 990288005034 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 990288005035 homodimer interface [polypeptide binding]; other site 990288005036 substrate-cofactor binding pocket; other site 990288005037 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288005038 catalytic residue [active] 990288005039 amidophosphoribosyltransferase; Provisional; Region: PRK09123 990288005040 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 990288005041 active site 990288005042 tetramer interface [polypeptide binding]; other site 990288005043 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 990288005044 Colicin V production protein; Region: Colicin_V; cl00567 990288005045 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 990288005046 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 990288005047 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 990288005048 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 990288005049 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 990288005050 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are...; Region: Tryptophan_synthase_alpha; cd04724 990288005051 substrate binding site [chemical binding]; other site 990288005052 active site 990288005053 catalytic residues [active] 990288005054 heterodimer interface [polypeptide binding]; other site 990288005055 tryptophan synthase, beta chain; Region: PLN02618 990288005056 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 990288005057 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288005058 catalytic residue [active] 990288005059 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric...; Region: PRAI; cd00405 990288005060 active site 990288005061 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1)...; Region: PseudoU_synth_EcTruA; cd02570 990288005062 dimerization interface 3.5A [polypeptide binding]; other site 990288005063 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 990288005064 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 990288005065 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 990288005066 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 990288005067 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 990288005068 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288005069 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 990288005070 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 990288005071 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 990288005072 GTP binding site [chemical binding]; other site 990288005073 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa...; Region: MobB; cd03116 990288005074 Walker A motif; other site 990288005075 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 990288005076 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 990288005077 dimer interface [polypeptide binding]; other site 990288005078 putative functional site; other site 990288005079 putative MPT binding site; other site 990288005080 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 990288005081 putative active site [active] 990288005082 catalytic site [active] 990288005083 Lumazine-binding domain; Region: Lumazine_bd; pfam12870 990288005084 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 990288005085 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 990288005086 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 990288005087 motif II; other site 990288005088 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 990288005089 DNA photolyase; Region: DNA_photolyase; pfam00875 990288005090 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 990288005091 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 990288005092 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 990288005093 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 990288005094 Outer membrane lipoprotein Slp family; Region: Slp; cl01164 990288005095 ABC-2 type transporter; Region: ABC2_membrane; cl11417 990288005096 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 990288005097 ABC-2 type transporter; Region: ABC2_membrane; cl11417 990288005098 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 990288005099 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 990288005100 Walker A/P-loop; other site 990288005101 ATP binding site [chemical binding]; other site 990288005102 Q-loop/lid; other site 990288005103 ABC transporter signature motif; other site 990288005104 Walker B; other site 990288005105 D-loop; other site 990288005106 H-loop/switch region; other site 990288005107 PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 990288005108 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 990288005109 Walker A/P-loop; other site 990288005110 ATP binding site [chemical binding]; other site 990288005111 Q-loop/lid; other site 990288005112 ABC transporter signature motif; other site 990288005113 Walker B; other site 990288005114 D-loop; other site 990288005115 H-loop/switch region; other site 990288005116 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 990288005117 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2...; Region: Biotinyl_lipoyl_domains; cl11404 990288005118 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 990288005119 D-galactonate transporter; Region: 2A0114; TIGR00893 990288005120 putative substrate translocation pore; other site 990288005121 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 990288005122 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 990288005123 Ligand Binding Site [chemical binding]; other site 990288005124 Amino acid permease; Region: AA_permease; pfam00324 990288005125 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 990288005126 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 990288005127 dimerization interface [polypeptide binding]; other site 990288005128 ATP binding site [chemical binding]; other site 990288005129 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 990288005130 dimerization interface [polypeptide binding]; other site 990288005131 ATP binding site [chemical binding]; other site 990288005132 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 990288005133 putative active site [active] 990288005134 catalytic triad [active] 990288005135 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 990288005136 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 990288005137 ATP binding site [chemical binding]; other site 990288005138 active site 990288005139 substrate binding site [chemical binding]; other site 990288005140 adenylosuccinate lyase; Provisional; Region: PRK07492 990288005141 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 990288005142 tetramer interface [polypeptide binding]; other site 990288005143 active site 990288005144 Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Region: Lyase_I_like; cl00013 990288005145 lipoprotein; Provisional; Region: PRK11679 990288005146 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 990288005147 dihydrodipicolinate synthase; Region: dapA; TIGR00674 990288005148 dimer interface [polypeptide binding]; other site 990288005149 active site 990288005150 catalytic residue [active] 990288005151 Uncharacterised protein family (UPF0227); Region: UPF0227; cl14886 990288005152 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts...; Region: cpn10; cd00320 990288005153 oligomerisation interface [polypeptide binding]; other site 990288005154 mobile loop; other site 990288005155 roof hairpin; other site 990288005156 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 990288005157 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 990288005158 ring oligomerisation interface [polypeptide binding]; other site 990288005159 ATP/Mg binding site [chemical binding]; other site 990288005160 stacking interactions; other site 990288005161 hinge regions; other site 990288005162 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 990288005163 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 990288005164 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated; Region: PRK05537 990288005165 active site 990288005166 nucleotide binding site [chemical binding]; other site 990288005167 HIGH motif; other site 990288005168 KMSKS motif; other site 990288005169 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically 'activated' sulfate form important for the assimilation...; Region: APSK; cd02027 990288005170 ligand-binding site [chemical binding]; other site 990288005171 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]; Region: COG1293 990288005172 Domain of unknown function (DUF814); Region: DUF814; pfam05670 990288005173 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 990288005174 Cytochrome c [Energy production and conversion]; Region: COG3258 990288005175 Cytochrome c [Energy production and conversion]; Region: COG3258 990288005176 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 990288005177 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 990288005178 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 990288005179 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 990288005180 active site 990288005181 metal binding site [ion binding]; metal-binding site 990288005182 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 990288005183 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 990288005184 Predicted secreted protein [Function unknown]; Region: COG5501; cl02313 990288005185 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 990288005186 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 990288005187 Subunit I/III interface [polypeptide binding]; other site 990288005188 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 990288005189 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily...; Region: Heme_Cu_Oxidase_I; cl00275 990288005190 D-pathway; other site 990288005191 Low-spin heme binding site [chemical binding]; other site 990288005192 Putative water exit pathway; other site 990288005193 Binuclear center (active site) [active] 990288005194 K-pathway; other site 990288005195 Putative proton exit pathway; other site 990288005196 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 990288005197 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 990288005198 transposase; Provisional; Region: PRK06526 990288005199 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288005200 Walker A motif; other site 990288005201 ATP binding site [chemical binding]; other site 990288005202 Walker B motif; other site 990288005203 Integrase core domain; Region: rve; cl01316 990288005204 SCP-2 sterol transfer family; Region: SCP2; cl01225 990288005205 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 990288005206 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 990288005207 GatB domain; Region: GatB_Yqey; cl11497 990288005208 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 990288005209 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 990288005210 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 990288005211 VacJ like lipoprotein; Region: VacJ; cl01073 990288005212 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; cl01074 990288005213 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 990288005214 hopanoid biosynthesis associated radical SAM protein HpnH; Region: HpnH; TIGR03470 990288005215 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 990288005216 FeS/SAM binding site; other site 990288005217 Domain of unknown function (DUF3463); Region: DUF3463; pfam11946 990288005218 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 990288005219 dinuclear metal binding motif [ion binding]; other site 990288005220 Uncharacterised protein family (UPF0104); Region: UPF0104; cl04219 990288005221 hopanoid biosynthesis associated RND transporter like protein HpnN; Region: HpnN; TIGR03480 990288005222 YdjC-like protein; Region: YdjC; cl01344 990288005223 hopanoid biosynthesis associated radical SAM protein HpnJ; Region: HpnJ; TIGR03471 990288005224 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase...; Region: B12-binding_like; cl00293 990288005225 B12 binding site [chemical binding]; other site 990288005226 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; cl15259 990288005227 hopanoid biosynthesis associated glycosyl transferase protein HpnI; Region: HpnI; TIGR03472 990288005228 Glucosylceramide synthase catalyzes the first glycosylation step of glycosphingolipid synthesis; Region: Glucosylceramide_synthase; cd02520 990288005229 ligand binding site [chemical binding]; other site 990288005230 hopanoid-associated sugar epimerase; Region: HpnA; TIGR03466 990288005231 uncharacterized subgroup of aldehyde reductase and flavonoid reductase related proteins, extended (e) SDRs; Region: AR_FR_like_1_SDR_e; cd05228 990288005232 putative NADP binding site [chemical binding]; other site 990288005233 putative substrate binding site [chemical binding]; other site 990288005234 active site 990288005235 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 990288005236 squalene-hopene cyclase; Region: hopene_cyclase; TIGR01507 990288005237 Squalene cyclase (SQCY) domain subgroup 1; found in class II terpene cyclases that have an alpha 6 - alpha 6 barrel fold. Squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY) are integral membrane proteins that catalyze a cationic cyclization...; Region: SQCY_1; cd02892 990288005238 Active site cavity [active] 990288005239 catalytic acid [active] 990288005240 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 990288005241 active site lid residues [active] 990288005242 substrate binding pocket [chemical binding]; other site 990288005243 catalytic residues [active] 990288005244 substrate-Mg2+ binding site; other site 990288005245 aspartate-rich region 1; other site 990288005246 aspartate-rich region 2; other site 990288005247 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 990288005248 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 990288005249 Walker A/P-loop; other site 990288005250 ATP binding site [chemical binding]; other site 990288005251 Q-loop/lid; other site 990288005252 ABC transporter signature motif; other site 990288005253 Walker B; other site 990288005254 D-loop; other site 990288005255 H-loop/switch region; other site 990288005256 Hydroxyneurosporene synthase (CrtC); Region: CrtC; cl12101 990288005257 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 990288005258 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...; Region: ThiF_MoeB_HesA_family; cd00757 990288005259 ATP binding site [chemical binding]; other site 990288005260 substrate interface [chemical binding]; other site 990288005261 MoeZ/MoeB domain; Region: MoeZ_MoeB; cl14816 990288005262 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 990288005263 putative catalytic site [active] 990288005264 putative metal binding site [ion binding]; other site 990288005265 putative phosphate binding site [ion binding]; other site 990288005266 Domain of unknown function DUF140; Region: DUF140; cl00510 990288005267 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 990288005268 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 990288005269 Walker A/P-loop; other site 990288005270 ATP binding site [chemical binding]; other site 990288005271 Q-loop/lid; other site 990288005272 ABC transporter signature motif; other site 990288005273 Walker B; other site 990288005274 D-loop; other site 990288005275 H-loop/switch region; other site 990288005276 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 990288005277 Outer membrane efflux protein; Region: OEP; pfam02321 990288005278 Outer membrane efflux protein; Region: OEP; pfam02321 990288005279 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 990288005280 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 990288005281 chorismate binding enzyme; Region: Chorismate_bind; cl10555 990288005282 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 990288005283 Glycogen_debranching_enzyme N-terminal domain. Glycogen debranching enzymes have both 4-alpha-glucanotransferase and amylo-1,6-glucosidase activities. As a transferase it transfers a segment of a 1,4-alpha-D-glucan to a new 4-position in an acceptor...; Region: Glycogen_debranching_enzyme_N_term; cd02856 990288005284 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 990288005285 Uncharacterised protein family (UPF0104); Region: UPF0104; cl04219 990288005286 Transposase, Mutator family; Region: Transposase_mut; pfam00872 990288005287 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 990288005288 Phd_YefM; Region: PhdYeFM; cl09153 990288005289 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 990288005290 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 990288005291 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 990288005292 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 990288005293 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 990288005294 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 990288005295 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 990288005296 DNA binding residues [nucleotide binding] 990288005297 DNA primase; Validated; Region: dnaG; PRK05667 990288005298 CHC2 zinc finger; Region: zf-CHC2; cl02597 990288005299 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 990288005300 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 990288005301 active site 990288005302 metal binding site [ion binding]; metal-binding site 990288005303 interdomain interaction site; other site 990288005304 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 990288005305 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 990288005306 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288005307 Walker A/P-loop; other site 990288005308 ATP binding site [chemical binding]; other site 990288005309 Q-loop/lid; other site 990288005310 ABC transporter signature motif; other site 990288005311 Walker B; other site 990288005312 D-loop; other site 990288005313 H-loop/switch region; other site 990288005314 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 990288005315 Smr domain; Region: Smr; cl02619 990288005316 GatB domain; Region: GatB_Yqey; cl11497 990288005317 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 990288005318 DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; Region: RpoD; COG0568 990288005319 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 990288005320 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 990288005321 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 Ham1-...; Region: HAM1; cd00515 990288005322 active site 990288005323 dimerization interface [polypeptide binding]; other site 990288005324 ribonuclease PH; Reviewed; Region: rph; PRK00173 990288005325 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 990288005326 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 990288005327 Protein of unknown function, DUF481; Region: DUF481; cl01213 990288005328 heat shock protein 90; Provisional; Region: PRK05218 990288005329 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 990288005330 ATP binding site [chemical binding]; other site 990288005331 Mg2+ binding site [ion binding]; other site 990288005332 G-X-G motif; other site 990288005333 Protein of unknown function (DUF423); Region: DUF423; cl01008 990288005334 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 990288005335 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 990288005336 putative NAD(P) binding site [chemical