-- dump date 20140619_104054 -- class Genbank::misc_feature -- table misc_feature_note -- id note 233412000001 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 233412000002 tRNA:m(5)U-54 methyltransferase; Region: gid_trmFO; TIGR00137 233412000003 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 233412000004 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 233412000005 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 233412000006 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 233412000007 S-adenosylmethionine binding site [chemical binding]; other site 233412000008 F0F1 ATP synthase subunit I; Validated; Region: PRK06099 233412000009 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 233412000010 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 233412000011 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 233412000012 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 233412000013 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 233412000014 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 233412000015 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 233412000016 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 233412000017 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 233412000018 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 233412000019 beta subunit interaction interface [polypeptide binding]; other site 233412000020 Walker A motif; other site 233412000021 ATP binding site [chemical binding]; other site 233412000022 Walker B motif; other site 233412000023 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 233412000024 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 233412000025 core domain interface [polypeptide binding]; other site 233412000026 delta subunit interface [polypeptide binding]; other site 233412000027 epsilon subunit interface [polypeptide binding]; other site 233412000028 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 233412000029 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 233412000030 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 233412000031 alpha subunit interaction interface [polypeptide binding]; other site 233412000032 Walker A motif; other site 233412000033 ATP binding site [chemical binding]; other site 233412000034 Walker B motif; other site 233412000035 inhibitor binding site; inhibition site 233412000036 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 233412000037 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 233412000038 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 233412000039 gamma subunit interface [polypeptide binding]; other site 233412000040 epsilon subunit interface [polypeptide binding]; other site 233412000041 LBP interface [polypeptide binding]; other site 233412000042 rRNA operon variant 1 difference region; HDprRNA1d 233412000043 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 233412000044 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 233412000045 active site 233412000046 Int/Topo IB signature motif; other site 233412000047 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 233412000048 Ligand Binding Site [chemical binding]; other site 233412000049 TilS substrate binding domain; Region: TilS; pfam09179 233412000050 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 233412000051 protease TldD; Provisional; Region: tldD; PRK10735 233412000052 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 233412000053 DNA methylase; Region: N6_N4_Mtase; cl17433 233412000054 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 233412000055 S-adenosylmethionine binding site [chemical binding]; other site 233412000056 conserved possible glucokinase regulatory protein, N-terminal fragment; HDp0017A 233412000057 conserved hypothetical protein, central fragment; HDp0019B 233412000058 conserved hypothetical protein, N-terminal fragment; HDp0019A 233412000059 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 233412000060 Major Facilitator Superfamily; Region: MFS_1; pfam07690 233412000061 putative substrate translocation pore; other site 233412000062 CrcB-like protein; Region: CRCB; cl09114 233412000063 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 233412000064 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK09412 233412000065 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 233412000066 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 233412000067 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 233412000068 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 233412000069 poxB regulator PoxA; Provisional; Region: PRK09350 233412000070 motif 1; other site 233412000071 dimer interface [polypeptide binding]; other site 233412000072 active site 233412000073 motif 2; other site 233412000074 motif 3; other site 233412000075 fumarate reductase flavoprotein subunit; Validated; Region: PRK09231 233412000076 L-aspartate oxidase; Provisional; Region: PRK06175 233412000077 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 233412000078 fumarate reductase iron-sulfur subunit; Provisional; Region: PRK12385 233412000079 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 233412000080 catalytic loop [active] 233412000081 iron binding site [ion binding]; other site 233412000082 Quinol:fumarate reductase (QFR) Type D subfamily, 15kD hydrophobic subunit C; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine...; Region: QFR_TypeD_subunitC; cd00546 233412000083 D-subunit interface [polypeptide binding]; other site 233412000084 Iron-sulfur protein interface; other site 233412000085 proximal quinone binding site [chemical binding]; other site 233412000086 distal quinone binding site [chemical binding]; other site 233412000087 Quinol:fumarate reductase (QFR) Type D subfamily, 13kD hydrophobic subunit D; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine...; Region: QFR_TypeD_subunitD; cd00547 233412000088 Iron-sulfur protein interface; other site 233412000089 proximal quinone binding site [chemical binding]; other site 233412000090 C-subunit interface; other site 233412000091 distal quinone binding site; other site 233412000092 Prokaryotic lipoprotein-attachment site; Region: LPAM_2; cl02361 233412000093 diaminopimelate decarboxylase; Region: lysA; TIGR01048 233412000094 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 233412000095 active site 233412000096 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 233412000097 substrate binding site [chemical binding]; other site 233412000098 catalytic residues [active] 233412000099 dimer interface [polypeptide binding]; other site 233412000100 putative heme utilization radical SAM enzyme HutW; Region: rSAM_HutW; TIGR04107 233412000101 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 233412000102 FeS/SAM binding site; other site 233412000103 putative heme utilization carrier protein HutX; Region: HutX; TIGR04108 233412000104 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 233412000105 NADH(P)-binding; Region: NAD_binding_10; pfam13460 233412000106 NAD(P) binding site [chemical binding]; other site 233412000107 active site 233412000108 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 233412000109 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 233412000110 trmE is a tRNA modification GTPase; Region: trmE; cd04164 233412000111 G1 box; other site 233412000112 GTP/Mg2+ binding site [chemical binding]; other site 233412000113 Switch I region; other site 233412000114 G2 box; other site 233412000115 Switch II region; other site 233412000116 G3 box; other site 233412000117 G4 box; other site 233412000118 G5 box; other site 233412000119 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 233412000120 membrane protein insertase; Provisional; Region: PRK01318 233412000121 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 233412000122 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 233412000123 CoenzymeA binding site [chemical binding]; other site 233412000124 subunit interaction site [polypeptide binding]; other site 233412000125 PHB binding site; other site 233412000126 outer membrane protein A; Reviewed; Region: PRK10808 233412000127 OmpA-like transmembrane domain; Region: OmpA_membrane; pfam01389 233412000128 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 233412000129 ligand binding site [chemical binding]; other site 233412000130 outer membrane protein A; Reviewed; Region: PRK10808 233412000131 OmpA-like transmembrane domain; Region: OmpA_membrane; pfam01389 233412000132 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 233412000133 ligand binding site [chemical binding]; other site 233412000134 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional; Region: PRK15018 233412000135 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 233412000136 putative acyl-acceptor binding pocket; other site 233412000137 FtsI repressor; Provisional; Region: PRK10883 233412000138 