binding]; other site 990288005337 active site 990288005338 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 990288005339 Sel1 repeat; Region: Sel1; cl02723 990288005340 Membrane glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: MdoH; COG2943 990288005341 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 990288005342 Ligand binding site [chemical binding]; other site 990288005343 DXD motif; other site 990288005344 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl01208 990288005345 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion]; Region: Lpd; COG1249 990288005346 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288005347 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 990288005348 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 990288005349 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 990288005350 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288005351 Walker A motif; other site 990288005352 ATP binding site [chemical binding]; other site 990288005353 Walker B motif; other site 990288005354 arginine finger; other site 990288005355 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 990288005356 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 990288005357 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 990288005358 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 990288005359 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 990288005360 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 990288005361 ThiC family; Region: ThiC; cl08031 990288005362 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-...; Region: SirA_YedF_YeeD; cl00436 990288005363 Phosphate-starvation-inducible E; Region: PsiE; cl01264 990288005364 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 990288005365 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 990288005366 dimerization interface [polypeptide binding]; other site 990288005367 domain crossover interface; other site 990288005368 redox-dependent activation switch; other site 990288005369 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...; Region: Alpha_ANH_like_II; cd01993 990288005370 Ligand Binding Site [chemical binding]; other site 990288005371 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 990288005372 putative ribose interaction site [chemical binding]; other site 990288005373 putative ADP binding site [chemical binding]; other site 990288005374 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 990288005375 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288005376 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 990288005377 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288005378 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 990288005379 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the...; Region: PNPsynthase; cd00003 990288005380 active site 990288005381 hydrophilic channel; other site 990288005382 dimerization interface [polypeptide binding]; other site 990288005383 catalytic residues [active] 990288005384 active site lid [active] 990288005385 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 990288005386 Recombination protein O C terminal; Region: RecO_C; pfam02565 990288005387 GTPase Era; Reviewed; Region: era; PRK00089 990288005388 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit...; Region: Era; cd04163 990288005389 G1 box; other site 990288005390 GTP/Mg2+ binding site [chemical binding]; other site 990288005391 Switch I region; other site 990288005392 G2 box; other site 990288005393 Switch II region; other site 990288005394 G3 box; other site 990288005395 G4 box; other site 990288005396 G5 box; other site 990288005397 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains...; Region: KH-I; cl00098 990288005398 ribonuclease III; Reviewed; Region: rnc; PRK00102 990288005399 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-...; Region: RIBOc; cd00593 990288005400 dimerization interface [polypeptide binding]; other site 990288005401 active site 990288005402 metal binding site [ion binding]; metal-binding site 990288005403 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase...; Region: DSRM; cd00048 990288005404 dsRNA binding site [nucleotide binding]; other site 990288005405 signal peptidase I; Provisional; Region: PRK10861 990288005406 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 990288005407 Catalytic site [active] 990288005408 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 990288005409 GTP-binding protein LepA; Provisional; Region: PRK05433 990288005410 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 990288005411 G1 box; other site 990288005412 putative GEF interaction site [polypeptide binding]; other site 990288005413 GTP/Mg2+ binding site [chemical binding]; other site 990288005414 Switch I region; other site 990288005415 G2 box; other site 990288005416 G3 box; other site 990288005417 Switch II region; other site 990288005418 G4 box; other site 990288005419 G5 box; other site 990288005420 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding...; Region: Translation_Factor_II_like; cl02787 990288005421 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 990288005422 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 990288005423 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 990288005424 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 990288005425 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 C-...; Region: PDZ_serine_protease; cd00987 990288005426 protein binding site [polypeptide binding]; other site 990288005427 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 C-...; Region: PDZ_serine_protease; cd00987 990288005428 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 990288005429 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 990288005430 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 990288005431 DNA binding residues [nucleotide binding] 990288005432 L-aspartate oxidase; Provisional; Region: PRK09077 990288005433 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288005434 domain; Region: Succ_DH_flav_C; pfam02910 990288005435 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 990288005436 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 990288005437 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 990288005438 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 990288005439 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288005440 Walker A/P-loop; other site 990288005441 ATP binding site [chemical binding]; other site 990288005442 Q-loop/lid; other site 990288005443 ABC transporter signature motif; other site 990288005444 Walker B; other site 990288005445 D-loop; other site 990288005446 H-loop/switch region; other site 990288005447 thiol reductant ABC exporter, CydD subunit; Region: CydD; TIGR02857 990288005448 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 990288005449 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288005450 Walker A/P-loop; other site 990288005451 ATP binding site [chemical binding]; other site 990288005452 Q-loop/lid; other site 990288005453 ABC transporter signature motif; other site 990288005454 Walker B; other site 990288005455 D-loop; other site 990288005456 H-loop/switch region; other site 990288005457 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4398 990288005458 FIST N domain; Region: FIST; cl10701 990288005459 FIST C domain; Region: FIST_C; pfam10442 990288005460 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 990288005461 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 990288005462 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and...; Region: RF3; cd04169 990288005463 G1 box; other site 990288005464 putative GEF interaction site [polypeptide binding]; other site 990288005465 GTP/Mg2+ binding site [chemical binding]; other site 990288005466 Switch I region; other site 990288005467 G2 box; other site 990288005468 G3 box; other site 990288005469 Switch II region; other site 990288005470 G4 box; other site 990288005471 G5 box; other site 990288005472 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 990288005473 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 990288005474 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 990288005475 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 990288005476 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288005477 DEAD_2; Region: DEAD_2; cl14887 990288005478 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288005479 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 990288005480 NlpC/P60 family; Region: NLPC_P60; cl11438 990288005481 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide...; Region: DsbA_DsbC_DsbG; cd03020 990288005482 catalytic residues [active] 990288005483 N-carbamolyputrescine amidase; Region: PLN02747 990288005484 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 990288005485 putative active site; other site 990288005486 catalytic triad [active] 990288005487 putative dimer interface [polypeptide binding]; other site 990288005488 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 990288005489 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 990288005490 putative active site [active] 990288005491 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 990288005492 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 990288005493 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 990288005494 conserved cys residue [active] 990288005495 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 990288005496 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288005497 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 990288005498 putative dimerization interface [polypeptide binding]; other site 990288005499 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 990288005500 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and...; Region: Aldo_ket_red; cd06660 990288005501 active site 990288005502 catalytic tetrad [active] 990288005503 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 990288005504 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 990288005505 metal ion-dependent adhesion site (MIDAS); other site 990288005506 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288005507 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 990288005508 Walker A motif; other site 990288005509 ATP binding site [chemical binding]; other site 990288005510 Walker B motif; other site 990288005511 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 990288005512 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 990288005513 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 990288005514 Biotin synthase-related enzyme [General function prediction only]; Region: COG2516 990288005515 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 990288005516 FeS/SAM binding site; other site 990288005517 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 990288005518 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288005519 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 990288005520 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 990288005521 Uncharacterized homolog of biotin synthetase [Function unknown]; Region: COG1856 990288005522 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; cl15259 990288005523 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 L-...; Region: GCS_H; cd06848 990288005524 lipoyl attachment site [posttranslational modification]; other site 990288005525 DsrE/DsrF-like family; Region: DrsE; cl00672 990288005526 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 L-...; Region: GCS_H; cd06848 990288005527 lipoyl attachment site [posttranslational modification]; other site 990288005528 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 990288005529 Cysteine-rich domain; Region: CCG; pfam02754 990288005530 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 990288005531 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 990288005532 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288005533 Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion]; Region: HdrA; COG1148 990288005534 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 990288005535 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 990288005536 Cysteine-rich domain; Region: CCG; pfam02754 990288005537 Heterodisulfide reductase, subunit C [Energy production and conversion]; Region: HdrC; COG1150 990288005538 DsrE/DsrF-like family; Region: DrsE; cl00672 990288005539 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-...; Region: SirA_YedF_YeeD; cd00291 990288005540 CPxP motif; other site 990288005541 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 990288005542 active site residue [active] 990288005543 molybdenum cofactor biosynthesis protein A, bacterial; Region: moaA; TIGR02666 990288005544 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 990288005545 FeS/SAM binding site; other site 990288005546 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 990288005547 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl04869 990288005548 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 990288005549 anaerobic dimethyl sulfoxide reductase subunit A; Provisional; Region: PRK14990 990288005550 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 990288005551 molybdopterin cofactor binding site; other site 990288005552 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 990288005553 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD...; Region: MopB_CT_2; cd02783 990288005554 putative molybdopterin cofactor binding site; other site 990288005555 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a...; Region: MoaC_PE; cd01420 990288005556 trimer interface [polypeptide binding]; other site 990288005557 dimer interface [polypeptide binding]; other site 990288005558 putative active site [active] 990288005559 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 990288005560 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 990288005561 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 trans-...; Region: HisKA; cd00082 990288005562 dimer interface [polypeptide binding]; other site 990288005563 phosphorylation site [posttranslational modification] 990288005564 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 990288005565 ATP binding site [chemical binding]; other site 990288005566 Mg2+ binding site [ion binding]; other site 990288005567 G-X-G motif; other site 990288005568 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 990288005569 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 990288005570 active site 990288005571 phosphorylation site [posttranslational modification] 990288005572 intermolecular recognition site; other site 990288005573 dimerization interface [polypeptide binding]; other site 990288005574 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288005575 Walker A motif; other site 990288005576 ATP binding site [chemical binding]; other site 990288005577 Walker B motif; other site 990288005578 arginine finger; other site 990288005579 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 990288005580 Cytochrome c; Region: Cytochrom_C; cl11414 990288005581 Predicted secreted protein [Function unknown]; Region: COG5501; cl02313 990288005582 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 990288005583 Cytochrome c [Energy production and conversion]; Region: COG3258 990288005584 Cytochrome c [Energy production and conversion]; Region: COG3258 990288005585 Domain of unknown function DUF302; Region: DUF302; cl01364 990288005586 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 990288005587 active site 990288005588 metal binding site [ion binding]; metal-binding site 990288005589 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 990288005590 rod shape-determining protein MreB; Provisional; Region: PRK13927 990288005591 hypothetical protein; Provisional; Region: PRK10039 990288005592 Cell division protein FtsA; Region: FtsA; cl11496 990288005593 rod shape-determining protein MreC; Provisional; Region: PRK13922 990288005594 rod shape-determining protein MreC; Region: MreC; pfam04085 990288005595 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 990288005596 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 990288005597 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 990288005598 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 990288005599 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 990288005600 Beta-lactamase; Region: Beta-lactamase; cl01009 990288005601 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 990288005602 Protein of unknown function (DUF493); Region: DUF493; cl01102 990288005603 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 990288005604 lipoyl synthase; Provisional; Region: PRK05481 990288005605 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; cl15259 990288005606 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 990288005607 putative active site [active] 990288005608 L,D-transpeptidase; Provisional; Region: PRK10190 990288005609 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 990288005610 Conserved hypothetical ATP binding protein; Region: ATP_bind_1; pfam03029 990288005611 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cd00882 990288005612 G1 box; other site 990288005613 GTP/Mg2+ binding site [chemical binding]; other site 990288005614 G2 box; other site 990288005615 Switch I region; other site 990288005616 G3 box; other site 990288005617 Switch II region; other site 990288005618 G4 box; other site 990288005619 G5 box; other site 990288005620 Roadblock/LC7 domain; Region: Robl_LC7; cl00886 990288005621 Roadblock/LC7 domain; Region: Robl_LC7; cl00886 990288005622 glycyl-tRNA synthetase, tetrameric type, alpha subunit; Region: glyQ; TIGR00388 990288005623 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 990288005624 dimer interface [polypeptide binding]; other site 990288005625 motif 1; other site 990288005626 active site 990288005627 motif 2; other site 990288005628 motif 3; other site 990288005629 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 990288005630 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 990288005631 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 990288005632 active site 990288005633 motif I; other site 990288005634 motif II; other site 990288005635 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 990288005636 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 990288005637 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 990288005638 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 990288005639 Cysteine-rich domain; Region: CCG; pfam02754 990288005640 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...; Region: TlpA_like_family; cd02966 990288005641 catalytic residues [active] 990288005642 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 990288005643 aromatic arch; other site 990288005644 DCoH dimer interaction site [polypeptide binding]; other site 990288005645 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 990288005646 DCoH tetramer interaction site [polypeptide binding]; other site 990288005647 substrate binding site [chemical binding]; other site 990288005648 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 990288005649 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 990288005650 amidase catalytic site [active] 990288005651 Zn binding residues [ion binding]; other site 990288005652 substrate binding site [chemical binding]; other site 990288005653 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 990288005654 catalytic residues [active] 990288005655 peroxiredoxin; Provisional; Region: PRK13189 990288005656 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 990288005657 dimer interface [polypeptide binding]; other site 990288005658 decamer (pentamer of dimers) interface [polypeptide binding]; other site 990288005659 catalytic triad [active] 990288005660 2-isopropylmalate synthase; Validated; Region: PRK00915 990288005661 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 990288005662 active site 990288005663 catalytic residues [active] 990288005664 metal binding site [ion binding]; metal-binding site 990288005665 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 990288005666 Domain of unknown function (DUF299); Region: DUF299; cl00780 990288005667 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 990288005668 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 990288005669 N-terminal plug; other site 990288005670 ligand-binding site [chemical binding]; other site 990288005671 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 990288005672 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 990288005673 Sulfatase; Region: Sulfatase; cl10460 990288005674 Transposase domain (DUF772); Region: DUF772; cl12084 990288005675 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288005676 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 990288005677 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl14655 990288005678 Cysteine-rich domain; Region: CCG; pfam02754 990288005679 Cysteine-rich domain; Region: CCG; pfam02754 990288005680 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 990288005681 FAD binding domain; Region: FAD_binding_4; pfam01565 990288005682 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 990288005683 FAD binding domain; Region: FAD_binding_4; pfam01565 990288005684 LamB/YcsF family; Region: LamB_YcsF; cl00664 990288005685 Protein of unknown function, DUF1537; Region: DUF1537; cl01345 990288005686 Phosphoketolase [Carbohydrate transport and metabolism]; Region: COG3957 990288005687 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 990288005688 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288005689 Bacterial transcriptional regulator; Region: IclR; pfam01614 990288005690 D-galactonate transporter; Region: 2A0114; TIGR00893 990288005691 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 990288005692 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 990288005693 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288005694 Walker A motif; other site 990288005695 ATP binding site [chemical binding]; other site 990288005696 Walker B motif; other site 990288005697 arginine finger; other site 990288005698 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 990288005699 DsrE/DsrF-like family; Region: DrsE; cl00672 990288005700 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-...; Region: SirA_YedF_YeeD; cd00291 990288005701 CPxP motif; other site 990288005702 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 990288005703 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(...; Region: Pep_deformylase; cd00487 990288005704 active site 990288005705 catalytic residues [active] 990288005706 metal binding site [ion binding]; metal-binding site 990288005707 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl09141 990288005708 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl09141 990288005709 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II)...; Region: Aldolase_II; cl00214 990288005710 intersubunit interface [polypeptide binding]; other site 990288005711 active site 990288005712 Zn2+ binding site [ion binding]; other site 990288005713 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 990288005714 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 990288005715 2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Region: RLP_DK-MTP-1-P-enolase; cd08209 990288005716 2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed; Region: mtnW; PRK09549 990288005717 dimer interface [polypeptide binding]; other site 990288005718 active site 990288005719 catalytic residue [active] 990288005720 metal binding site [ion binding]; metal-binding site 990288005721 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1791 990288005722 Cupin domain; Region: Cupin_2; cl09118 990288005723 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 990288005724 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 990288005725 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 990288005726 active site 990288005727 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 990288005728 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl00412 990288005729 NAD synthetase; Provisional; Region: PRK13981 990288005730 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 990288005731 multimer interface [polypeptide binding]; other site 990288005732 active site 990288005733 catalytic triad [active] 990288005734 protein interface 1 [polypeptide binding]; other site 990288005735 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to...; Region: NAD_synthase; cd00553 990288005736 homodimer interface [polypeptide binding]; other site 990288005737 NAD binding pocket [chemical binding]; other site 990288005738 ATP binding pocket [chemical binding]; other site 990288005739 Mg binding site [ion binding]; other site 990288005740 active-site loop [active] 990288005741 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 990288005742 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288005743 CoA-ligase; Region: Ligase_CoA; pfam00549 990288005744 peptide chain release factor 1; Validated; Region: prfA; PRK00591 990288005745 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 990288005746 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 990288005747 CoA-ligase; Region: Ligase_CoA; pfam00549 990288005748 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 990288005749 isocitrate dehydrogenase; Validated; Region: PRK06451 990288005750 aconitate hydratase; Validated; Region: PRK07229 990288005751 Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: AcnA_Bact; cd01585 990288005752 substrate binding site [chemical binding]; other site 990288005753 ligand binding site [chemical binding]; other site 990288005754 Bacterial Aconitase-like swivel domain. Aconitase (aconitate hydratase or citrate hydrolyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Cis-aconitate is formed as an intermediate product during the...; Region: AcnA_Bact_Swivel; cd01579 990288005755 substrate binding site [chemical binding]; other site 990288005756 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 990288005757 Sulfate transporter family; Region: Sulfate_transp; cl00967 990288005758 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 990288005759 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 990288005760 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 990288005761 active site 990288005762 HIGH motif; other site 990288005763 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 990288005764 active site 990288005765 KMSKS motif; other site 990288005766 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 990288005767 N-acetyl-D-glucosamine binding site [chemical binding]; other site 990288005768 catalytic residue [active] 990288005769 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 990288005770 putative peptidoglycan binding site; other site 990288005771 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 990288005772 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 990288005773 putative peptidoglycan binding site; other site 990288005774 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 990288005775 putative peptidoglycan binding site; other site 990288005776 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 990288005777 putative peptidoglycan binding site; other site 990288005778 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 990288005779 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 990288005780 NAD binding site [chemical binding]; other site 990288005781 homotetramer interface [polypeptide binding]; other site 990288005782 homodimer interface [polypeptide binding]; other site 990288005783 substrate binding site [chemical binding]; other site 990288005784 active site 990288005785 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 990288005786 putative active site [active] 990288005787 transaldolase; Provisional; Region: PRK03903 990288005788 catalytic residue [active] 990288005789 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 990288005790 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 990288005791 substrate binding site [chemical binding]; other site 990288005792 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 990288005793 putative active site [active] 990288005794 putative metal binding site [ion binding]; other site 990288005795 aspartate kinase; Reviewed; Region: PRK06635 990288005796 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 990288005797 putative nucleotide binding site [chemical binding]; other site 990288005798 putative catalytic residues [active] 990288005799 putative Mg ion binding site [ion binding]; other site 990288005800 putative aspartate binding site [chemical binding]; other site 990288005801 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 990288005802 putative allosteric regulatory site; other site 990288005803 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 990288005804 putative allosteric regulatory residue; other site 990288005805 acetylornithine aminotransferase; Provisional; Region: PRK02627 990288005806 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 990288005807 inhibitor-cofactor binding pocket; inhibition site 990288005808 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288005809 catalytic residue [active] 990288005810 ornithine carbamoyltransferase; Provisional; Region: PRK00779 990288005811 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 990288005812 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288005813 argininosuccinate synthase; Provisional; Region: PLN00200 990288005814 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 990288005815 ANP binding site [chemical binding]; other site 990288005816 Substrate Binding Site II [chemical binding]; other site 990288005817 Substrate Binding Site I [chemical binding]; other site 990288005818 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 990288005819 dimer interface [polypeptide binding]; other site 990288005820 active site 990288005821 metal binding site [ion binding]; metal-binding site 990288005822 glutathione binding site [chemical binding]; other site 990288005823 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 990288005824 active site 990288005825 substrate binding site [chemical binding]; other site 990288005826 catalytic site [active] 990288005827 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 990288005828 RNA/DNA hybrid binding site [nucleotide binding]; other site 990288005829 active site 990288005830 hypothetical protein; Provisional; Region: PRK08317 990288005831 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288005832 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 990288005833 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 990288005834 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 990288005835 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 990288005836 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 990288005837 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 990288005838 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 990288005839 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 990288005840 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 990288005841 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 990288005842 putative nucleic acid binding region [nucleotide binding]; other site 990288005843 G-X-X-G motif; other site 990288005844 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 990288005845 RNA binding site [nucleotide binding]; other site 990288005846 domain interface; other site 990288005847 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole...; Region: Ribosomal_S15p_S13e; cd00353 990288005848 16S/18S rRNA binding site [nucleotide binding]; other site 990288005849 S13e-L30e interaction site [polypeptide binding]; other site 990288005850 25S rRNA binding site [nucleotide binding]; other site 990288005851 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 990288005852 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of...; Region: PseudoU_synth_EcTruB; cd02573 990288005853 RNA binding site [nucleotide binding]; other site 990288005854 active site 990288005855 Ribosome-binding factor A; Region: RBFA; cl00542 990288005856 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 990288005857 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 990288005858 translation initiation factor IF-2; Region: IF-2; TIGR00487 990288005859 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 990288005860 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases...; Region: IF2_eIF5B; cd01887 990288005861 G1 box; other site 990288005862 putative GEF interaction site [polypeptide binding]; other site 990288005863 GTP/Mg2+ binding site [chemical binding]; other site 990288005864 Switch I region; other site 990288005865 G2 box; other site 990288005866 G3 box; other site 990288005867 Switch II region; other site 990288005868 G4 box; other site 990288005869 G5 box; other site 990288005870 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the...; Region: IF2_mtIF2_II; cd03702 990288005871 Translation-initiation factor 2; Region: IF-2; pfam11987 990288005872 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation...; Region: mtIF2_IVc; cd03692 990288005873 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 990288005874 NusA N-terminal domain; Region: NusA_N; pfam08529 990288005875 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and...; Region: S1_NusA; cd04455 990288005876 RNA binding site [nucleotide binding]; other site 990288005877 homodimer interface [polypeptide binding]; other site 990288005878 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 990288005879 G-X-X-G motif; other site 990288005880 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 990288005881 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 990288005882 ribosome maturation protein RimP; Reviewed; Region: PRK00092 990288005883 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 990288005884 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 990288005885 Sm1 motif; other site 990288005886 D3 - B interaction site; other site 990288005887 D1 - D2 interaction site; other site 990288005888 Hfq - Hfq interaction site; other site 990288005889 RNA binding pocket [nucleotide binding]; other site 990288005890 Sm2 motif; other site 990288005891 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 990288005892 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 990288005893 Walker A/P-loop; other site 990288005894 ATP binding site [chemical binding]; other site 990288005895 Q-loop/lid; other site 990288005896 ABC transporter signature motif; other site 990288005897 Walker B; other site 990288005898 D-loop; other site 990288005899 H-loop/switch region; other site 990288005900 CAAX amino terminal protease self- immunity; Region: Abi; cl00558 990288005901 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 990288005902 putative peptidoglycan binding site; other site 990288005903 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 990288005904 seryl-tRNA synthetase; Provisional; Region: PRK05431 990288005905 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 990288005906 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 990288005907 dimer interface [polypeptide binding]; other site 990288005908 active site 990288005909 motif 1; other site 990288005910 motif 2; other site 990288005911 motif 3; other site 990288005912 recombination factor protein RarA; Reviewed; Region: PRK13342 990288005913 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288005914 Walker A motif; other site 990288005915 ATP binding site [chemical binding]; other site 990288005916 Walker B motif; other site 990288005917 arginine finger; other site 990288005918 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 990288005919 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 990288005920 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 990288005921 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 990288005922 DNA translocase FtsK; Provisional; Region: PRK10263 990288005923 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288005924 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 990288005925 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 990288005926 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288005927 Smr domain; Region: Smr; cl02619 990288005928 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 990288005929 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 990288005930 DNA binding residues [nucleotide binding] 990288005931 dimer interface [polypeptide binding]; other site 990288005932 metal binding site [ion binding]; metal-binding site 990288005933 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 990288005934 PseudoU_synth_EcTruD: Pseudouridine synthase, TruD family. This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_EcTruD; cd02575 990288005935 Permutation of conserved domain; other site 990288005936 active site 990288005937 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 990288005938 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...; Region: MECDP_synthase; cd00554 990288005939 homotrimer interaction site [polypeptide binding]; other site 990288005940 zinc binding site [ion binding]; other site 990288005941 CDP-binding sites; other site 990288005942 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 990288005943 substrate binding site [chemical binding]; other site 990288005944 dimer interface [polypeptide binding]; other site 990288005945 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 990288005946 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 990288005947 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 990288005948 ATP binding site [chemical binding]; other site 990288005949 putative Mg++ binding site [ion binding]; other site 990288005950 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 990288005951 nucleotide binding region [chemical binding]; other site 990288005952 ATP-binding site [chemical binding]; other site 990288005953 TRCF domain; Region: TRCF; cl04088 990288005954 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 990288005955 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 990288005956 motif II; other site 990288005957 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 990288005958 catalytic triad [active] 990288005959 dimer interface [polypeptide binding]; other site 990288005960 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288005961 glutathione reductase; Validated; Region: PRK06116 990288005962 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288005963 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 990288005964 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 990288005965 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 990288005966 DsrE/DsrF-like family; Region: DrsE; cl00672 990288005967 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 990288005968 hypothetical protein; Reviewed; Region: PRK00024 990288005969 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 990288005970 MPN+ (JAMM) motif; other site 990288005971 Zinc-binding site [ion binding]; other site 990288005972 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 990288005973 Flavoprotein; Region: Flavoprotein; cl08021 990288005974 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 990288005975 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 990288005976 trimer interface [polypeptide binding]; other site 990288005977 active site 990288005978 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 990288005979 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 990288005980 trimer interface [polypeptide binding]; other site 990288005981 active site 990288005982 antiporter inner membrane protein; Provisional; Region: PRK11670 990288005983 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 990288005984 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 990288005985 dihydrodipicolinate reductase; Provisional; Region: PRK00048 990288005986 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288005987 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 990288005988 chaperone protein DnaJ; Provisional; Region: PRK10767 990288005989 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of...; Region: DnaJ; cd06257 990288005990 HSP70 interaction site [polypeptide binding]; other site 990288005991 DnaJ central domain; Region: DnaJ_CXXCXGXG; cl14908 990288005992 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 990288005993 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 990288005994 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 990288005995 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 990288005996 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 990288005997 dimer interface [polypeptide binding]; other site 990288005998 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 990288005999 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 990288006000 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288006001 HrcA protein C terminal domain; Region: HrcA; pfam01628 990288006002 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 990288006003 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 990288006004 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 990288006005 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 990288006006 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 990288006007 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288006008 Protein of unknown function (DUF1365); Region: DUF1365; cl01388 990288006009 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 990288006010 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 990288006011 S-adenosylmethionine binding site [chemical binding]; other site 990288006012 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 990288006013 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 990288006014 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 990288006015 classical (c) SDRs; Region: SDR_c; cd05233 990288006016 NAD(P) binding site [chemical binding]; other site 990288006017 active site 990288006018 AMP-binding enzyme; Region: AMP-binding; pfam00501 990288006019 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 990288006020 PAS fold; Region: PAS; pfam00989 990288006021 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 990288006022 DNA binding residues [nucleotide binding] 990288006023 Predicted flavoproteins [General function prediction only]; Region: COG2081 990288006024 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288006025 Heterodisulfide reductase, subunit A and related polyferredoxins [Energy production and conversion]; Region: HdrA; COG1148 990288006026 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 990288006027 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288006028 NAD(P) binding site [chemical binding]; other site 990288006029 active site 990288006030 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 990288006031 substrate binding site [chemical binding]; other site 990288006032 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 990288006033 dimer interface [polypeptide binding]; other site 990288006034 putative radical transfer pathway; other site 990288006035 diiron center [ion binding]; other site 990288006036 tyrosyl radical; other site 990288006037 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 990288006038 ATP cone domain; Region: ATP-cone; pfam03477 990288006039 ATP cone domain; Region: ATP-cone; pfam03477 990288006040 Class I ribonucleotide reductase; Region: RNR_I; cd01679 990288006041 active site 990288006042 dimer interface [polypeptide binding]; other site 990288006043 catalytic residues [active] 990288006044 effector binding site; other site 990288006045 R2 peptide binding site; other site 990288006046 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 990288006047 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 990288006048 FtsH Extracellular; Region: FtsH_ext; pfam06480 990288006049 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 990288006050 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288006051 Walker A motif; other site 990288006052 ATP binding site [chemical binding]; other site 990288006053 Walker B motif; other site 990288006054 arginine finger; other site 990288006055 Peptidase family M41; Region: Peptidase_M41; pfam01434 990288006056 dihydropteroate synthase; Region: DHPS; TIGR01496 990288006057 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 990288006058 substrate binding pocket [chemical binding]; other site 990288006059 dimer interface [polypeptide binding]; other site 990288006060 inhibitor binding site; inhibition site 990288006061 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 990288006062 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 UDP-N-...; Region: GlmM; cd05802 990288006063 active site 990288006064 substrate binding site [chemical binding]; other site 990288006065 metal binding site [ion binding]; metal-binding site 990288006066 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 990288006067 dimer interface [polypeptide binding]; other site 990288006068 substrate binding site [chemical binding]; other site 990288006069 catalytic triad [active] 990288006070 Preprotein translocase SecG subunit; Region: SecG; cl09123 990288006071 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 990288006072 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 990288006073 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 990288006074 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 990288006075 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 990288006076 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...; Region: TRX_Fd_NuoE; cd03064 990288006077 putative dimer interface [polypeptide binding]; other site 990288006078 [2Fe-2S] cluster binding site [ion binding]; other site 990288006079 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 990288006080 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 990288006081 SLBB domain; Region: SLBB; pfam10531 990288006082 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 990288006083 NADH dehydrogenase subunit G; Validated; Region: PRK09129 990288006084 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 990288006085 catalytic loop [active] 990288006086 iron binding site [ion binding]; other site 990288006087 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 990288006088 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 990288006089 molybdopterin cofactor binding site; other site 990288006090 NADH dehydrogenase; Region: NADHdh; cl00469 990288006091 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 990288006092 4Fe-4S binding domain; Region: Fer4; cl02805 990288006093 4Fe-4S binding domain; Region: Fer4; cl02805 990288006094 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 990288006095 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 990288006096 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 990288006097 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 990288006098 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 990288006099 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 990288006100 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 990288006101 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 990288006102 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 990288006103 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 990288006104 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 990288006105 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase...; Region: TGS_ThrRS_N; cd01667 990288006106 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 990288006107 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 990288006108 active site 990288006109 dimer interface [polypeptide binding]; other site 990288006110 motif 1; other site 990288006111 motif 2; other site 990288006112 motif 3; other site 990288006113 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 990288006114 anticodon binding site; other site 990288006115 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 990288006116 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 990288006117 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 990288006118 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 990288006119 23S rRNA binding site [nucleotide binding]; other site 990288006120 L21 binding site [polypeptide binding]; other site 990288006121 L13 binding site [polypeptide binding]; other site 990288006122 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 990288006123 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 990288006124 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 990288006125 dimer interface [polypeptide binding]; other site 990288006126 motif 1; other site 990288006127 active site 990288006128 motif 2; other site 990288006129 motif 3; other site 990288006130 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 990288006131 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 990288006132 putative tRNA-binding site [nucleotide binding]; other site 990288006133 B3/4 domain; Region: B3_4; cl11458 990288006134 tRNA synthetase B5 domain; Region: B5; cl08394 990288006135 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 990288006136 dimer interface [polypeptide binding]; other site 990288006137 motif 1; other site 990288006138 motif 3; other site 990288006139 motif 2; other site 990288006140 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 990288006141 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 990288006142 IHF - DNA interface [nucleotide binding]; other site 990288006143 IHF dimer interface [polypeptide binding]; other site 990288006144 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 990288006145 DNA binding residues [nucleotide binding] 990288006146 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 990288006147 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 990288006148 Walker A/P-loop; other site 990288006149 ATP binding site [chemical binding]; other site 990288006150 Q-loop/lid; other site 990288006151 ABC transporter signature motif; other site 990288006152 Walker B; other site 990288006153 D-loop; other site 990288006154 H-loop/switch region; other site 990288006155 Uncharacterized conserved protein [Function unknown]; Region: COG4754 990288006156 ABC nitrate/sulfonate/bicarbonate family transporter, ATPase subunit; Region: ABC_transp; pfam09821 990288006157 ABC-type anion transport system, duplicated permease component [Inorganic ion transport and metabolism]; Region: COG4986 990288006158 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 990288006159 dimer interface [polypeptide binding]; other site 990288006160 conserved gate region; other site 990288006161 putative PBP binding loops; other site 990288006162 ABC-ATPase subunit interface; other site 990288006163 pyruvate kinase; Validated; Region: PRK08187 990288006164 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 990288006165 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 990288006166 domain interfaces; other site 990288006167 active site 990288006168 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 990288006169 dinuclear metal binding motif [ion binding]; other site 990288006170 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 990288006171 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 990288006172 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional; Region: PRK11742 990288006173 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 990288006174 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 990288006175 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 990288006176 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...; Region: TRX_Fd_NuoE; cd03064 990288006177 putative dimer interface [polypeptide binding]; other site 990288006178 [2Fe-2S] cluster binding site [ion binding]; other site 990288006179 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 990288006180 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 990288006181 SLBB domain; Region: SLBB; pfam10531 990288006182 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 990288006183 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 990288006184 NADH dehydrogenase subunit G; Validated; Region: PRK08166 990288006185 catalytic loop [active] 990288006186 iron binding site [ion binding]; other site 990288006187 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 990288006188 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 990288006189 molybdopterin cofactor binding site; other site 990288006190 NADH dehydrogenase; Region: NADHdh; cl00469 990288006191 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 990288006192 4Fe-4S binding domain; Region: Fer4; cl02805 990288006193 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 990288006194 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 990288006195 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 990288006196 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 990288006197 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 990288006198 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 990288006199 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK08376 990288006200 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 990288006201 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 990288006202 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 990288006203 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 990288006204 S-adenosylmethionine binding site [chemical binding]; other site 990288006205 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 990288006206 Histidine phosphatase superfamily (branch 1); Region: His_Phos_1; pfam00300 990288006207 catalytic core [active] 990288006208 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; cl01951 990288006209 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 990288006210 metal binding site 2 [ion binding]; metal-binding site 990288006211 putative DNA binding helix; other site 990288006212 metal binding site 1 [ion binding]; metal-binding site 990288006213 dimer interface [polypeptide binding]; other site 990288006214 structural Zn2+ binding site [ion binding]; other site 990288006215 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 990288006216 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 990288006217 putative coenzyme Q binding site [chemical binding]; other site 990288006218 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 990288006219 putative active site [active] 990288006220 catalytic site [active] 990288006221 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 990288006222 putative active site [active] 990288006223 catalytic site [active] 990288006224 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 990288006225 SmpB-tmRNA interface; other site 990288006226 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT; cl01961 990288006227 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288006228 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 990288006229 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 990288006230 AIR carboxylase; Region: AIRC; cl00310 990288006231 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 990288006232 S-adenosylmethionine binding site [chemical binding]; other site 990288006233 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 990288006234 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 990288006235 ligand binding site [chemical binding]; other site 990288006236 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 990288006237 putative switch regulator; other site 990288006238 non-specific DNA interactions [nucleotide binding]; other site 990288006239 DNA binding site [nucleotide binding] 990288006240 sequence specific DNA binding site [nucleotide binding]; other site 990288006241 putative cAMP binding site [chemical binding]; other site 990288006242 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 990288006243 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 990288006244 potential frameshift: common BLAST hit: gi|218668135|ref|YP_002424773.1| glycosyl transferase, group 2 family protein 990288006245 hopene-associated glycosyltransferase HpnB; Region: HpnB; TIGR03469 990288006246 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 990288006247 active site 990288006248 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 990288006249 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 990288006250 Walker A motif; other site 990288006251 ATP binding site [chemical binding]; other site 990288006252 Walker B motif; other site 990288006253 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 990288006254 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 990288006255 Walker A motif; other site 990288006256 ATP binding site [chemical binding]; other site 990288006257 Walker B motif; other site 990288006258 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 990288006259 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 990288006260 catalytic residue [active] 990288006261 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288006262 YGGT family; Region: YGGT; cl00508 990288006263 Uncharacterised ACR, YggU family COG1872; Region: DUF167; cl00811 990288006264 biotin synthase; Provisional; Region: PRK15108 990288006265 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 990288006266 FeS/SAM binding site; other site 990288006267 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 990288006268 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 990288006269 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 990288006270 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 990288006271 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 990288006272 active site 990288006273 motif I; other site 990288006274 motif II; other site 990288006275 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...; Region: AAK_NAGK-C; cd04250 990288006276 feedback inhibition sensing region; other site 990288006277 homohexameric interface [polypeptide binding]; other site 990288006278 nucleotide binding site [chemical binding]; other site 990288006279 N-acetyl-L-glutamate binding site [chemical binding]; other site 990288006280 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 990288006281 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 990288006282 Putative zinc ribbon domain; Region: Zn_ribbon_2; pfam12674 990288006283 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 990288006284 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 990288006285 catalytic loop [active] 990288006286 iron binding site [ion binding]; other site 990288006287 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD...; Region: flavin_oxioreductase; cd06189 990288006288 FAD binding pocket [chemical binding]; other site 990288006289 FAD binding motif [chemical binding]; other site 990288006290 phosphate binding motif [ion binding]; other site 990288006291 beta-alpha-beta structure motif; other site 990288006292 NAD binding pocket [chemical binding]; other site 990288006293 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 990288006294 active site 990288006295 catalytic site [active] 990288006296 substrate binding site [chemical binding]; other site 990288006297 Uncharacterised protein family (UPF0014); Region: UPF0014; cl00424 990288006298 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 990288006299 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 990288006300 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 990288006301 Leucyl/phenylalanyl-tRNA protein transferase; Region: Leu_Phe_trans; cl01006 990288006302 Peptidase family M48; Region: Peptidase_M48; cl12018 990288006303 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 990288006304 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 990288006305 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 990288006306 S-adenosylmethionine binding site [chemical binding]; other site 990288006307 putative pimeloyl-BioC--CoA transferase BioH; Region: bioH; TIGR01738 990288006308 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 990288006309 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 990288006310 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 990288006311 catalytic residue [active] 990288006312 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 990288006313 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 990288006314 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 990288006315 phosphate:H+ symporter; Region: 2A0109; TIGR00887 990288006316 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 990288006317 putative substrate translocation pore; other site 990288006318 DinB superfamily; Region: DinB_2; cl00986 990288006319 TIGR03440 family protein; Region: unchr_TIGR03440 990288006320 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl00556 990288006321 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 990288006322 S-adenosylmethionine binding site [chemical binding]; other site 990288006323 aspartate aminotransferase; Provisional; Region: PRK08361 990288006324 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 990288006325 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288006326 homodimer interface [polypeptide binding]; other site 990288006327 catalytic residue [active] 990288006328 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (; Region: PTPc; cl00053 990288006329 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 990288006330 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 990288006331 putative active site [active] 990288006332 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 990288006333 putative metal binding site [ion binding]; other site 990288006334 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 990288006335 Probable Catalytic site [active] 990288006336 metal binding site [ion binding]; metal-binding site 990288006337 O-Antigen ligase; Region: Wzy_C; cl04850 990288006338 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 990288006339 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 990288006340 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 990288006341 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cl04270 990288006342 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 990288006343 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 990288006344 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 990288006345 Ligand binding site [chemical binding]; other site 990288006346 Putative Catalytic site [active] 990288006347 DXD motif; other site 990288006348 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 990288006349 active site 990288006350 8-oxo-dGMP binding site [chemical binding]; other site 990288006351 nudix motif; other site 990288006352 metal binding site [ion binding]; metal-binding site 990288006353 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- (beta-...; Region: TMP_TenI; cd00564 990288006354 thiamine phosphate binding site [chemical binding]; other site 990288006355 active site 990288006356 pyrophosphate binding site [ion binding]; other site 990288006357 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...; Region: OAT; cd02152 990288006358 heterotetramer interface [polypeptide binding]; other site 990288006359 active site pocket [active] 990288006360 cleavage site 990288006361 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 990288006362 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288006363 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 990288006364 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288006365 nucleotide binding region [chemical binding]; other site 990288006366 ATP-binding site [chemical binding]; other site 990288006367 SEC-C motif; Region: SEC-C; cl12132 990288006368 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 990288006369 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 990288006370 stringent starvation protein A; Provisional; Region: sspA; PRK09481 990288006371 GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival...; Region: GST_N_SspA; cd03059 990288006372 C-terminal domain interface [polypeptide binding]; other site 990288006373 putative GSH binding site (G-site) [chemical binding]; other site 990288006374 dimer interface [polypeptide binding]; other site 990288006375 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 990288006376 N-terminal domain interface [polypeptide binding]; other site 990288006377 dimer interface [polypeptide binding]; other site 990288006378 substrate binding pocket (H-site) [chemical binding]; other site 990288006379 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 990288006380 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 990288006381 cell division protein MraZ; Reviewed; Region: PRK00326 990288006382 MraZ protein; Region: MraZ; pfam02381 990288006383 MraZ protein; Region: MraZ; pfam02381 990288006384 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 990288006385 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288006386 Septum formation initiator; Region: DivIC; cl11433 990288006387 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 990288006388 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 990288006389 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 990288006390 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 990288006391 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 990288006392 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 990288006393 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 990288006394 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 990288006395 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 990288006396 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 990288006397 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 990288006398 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 undecaprenyl-pyrophosphoryl-N-...; Region: GT_MraY; cd06852 990288006399 Mg++ binding site [ion binding]; other site 990288006400 putative catalytic motif [active] 990288006401 putative substrate binding site [chemical binding]; other site 990288006402 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 990288006403 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 990288006404 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 990288006405 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 990288006406 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...; Region: GT1_MurG; cd03785 990288006407 active site 990288006408 homodimer interface [polypeptide binding]; other site 990288006409 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 990288006410 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 990288006411 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 990288006412 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 990288006413 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 990288006414 FAD binding domain; Region: FAD_binding_4; pfam01565 990288006415 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 990288006416 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 990288006417 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 990288006418 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 990288006419 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 990288006420 Cell division protein FtsQ; Region: FtsQ; pfam03799 990288006421 cell division protein FtsA; Region: ftsA; TIGR01174 990288006422 Cell division protein FtsA; Region: FtsA; cl11496 990288006423 Cell division protein FtsA; Region: FtsA; cl11496 990288006424 cell division protein FtsZ; Validated; Region: PRK09330 990288006425 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum...; Region: FtsZ_type1; cd02201 990288006426 nucleotide binding site [chemical binding]; other site 990288006427 SulA interaction site; other site 990288006428 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 990288006429 homodimer interface [polypeptide binding]; other site 990288006430 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 990288006431 active site pocket [active] 990288006432 Sulfatase; Region: Sulfatase; cl10460 990288006433 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 990288006434 Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; Region: Cenp-F_leu_zip; pfam10473 990288006435 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 990288006436 Peptidase family M23; Region: Peptidase_M23; pfam01551 990288006437 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 990288006438 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 990288006439 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 990288006440 protein binding site [polypeptide binding]; other site 990288006441 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 990288006442 Catalytic dyad [active] 990288006443 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 990288006444 conserved cys residue [active] 990288006445 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 990288006446 PPIC-type PPIASE domain; Region: Rotamase; cl08278 990288006447 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 990288006448 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 990288006449 Clp amino terminal domain; Region: Clp_N; pfam02861 990288006450 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288006451 Walker A motif; other site 990288006452 ATP binding site [chemical binding]; other site 990288006453 Walker B motif; other site 990288006454 arginine finger; other site 990288006455 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288006456 Walker A motif; other site 990288006457 ATP binding site [chemical binding]; other site 990288006458 Walker B motif; other site 990288006459 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 990288006460 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 990288006461 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 990288006462 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288006463 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288006464 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 990288006465 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 990288006466 N-terminal domain interface [polypeptide binding]; other site 990288006467 dimer interface [polypeptide binding]; other site 990288006468 substrate binding pocket (H-site) [chemical binding]; other site 990288006469 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 990288006470 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 990288006471 S-adenosylmethionine binding site [chemical binding]; other site 990288006472 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 990288006473 N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by...; Region: CIMS_N_terminal_like; cd03312 990288006474 THF binding site; other site 990288006475 C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by...; Region: CIMS_C_terminal_like; cd03311 990288006476 substrate binding site [chemical binding]; other site 990288006477 THF binding site; other site 990288006478 zinc-binding site [ion binding]; other site 990288006479 lipid-transfer protein; Provisional; Region: PRK07937 990288006480 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cd00882 990288006481 G1 box; other site 990288006482 GTP/Mg2+ binding site [chemical binding]; other site 990288006483 G2 box; other site 990288006484 Switch I region; other site 990288006485 G3 box; other site 990288006486 Switch II region; other site 990288006487 G4 box; other site 990288006488 G5 box; other site 990288006489 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 990288006490 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 990288006491 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 990288006492 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 990288006493 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 990288006494 voltage-gated potassium channel; Provisional; Region: PRK10537 990288006495 Ion channel; Region: Ion_trans_2; cl11596 990288006496 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288006497 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 990288006498 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 990288006499 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 990288006500 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 990288006501 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 990288006502 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 990288006503 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 C-...; Region: PDZ_serine_protease; cd00987 990288006504 protein binding site [polypeptide binding]; other site 990288006505 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 C-...; Region: PDZ_serine_protease; cd00987 990288006506 protein binding site [polypeptide binding]; other site 990288006507 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 990288006508 Beta-lactamase; Region: Beta-lactamase; cl01009 990288006509 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 990288006510 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 990288006511 TolB amino-terminal domain; Region: TolB_N; pfam04052 990288006512 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 990288006513 Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes sulfite sensitivity protein (sulfite efflux pump; SSU1); Region: TDT_SSU1; cd09318 990288006514 C4-dicarboxylate transporter/malic acid transport protein; Region: C4dic_mal_tran; pfam03595 990288006515 gating phenylalanine in ion channel; other site 990288006516 Transcriptional regulator [Transcription]; Region: LysR; COG0583 990288006517 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288006518 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 990288006519 dimerization interface [polypeptide binding]; other site 990288006520 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 990288006521 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 990288006522 Obg family GTPase CgtA; Region: Obg_CgtA; TIGR02729 990288006523 GTP1/OBG; Region: GTP1_OBG; pfam01018 990288006524 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 990288006525 G1 box; other site 990288006526 GTP/Mg2+ binding site [chemical binding]; other site 990288006527 Switch I region; other site 990288006528 G2 box; other site 990288006529 G3 box; other site 990288006530 Switch II region; other site 990288006531 G4 box; other site 990288006532 G5 box; other site 990288006533 gamma-glutamyl kinase; Provisional; Region: PRK05429 990288006534 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 990288006535 nucleotide binding site [chemical binding]; other site 990288006536 homotetrameric interface [polypeptide binding]; other site 990288006537 putative phosphate binding site [ion binding]; other site 990288006538 putative allosteric binding site; other site 990288006539 PUA domain; Region: PUA; cl00607 990288006540 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 990288006541 ligand binding site [chemical binding]; other site 990288006542 spermidine synthase; Provisional; Region: PRK00811 990288006543 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 990288006544 S-adenosylmethionine binding site [chemical binding]; other site 990288006545 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 990288006546 diaminopimelate decarboxylase; Region: lysA; TIGR01048 990288006547 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 990288006548 active site 990288006549 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 990288006550 substrate binding site [chemical binding]; other site 990288006551 catalytic residues [active] 990288006552 dimer interface [polypeptide binding]; other site 990288006553 argininosuccinate lyase; Provisional; Region: PRK00855 990288006554 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 990288006555 active sites [active] 990288006556 tetramer interface [polypeptide binding]; other site 990288006557 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; cl00859 990288006558 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 990288006559 Phosphotransferase enzyme family; Region: APH; pfam01636 990288006560 putative active site [active] 990288006561 putative substrate binding site [chemical binding]; other site 990288006562 ATP binding site [chemical binding]; other site 990288006563 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 990288006564 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 990288006565 DNA polymerase I; Provisional; Region: PRK05755 990288006566 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 990288006567 active site 990288006568 metal binding site 1 [ion binding]; metal-binding site 990288006569 putative 5' ssDNA interaction site; other site 990288006570 metal binding site 3; metal-binding site 990288006571 metal binding site 2 [ion binding]; metal-binding site 990288006572 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 990288006573 putative DNA binding site [nucleotide binding]; other site 990288006574 putative metal binding site [ion binding]; other site 990288006575 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 990288006576 active site 990288006577 catalytic site [active] 990288006578 substrate binding site [chemical binding]; other site 990288006579 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 990288006580 active site 990288006581 DNA binding site [nucleotide binding] 990288006582 catalytic site [active] 990288006583 voltage-gated potassium channel; Provisional; Region: PRK10537 990288006584 Ion channel; Region: Ion_trans_2; cl11596 990288006585 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288006586 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 990288006587 G1 box; other site 990288006588 GTP/Mg2+ binding site [chemical binding]; other site 990288006589 Switch I region; other site 990288006590 G2 box; other site 990288006591 G3 box; other site 990288006592 Switch II region; other site 990288006593 G4 box; other site 990288006594 G5 box; other site 990288006595 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 990288006596 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 990288006597 Major Facilitator Superfamily; Region: MFS_1; pfam07690 990288006598 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 990288006599 tetramerization interface [polypeptide binding]; other site 990288006600 active site 990288006601 plasma-membrane proton-efflux P-type ATPase; Region: ATPase-IIIA_H; TIGR01647 990288006602 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 990288006603 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 990288006604 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 990288006605 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 990288006606 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 990288006607 gluconate kinases; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_GntK; cd07770 990288006608 N- and C-terminal domain interface [polypeptide binding]; other site 990288006609 putative active site [active] 990288006610 catalytic site [active] 990288006611 metal binding site [ion binding]; metal-binding site 990288006612 carbohydrate binding site [chemical binding]; other site 990288006613 ATP binding site [chemical binding]; other site 990288006614 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 990288006615 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 990288006616 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 990288006617 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 990288006618 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288006619 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 990288006620 ABC transporter; Region: ABC_tran_2; pfam12848 990288006621 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 990288006622 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 990288006623 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288006624 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288006625 Transposase domain (DUF772); Region: DUF772; cl12084 990288006626 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288006627 hypothetical protein; Provisional; Region: PRK06148 990288006628 Peptidase family M23; Region: Peptidase_M23; pfam01551 990288006629 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases...; Region: lysozyme_like; cl00222 990288006630 Peptidase family M23; Region: Peptidase_M23; pfam01551 990288006631 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 990288006632 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases...; Region: lysozyme_like; cl00222 990288006633 Uncharacterized ACR, COG1430; Region: DUF192; cl00627 990288006634 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 990288006635 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 990288006636 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 990288006637 phosphopeptide binding site; other site 990288006638 Type II/IV secretion system protein; Region: GSPII_E; pfam00437 990288006639 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...; Region: VirB11-like_ATPase; cd01130 990288006640 ATP binding site [chemical binding]; other site 990288006641 Walker A motif; other site 990288006642 hexamer interface [polypeptide binding]; other site 990288006643 Walker B motif; other site 990288006644 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 990288006645 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 990288006646 SAF domain; Region: SAF; cl00555 990288006647 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 990288006648 Predicted methyltransferases [General function prediction only]; Region: COG0313 990288006649 LppC putative lipoprotein; Region: LppC; pfam04348 990288006650 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 990288006651 Uncharacterised protein family UPF0102; Region: UPF0102; cl00516 990288006652 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 990288006653 dimer interface [polypeptide binding]; other site 990288006654 active site 990288006655 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 990288006656 active site 990288006657 nucleotide binding site [chemical binding]; other site 990288006658 HIGH motif; other site 990288006659 KMSKS motif; other site 990288006660 FAD binding domain; Region: FAD_binding_4; pfam01565 990288006661 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 990288006662 Uncharacterised ACR, YagE family COG1723; Region: DUF155; cl00751 990288006663 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 990288006664 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 990288006665 putative active site [active] 990288006666 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 990288006667 ligand binding site [chemical binding]; other site 990288006668 outer membrane porin, OprD family; Region: OprD; pfam03573 990288006669 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 990288006670 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288006671 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 990288006672 putative dimerization interface [polypeptide binding]; other site 990288006673 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 990288006674 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 990288006675 FeS/SAM binding site; other site 990288006676 HemN C-terminal region; Region: HemN_C; pfam06969 990288006677 Uncharacterized conserved protein [Function unknown]; Region: COG1565 990288006678 Uncharacterized ACR, COG1565; Region: DUF185; pfam02636 990288006679 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288006680 NAD(P) binding site [chemical binding]; other site 990288006681 active site 990288006682 NifU-like domain; Region: NifU; cl00484 990288006683 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 990288006684 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 990288006685 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 990288006686 FeS/SAM binding site; other site 990288006687 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cl00233 990288006688 catalytic center binding site [active] 990288006689 ATP binding site [chemical binding]; other site 990288006690 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines...; Region: DHNA_DHNTPE; cd00534 990288006691 homooctamer interface [polypeptide binding]; other site 990288006692 active site 990288006693 Domain of unknown function (DUF205); Region: DUF205; cl00410 990288006694 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 990288006695 binding surface 990288006696 TPR motif; other site 990288006697 UGMP family protein; Validated; Region: PRK09604 990288006698 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 990288006699 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 990288006700 dinuclear metal binding motif [ion binding]; other site 990288006701 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue...; Region: GSH_Peroxidase; cd00340 990288006702 catalytic residues [active] 990288006703 dimer interface [polypeptide binding]; other site 990288006704 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 990288006705 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 990288006706 active site 990288006707 HIGH motif; other site 990288006708 dimer interface [polypeptide binding]; other site 990288006709 KMSKS motif; other site 990288006710 DsrE/DsrF-like family; Region: DrsE; cl00672 990288006711 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 990288006712 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 990288006713 Domain of unknown function DUF; Region: DUF202; cl09954 990288006714 Domain of unknown function DUF; Region: DUF202; cl09954 990288006715 MarC family integral membrane protein; Region: MarC; cl00919 990288006716 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 990288006717 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 990288006718 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 990288006719 dimer interface [polypeptide binding]; other site 990288006720 anticodon binding site; other site 990288006721 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 990288006722 homodimer interface [polypeptide binding]; other site 990288006723 motif 1; other site 990288006724 active site 990288006725 motif 2; other site 990288006726 GAD domain; Region: GAD; pfam02938 990288006727 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 990288006728 motif 3; other site 990288006729 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or...; Region: Nudix_Hydrolase; cl00447 990288006730 nudix motif; other site 990288006731 Quinolinate synthetase A protein; Region: NadA; cl00420 990288006732 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 990288006733 putative acyl-acceptor binding pocket; other site 990288006734 Domain of unknown function DUF28; Region: DUF28; cl00361 990288006735 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 990288006736 active site 990288006737 putative DNA-binding cleft [nucleotide binding]; other site 990288006738 dimer interface [polypeptide binding]; other site 990288006739 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 990288006740 RuvA N terminal domain; Region: RuvA_N; pfam01330 990288006741 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 990288006742 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 990288006743 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288006744 Walker A motif; other site 990288006745 ATP binding site [chemical binding]; other site 990288006746 Walker B motif; other site 990288006747 arginine finger; other site 990288006748 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 990288006749 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...; Region: 4HBT; cd00586 990288006750 active site 990288006751 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 990288006752 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 990288006753 Gram-negative bacterial tonB protein; Region: TonB; cl10048 990288006754 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 990288006755 TolB amino-terminal domain; Region: TolB_N; pfam04052 990288006756 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 990288006757 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 990288006758 Ligand Binding Site [chemical binding]; other site 990288006759 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 990288006760 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 990288006761 FeS/SAM binding site; other site 990288006762 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 990288006763 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi...; Region: TPR; cl02429 990288006764 binding surface 990288006765 TPR motif; other site 990288006766 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 990288006767 ligand binding site [chemical binding]; other site 990288006768 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 990288006769 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl03189 990288006770 domain interfaces; other site 990288006771 active site 990288006772 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations...; Region: HemD; cd06578 990288006773 active site 990288006774 Uroporphyrinogen-III synthase HemD; Region: HEM4; pfam02602 990288006775 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS; cd00384 990288006776 dimer interface [polypeptide binding]; other site 990288006777 active site 990288006778 Schiff base residues; other site 990288006779 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 990288006780 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; cl00290 990288006781 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 990288006782 benzoate transport; Region: 2A0115; TIGR00895 990288006783 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 990288006784 putative substrate translocation pore; other site 990288006785 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 990288006786 Haemolysin-III related; Region: HlyIII; cl03831 990288006787 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 990288006788 metal-binding site [ion binding] 990288006789 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 990288006790 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 990288006791 metal-binding site [ion binding] 990288006792 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 990288006793 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 990288006794 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 990288006795 metal-binding site [ion binding] 990288006796 ribonuclease G; Provisional; Region: PRK11712 990288006797 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 990288006798 homodimer interface [polypeptide binding]; other site 990288006799 oligonucleotide binding site [chemical binding]; other site 990288006800 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 990288006801 active site 990288006802 dimer interface [polypeptide binding]; other site 990288006803 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 990288006804 Domain of unknown function DUF143; Region: DUF143; cl00519 990288006805 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 990288006806 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 990288006807 active site 990288006808 (T/H)XGH motif; other site 990288006809 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 990288006810 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 990288006811 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface...; Region: TroA-like; cl00262 990288006812 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 990288006813 intersubunit interface [polypeptide binding]; other site 990288006814 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 990288006815 putative acyl-acceptor binding pocket; other site 990288006816 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 990288006817 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are...; Region: ACD_sHsps-like; cd06464 990288006818 putative dimer interface [polypeptide binding]; other site 990288006819 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 990288006820 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 990288006821 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 990288006822 G1 box; other site 990288006823 GTP/Mg2+ binding site [chemical binding]; other site 990288006824 Switch I region; other site 990288006825 G2 box; other site 990288006826 Switch II region; other site 990288006827 G3 box; other site 990288006828 G4 box; other site 990288006829 G5 box; other site 990288006830 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 990288006831 membrane protein insertase; Provisional; Region: PRK01318 990288006832 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 990288006833 Domain of unknown function DUF37; Region: DUF37; cl00506 990288006834 Ribonuclease P; Region: Ribonuclease_P; cl00457 990288006835 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 990288006836 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 990288006837 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 990288006838 Walker A/P-loop; other site 990288006839 ATP binding site [chemical binding]; other site 990288006840 Q-loop/lid; other site 990288006841 ABC transporter signature motif; other site 990288006842 Walker B; other site 990288006843 D-loop; other site 990288006844 H-loop/switch region; other site 990288006845 Domain of unknown function DUF140; Region: DUF140; cl00510 990288006846 mce related protein; Region: MCE; pfam02470 990288006847 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; cl01074 990288006848 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 990288006849 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 990288006850 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency...; Region: ABC_subfamily_A; cd03263 990288006851 Walker A/P-loop; other site 990288006852 ATP binding site [chemical binding]; other site 990288006853 Q-loop/lid; other site 990288006854 ABC transporter signature motif; other site 990288006855 Walker B; other site 990288006856 D-loop; other site 990288006857 H-loop/switch region; other site 990288006858 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 990288006859 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 990288006860 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 990288006861 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins...; Region: HNHc; cd00085 990288006862 active site 990288006863 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 990288006864 Family of unknown function (DUF1790); Region: DUF1790; cl02283 990288006865 Sporulation related domain; Region: SPOR; cl10051 990288006866 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 990288006867 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 990288006868 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 990288006869 active site 990288006870 HIGH motif; other site 990288006871 nucleotide binding site [chemical binding]; other site 990288006872 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 990288006873 KMSK motif region; other site 990288006874 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 990288006875 tRNA binding surface [nucleotide binding]; other site 990288006876 anticodon binding site; other site 990288006877 Major Facilitator Superfamily; Region: MFS_1; pfam07690 990288006878 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; cl11420 990288006879 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 990288006880 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288006881 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 990288006882 dimerization interface [polypeptide binding]; other site 990288006883 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 990288006884 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 990288006885 S-adenosylmethionine binding site [chemical binding]; other site 990288006886 Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Mth212-like_AP-endo; cd09085 990288006887 active site 990288006888 phosphate binding site A [ion binding]; other site 990288006889 putative catalytic site [active] 990288006890 DNA binding site [nucleotide binding] 990288006891 metal binding site A [ion binding]; metal-binding site 990288006892 putative AP binding site [nucleotide binding]; other site 990288006893 putative metal binding site B [ion binding]; other site 990288006894 phosphate binding site B [ion binding]; other site 990288006895 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; cl01820 990288006896 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 990288006897 putative glutathione S-transferase; Provisional; Region: PRK10357 990288006898 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 990288006899 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 990288006900 N-terminal domain interface [polypeptide binding]; other site 990288006901 dimer interface [polypeptide binding]; other site 990288006902 substrate binding pocket (H-site) [chemical binding]; other site 990288006903 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 990288006904 putative phosphate binding site [ion binding]; other site 990288006905 putative catalytic site [active] 990288006906 active site 990288006907 metal binding site A [ion binding]; metal-binding site 990288006908 DNA binding site [nucleotide binding] 990288006909 putative AP binding site [nucleotide binding]; other site 990288006910 putative metal binding site B [ion binding]; other site 990288006911 ferrochelatase; Reviewed; Region: hemH; PRK00035 990288006912 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 990288006913 C-terminal domain interface [polypeptide binding]; other site 990288006914 active site 990288006915 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 990288006916 active site 990288006917 N-terminal domain interface [polypeptide binding]; other site 990288006918 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 990288006919 Uncharacterised protein family (UPF0075); Region: UPF0075; cl04217 990288006920 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 990288006921 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 990288006922 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 990288006923 shikimate binding site; other site 990288006924 NAD(P) binding site [chemical binding]; other site 990288006925 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 990288006926 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 990288006927 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 990288006928 Walker A motif; other site 990288006929 ATP binding site [chemical binding]; other site 990288006930 Walker B motif; other site 990288006931 sensory histidine kinase AtoS; Provisional; Region: PRK11360 990288006932 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 trans-...; Region: HisKA; cd00082 990288006933 dimer interface [polypeptide binding]; other site 990288006934 phosphorylation site [posttranslational modification] 990288006935 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 990288006936 ATP binding site [chemical binding]; other site 990288006937 Mg2+ binding site [ion binding]; other site 990288006938 G-X-G motif; other site 990288006939 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 990288006940 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 990288006941 active site 990288006942 phosphorylation site [posttranslational modification] 990288006943 intermolecular recognition site; other site 990288006944 dimerization interface [polypeptide binding]; other site 990288006945 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288006946 Walker A motif; other site 990288006947 ATP binding site [chemical binding]; other site 990288006948 Walker B motif; other site 990288006949 arginine finger; other site 990288006950 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 990288006951 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 990288006952 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 990288006953 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 990288006954 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 990288006955 CoA-binding site [chemical binding]; other site 990288006956 ATP-binding [chemical binding]; other site 990288006957 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 990288006958 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1,7-...; Region: FBPase; cd00354 990288006959 AMP binding site [chemical binding]; other site 990288006960 metal binding site [ion binding]; metal-binding site 990288006961 active site 990288006962 Enterobacterial TraT complement resistance protein; Region: TraT; cl05410 990288006963 Stringent starvation protein B; Region: SspB; cl01120 990288006964 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 990288006965 N-acetyl-D-glucosamine binding site [chemical binding]; other site 990288006966 catalytic residue [active] 990288006967 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 990288006968 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 990288006969 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 990288006970 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 990288006971 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 990288006972 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 990288006973 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 990288006974 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 990288006975 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 990288006976 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 990288006977 carboxyltransferase (CT) interaction site; other site 990288006978 biotinylation site [posttranslational modification]; other site 990288006979 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 990288006980 trimer interface [polypeptide binding]; other site 990288006981 active site 990288006982 dimer interface [polypeptide binding]; other site 990288006983 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 990288006984 dimer interface [polypeptide binding]; other site 990288006985 FMN binding site [chemical binding]; other site 990288006986 comEA protein; Region: comE; TIGR01259 990288006987 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 990288006988 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the...; Region: HIT_like; cl00228 990288006989 nucleotide binding site/active site [active] 990288006990 HIT family signature motif; other site 990288006991 catalytic residue [active] 990288006992 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 990288006993 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 990288006994 inhibitor-cofactor binding pocket; inhibition site 990288006995 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288006996 catalytic residue [active] 990288006997 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- (beta-...; Region: TMP_TenI; cd00564 990288006998 thiamine phosphate binding site [chemical binding]; other site 990288006999 active site 990288007000 pyrophosphate binding site [ion binding]; other site 990288007001 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 990288007002 substrate binding site [chemical binding]; other site 990288007003 dimer interface [polypeptide binding]; other site 990288007004 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288007005 NAD(P) binding site [chemical binding]; other site 990288007006 active site 990288007007 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 990288007008 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 990288007009 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 990288007010 Gram-negative bacterial tonB protein; Region: TonB; cl10048 990288007011 Sodium:solute symporter family; Region: SSF; cl00456 990288007012 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...; Region: metallo-dependent_hydrolases; cl00281 990288007013 active site 990288007014 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 990288007015 active site 990288007016 purine riboside binding site [chemical binding]; other site 990288007017 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 990288007018 Transposase domain (DUF772); Region: DUF772; cl12084 990288007019 Integrase core domain; Region: rve; cl01316 990288007020 Integrase core domain; Region: rve; cl01316 990288007021 Transposase domain (DUF772); Region: DUF772; cl12084 990288007022 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 990288007023 IstB-like ATP binding N-terminal; Region: IstB_IS21_ATP; pfam08483 990288007024 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288007025 Integrase core domain; Region: rve; cl01316 990288007026 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 990288007027 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288007028 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 990288007029 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 990288007030 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 990288007031 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16...; Region: OM_channels; cl00284 990288007032 Transposase domain (DUF772); Region: DUF772; cl12084 990288007033 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 990288007034 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 990288007035 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 990288007036 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 990288007037 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 990288007038 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 990288007039 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 990288007040 Ureidoglycolate hydrolase; Region: Ureidogly_hydro; cl01250 990288007041 Amidohydrolase ring-opening protein (Amido_AtzD_TrzD); Region: Amido_AtzD_TrzD; pfam09663 990288007042 ring-opening amidohydrolases; Region: amido_AtzD_TrzD; TIGR02714 990288007043 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 990288007044 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 990288007045 amidase; Provisional; Region: PRK09201 990288007046 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 990288007047 Protein of unknown function (DUF3225); Region: DUF3225; pfam11533 990288007048 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 990288007049 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 990288007050 Transcriptional regulator [Transcription]; Region: LysR; COG0583 990288007051 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288007052 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 990288007053 dimerization interface [polypeptide binding]; other site 990288007054 Transposase domain (DUF772); Region: DUF772; cl12084 990288007055 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288007056 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 (...; Region: S24_LexA-like; cd06529 990288007057 Catalytic site [active] 990288007058 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 990288007059 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 990288007060 DNA binding site [nucleotide binding] 990288007061 Int/Topo IB signature motif; other site 990288007062 active site 990288007063 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 990288007064 IHF dimer interface [polypeptide binding]; other site 990288007065 IHF - DNA interface [nucleotide binding]; other site 990288007066 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 990288007067 IHF - DNA interface [nucleotide binding]; other site 990288007068 IHF dimer interface [polypeptide binding]; other site 990288007069 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 990288007070 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 990288007071 active site 990288007072 Fe-S cluster binding site [ion binding]; other site 990288007073 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 990288007074 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 990288007075 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 990288007076 putative active site [active] 990288007077 catalytic site [active] 990288007078 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 990288007079 Integrase core domain; Region: rve; cl01316 990288007080 HipA N-terminal domain; Region: couple_hipA; TIGR03071 990288007081 HipA-like N-terminal domain; Region: HipA_N; pfam07805 990288007082 HipA-like C-terminal domain; Region: HipA_C; pfam07804 990288007083 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 990288007084 UvrD/REP helicase; Region: UvrD-helicase; cl14126 990288007085 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 990288007086 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 four-...; Region: RecG_wedge_OBF; cd04488 990288007087 ssDNA binding site; other site 990288007088 generic binding surface II; other site 990288007089 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 990288007090 ATP binding site [chemical binding]; other site 990288007091 putative Mg++ binding site [ion binding]; other site 990288007092 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 990288007093 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 990288007094 nucleotide binding region [chemical binding]; other site 990288007095 ATP-binding site [chemical binding]; other site 990288007096 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 990288007097 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 990288007098 SpoVT / AbrB like domain; Region: SpoVT_AbrB; cl00877 990288007099 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 990288007100 metal binding site [ion binding]; metal-binding site 990288007101 active site 990288007102 I-site; other site 990288007103 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 990288007104 Putative transposase; Region: Y2_Tnp; pfam04986 990288007105 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 990288007106 Outer membrane efflux protein; Region: OEP; pfam02321 990288007107 Outer membrane efflux protein; Region: OEP; pfam02321 990288007108 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288007109 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 990288007110 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 990288007111 homodimer interface [polypeptide binding]; other site 990288007112 substrate-cofactor binding pocket; other site 990288007113 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288007114 catalytic residue [active] 990288007115 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 990288007116 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 990288007117 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288007118 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288007119 Natural resistance-associated macrophage protein; Region: Nramp; cl00836 990288007120 Cation efflux family; Region: Cation_efflux; cl00316 990288007121 Cation efflux family; Region: Cation_efflux; cl00316 990288007122 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 990288007123 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 990288007124 DNA binding residues [nucleotide binding] 990288007125 Cation efflux family; Region: Cation_efflux; cl00316 990288007126 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 990288007127 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; cl00859 990288007128 Protein of unknown function DUF124; Region: DUF124; cl00884 990288007129 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 990288007130 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 990288007131 Outer membrane efflux protein; Region: OEP; pfam02321 990288007132 Outer membrane efflux protein; Region: OEP; pfam02321 990288007133 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288007134 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288007135 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 990288007136 metal-binding site [ion binding] 990288007137 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 990288007138 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 990288007139 metal-binding site [ion binding] 990288007140 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 990288007141 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 990288007142 Domain of unknown function DUF302; Region: DUF302; cl01364 990288007143 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 990288007144 metal-binding site [ion binding] 990288007145 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...; Region: NrdH; cd02976 990288007146 catalytic residues [active] 990288007147 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 990288007148 putative substrate translocation pore; other site 990288007149 Protein of unknown function (DUF330); Region: DUF330; cl01135 990288007150 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 990288007151 mce related protein; Region: MCE; pfam02470 990288007152 mce related protein; Region: MCE; pfam02470 990288007153 mce related protein; Region: MCE; pfam02470 990288007154 Paraquat-inducible protein A; Region: PqiA; pfam04403 990288007155 Paraquat-inducible protein A; Region: PqiA; pfam04403 990288007156 Sel1 repeat; Region: Sel1; cl02723 990288007157 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288007158 Walker A motif; other site 990288007159 ATP binding site [chemical binding]; other site 990288007160 Bacterial TniB protein; Region: TniB; pfam05621 990288007161 Walker B motif; other site 990288007162 Tn7 transposition regulator TnsC; Region: Tn7_TnsC_Int; pfam11426 990288007163 Integrase core domain; Region: rve; cl01316 990288007164 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; cl07370 990288007165 TnsA endonuclease C terminal; Region: Tn7_Tnp_TnsA_C; pfam08721 990288007166 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288007167 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288007168 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 990288007169 IstB-like ATP binding N-terminal; Region: IstB_IS21_ATP; pfam08483 990288007170 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288007171 Integrase core domain; Region: rve; cl01316 990288007172 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 990288007173 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 990288007174 Coenzyme A binding pocket [chemical binding]; other site 990288007175 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 990288007176 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 990288007177 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 990288007178 dimerization interface [polypeptide binding]; other site 990288007179 putative DNA binding site [nucleotide binding]; other site 990288007180 putative Zn2+ binding site [ion binding]; other site 990288007181 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 990288007182 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 990288007183 N-acetyl-D-glucosamine binding site [chemical binding]; other site 990288007184 catalytic residue [active] 990288007185 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 990288007186 putative peptidoglycan binding site; other site 990288007187 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 990288007188 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 990288007189 DHH family; Region: DHH; pfam01368 990288007190 DHHA1 domain; Region: DHHA1; pfam02272 990288007191 NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]; Region: Lig; COG0272 990288007192 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; cl03295 990288007193 nucleotide binding pocket [chemical binding]; other site 990288007194 K-X-D-G motif; other site 990288007195 catalytic site [active] 990288007196 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 990288007197 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 990288007198 Dimer interface [polypeptide binding]; other site 990288007199 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 990288007200 S-adenosylmethionine binding site [chemical binding]; other site 990288007201 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins...; Region: HNHc; cd00085 990288007202 active site 990288007203 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 990288007204 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 990288007205 Mg2+ binding site [ion binding]; other site 990288007206 G-X-G motif; other site 990288007207 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 990288007208 anchoring element; other site 990288007209 dimer interface [polypeptide binding]; other site 990288007210 ATP binding site [chemical binding]; other site 990288007211 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of...; Region: TOPRIM_TopoIIA_GyrB; cd03366 990288007212 active site 990288007213 putative metal-binding site [ion binding]; other site 990288007214 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 990288007215 DNA gyrase subunit A; Validated; Region: PRK05560 990288007216 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in...; Region: TOP4c; cd00187 990288007217 CAP-like domain; other site 990288007218 Active site [active] 990288007219 primary dimer interface [polypeptide binding]; other site 990288007220 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 990288007221 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 990288007222 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 990288007223 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 990288007224 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 990288007225 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 990288007226 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 990288007227 dimer interface [polypeptide binding]; other site 990288007228 ssDNA binding site [nucleotide binding]; other site 990288007229 tetramer (dimer of dimers) interface [polypeptide binding]; other site 990288007230 SprT homologues; Region: SprT; cl01182 990288007231 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 990288007232 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl15270 990288007233 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 990288007234 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 990288007235 DNA binding site [nucleotide binding] 990288007236 Int/Topo IB signature motif; other site 990288007237 active site 990288007238 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 990288007239 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 990288007240 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]; Region: COG1205 990288007241 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 990288007242 ATP binding site [chemical binding]; other site 990288007243 putative Mg++ binding site [ion binding]; other site 990288007244 Superfamily II DNA helicase [DNA replication, recombination, and repair]; Region: RecQ; COG0514 990288007245 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]; Region: COG1205 990288007246 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 990288007247 ATP-binding site [chemical binding]; other site 990288007248 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 990288007249 transposase; Provisional; Region: PRK06526 990288007250 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288007251 Walker A motif; other site 990288007252 ATP binding site [chemical binding]; other site 990288007253 Walker B motif; other site 990288007254 Integrase core domain; Region: rve; cl01316 990288007255 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 990288007256 ATP binding site [chemical binding]; other site 990288007257 putative Mg++ binding site [ion binding]; other site 990288007258 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 990288007259 nucleotide binding region [chemical binding]; other site 990288007260 ATP-binding site [chemical binding]; other site 990288007261 Phd_YefM; Region: PhdYeFM; cl09153 990288007262 PIN domain of the hypothetical protein MT3492 of Mycobacterium tuberculosis CDC1551 and other uncharacterized, annotated PilT protein domain proteins; Region: PIN_MT3492; cd09874 990288007263 putative active site [active] 990288007264 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 990288007265 Predicted restriction endonuclease [Defense mechanisms]; Region: COG3440 990288007266 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 990288007267 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 990288007268 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 990288007269 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 990288007270 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 990288007271 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 990288007272 Transposase; Region: DEDD_Tnp_IS110; pfam01548 990288007273 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 990288007274 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 990288007275 RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons...; Region: RT_like; cl02808 990288007276 transposase/IS protein; Provisional; Region: PRK09183 990288007277 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288007278 Walker A motif; other site 990288007279 ATP binding site [chemical binding]; other site 990288007280 Walker B motif; other site 990288007281 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 990288007282 Integrase core domain; Region: rve; cl01316 990288007283 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 990288007284 putative active site [active] 990288007285 putative NTP binding site [chemical binding]; other site 990288007286 putative nucleic acid binding site [nucleotide binding]; other site 990288007287 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 990288007288 Outer membrane lipoprotein Slp family; Region: Slp; cl01164 990288007289 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 990288007290 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 990288007291 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 990288007292 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288007293 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288007294 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16...; Region: OM_channels; cl00284 990288007295 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 990288007296 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288007297 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288007298 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 990288007299 Transposase domain (DUF772); Region: DUF772; cl12084 990288007300 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288007301 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 990288007302 IstB-like ATP binding N-terminal; Region: IstB_IS21_ATP; pfam08483 990288007303 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288007304 Integrase core domain; Region: rve; cl01316 990288007305 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 990288007306 Transposase domain (DUF772); Region: DUF772; cl12084 990288007307 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288007308 RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons...; Region: RT_like; cl02808 990288007309 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 990288007310 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 990288007311 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 990288007312 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 990288007313 putative active site [active] 990288007314 putative NTP binding site [chemical binding]; other site 990288007315 putative nucleic acid binding site [nucleotide binding]; other site 990288007316 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 990288007317 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288007318 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288007319 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 990288007320 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 990288007321 inhibitor-cofactor binding pocket; inhibition site 990288007322 pyridoxal 5'-phosphate binding site [chemical binding]; other site 990288007323 catalytic residue [active] 990288007324 Transposase, Mutator family; Region: Transposase_mut; pfam00872 990288007325 MULE transposase domain; Region: MULE; pfam10551 990288007326 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288007327 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288007328 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 990288007329 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 990288007330 N-terminal plug; other site 990288007331 ligand-binding site [chemical binding]; other site 990288007332 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 990288007333 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 990288007334 Transposase domain (DUF772); Region: DUF772; cl12084 990288007335 IstB-like ATP binding N-terminal; Region: IstB_IS21_ATP; pfam08483 990288007336 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 990288007337 Integrase core domain; Region: rve; cl01316 990288007338 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 990288007339 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288007340 Transposase, Mutator family; Region: Transposase_mut; pfam00872 990288007341 MULE transposase domain; Region: MULE; pfam10551 990288007342 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl01116 990288007343 Integrase core domain; Region: rve; cl01316 990288007344 Transposase domain (DUF772); Region: DUF772; cl12084 990288007345 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288007346 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 990288007347 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 990288007348 Walker A motif; other site 990288007349 ATP binding site [chemical binding]; other site 990288007350 Walker B motif; other site 990288007351 Transposase domain (DUF772); Region: DUF772; cl12084 990288007352 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 990288007353 putative toxin-antitoxin system antitoxin component, TIGR02293 family; Region: TAS_TIGR02293 990288007354 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 990288007355 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 990288007356 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 990288007357 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 990288007358 P loop; other site 990288007359 Nucleotide binding site [chemical binding]; other site 990288007360 DTAP/Switch II; other site 990288007361 Switch I; other site 990288007362 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...; Region: ParA; cd02042 990288007363 Magnesium ion binding site [ion binding]; other site 990288007364 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 990288007365 ParB-like nuclease domain; Region: ParBc; cl02129 990288007366 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 990288007367 dimer interface [polypeptide binding]; other site 990288007368 putative radical transfer pathway; other site 990288007369 diiron center [ion binding]; other site 990288007370 tyrosyl radical; other site 990288007371 Protein of unknown function (DUF1640); Region: DUF1640; pfam07798 990288007372 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15258 990288007373 HipA N-terminal domain; Region: couple_hipA; TIGR03071 990288007374 HipA-like N-terminal domain; Region: HipA_N; pfam07805 990288007375 HipA-like C-terminal domain; Region: HipA_C; pfam07804 990288007376 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 990288007377 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 990288007378 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; cl14891 990288007379 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 990288007380 Transposase; Region: DEDD_Tnp_IS110; pfam01548 990288007381 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 990288007382 potential frameshift: common BLAST hit: gi|198283446|ref|YP_002219767.1| transposase IS66 990288007383 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 990288007384 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 990288007385 Transposase, Mutator family; Region: Transposase_mut; pfam00872 990288007386 Protein of unknown function (DUF1275); Region: DUF1275; cl01453 990288007387 Relaxase/Mobilisation nuclease domain; Region: Relaxase; cl01584 990288007388 Predicted DNA-binding protein with an HTH domain [General function prediction only]; Region: COG4710 990288007389 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 990288007390 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 990288007391 Transposase IS200 like; Region: Y1_Tnp; cl00848 990288007392 Replication protein C (RepC); Region: RepC; pfam06504 990288007393 Hexameric Replicative Helicase RepA. RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent; Region: repA; cd01125 990288007394 Walker A motif; other site 990288007395 NTP binding site [chemical binding]; other site 990288007396 hexamer interface [polypeptide binding]; other site 990288007397 Walker B motif; other site 990288007398 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 990288007399 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 990288007400 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 990288007401 IHF - DNA interface [nucleotide binding]; other site 990288007402 IHF dimer interface [polypeptide binding]; other site 990288007403 Conjugal transfer protein TraD; Region: TraD; cl05753 990288007404 MobA/MobL family; Region: MobA_MobL; pfam03389 990288007405 conjugal transfer relaxase TraI; Provisional; Region: PRK13878 990288007406 DsrE/DsrF-like family; Region: DrsE; cl00672 990288007407 Protein of unknown function (DUF2283); Region: DUF2283; cl02251 990288007408 Phosphate-selective porin O and P; Region: Porin_O_P; cl01524 990288007409 multiple promoter invertase; Provisional; Region: mpi; PRK13413 990288007410 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 990288007411 catalytic residues [active] 990288007412 catalytic nucleophile [active] 990288007413 Presynaptic Site I dimer interface [polypeptide binding]; other site 990288007414 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 990288007415 Synaptic Flat tetramer interface [polypeptide binding]; other site 990288007416 Synaptic Site I dimer interface [polypeptide binding]; other site 990288007417 DNA binding site [nucleotide binding] 990288007418 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 990288007419 DNA-binding interface [nucleotide binding]; DNA binding site 990288007420 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...; Region: ParA; cd02042 990288007421 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 990288007422 P-loop; other site 990288007423 Magnesium ion binding site [ion binding]; other site 990288007424 ParG; Region: ParG; pfam09274 990288007425 Plasmid encoded RepA protein; Region: RepA_C; pfam04796 990288007426 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 990288007427 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 990288007428 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 990288007429 flagellar motor protein MotB; Validated; Region: motB; PRK05996 990288007430 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314; cl02193 990288007431 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 990288007432 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288007433 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 990288007434 Anion-transporting ATPase; Region: ArsA_ATPase; pfam02374 990288007435 Oxyanion-translocating ATPase (ArsA). This ATPase is involved in transport of arsenite, antimonite or other oxyanions across biological membranes in all three kingdoms of life. ArsA contains a highly conserved AAA motif present in the AAA+ ATPase...; Region: ArsA_ATPase; cd00550 990288007436 ATP binding site [chemical binding]; other site 990288007437 dimerization interface [polypeptide binding]; other site 990288007438 Metal binding site [ion binding]; metal-binding site 990288007439 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 990288007440 arsenite-activated ATPase ArsA; Region: arsA; TIGR00345 990288007441 dimerization interface [polypeptide binding]; other site 990288007442 Metal binding site [ion binding]; metal-binding site 990288007443 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 990288007444 Low molecular weight phosphatase family; Region: LMWPc; cd00115 990288007445 Active site [active] 990288007446 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 990288007447 dimerization interface [polypeptide binding]; other site 990288007448 putative DNA binding site [nucleotide binding]; other site 990288007449 putative Zn2+ binding site [ion binding]; other site 990288007450 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 990288007451 multiple promoter invertase; Provisional; Region: mpi; PRK13413 990288007452 catalytic residues [active] 990288007453 catalytic nucleophile [active] 990288007454 Presynaptic Site I dimer interface [polypeptide binding]; other site 990288007455 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 990288007456 Synaptic Flat tetramer interface [polypeptide binding]; other site 990288007457 Synaptic Site I dimer interface [polypeptide binding]; other site 990288007458 DNA binding site [nucleotide binding] 990288007459 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 990288007460 DNA-binding interface [nucleotide binding]; DNA binding site 990288007461 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 990288007462 IHF - DNA interface [nucleotide binding]; other site 990288007463 IHF dimer interface [polypeptide binding]; other site 990288007464 Conjugal transfer protein TraD; Region: TraD; cl05753 990288007465 MobA/MobL family; Region: MobA_MobL; pfam03389 990288007466 conjugal transfer relaxase TraI; Provisional; Region: PRK13878 990288007467 SpoVT / AbrB like domain; Region: SpoVT_AbrB; cl00877 990288007468 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 990288007469 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 990288007470 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 990288007471 Transposase; Region: DDE_Tnp_ISL3; pfam01610 990288007472 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 990288007473 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 990288007474 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 990288007475 DNA-binding site [nucleotide binding]; DNA binding site 990288007476 UTRA domain; Region: UTRA; cl01230 990288007477 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 990288007478 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 990288007479 catalytic residues [active] 990288007480 catalytic nucleophile [active] 990288007481 Presynaptic Site I dimer interface [polypeptide binding]; other site 990288007482 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 990288007483 Synaptic Flat tetramer interface [polypeptide binding]; other site 990288007484 Synaptic Site I dimer interface [polypeptide binding]; other site 990288007485 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 990288007486 DNA-binding interface [nucleotide binding]; DNA binding site 990288007487 WGR domain of molybdate metabolism regulator and related proteins; Region: WGR_MMR_like; cd07996 990288007488 FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 990288007489 putative active site [active] 990288007490 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 990288007491 SpoVT / AbrB like domain; Region: SpoVT_AbrB; cl00877 990288007492 ParA-like protein; Provisional; Region: PHA02518 990288007493 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...; Region: ParA; cd02042 990288007494 P-loop; other site 990288007495 Magnesium ion binding site [ion binding]; other site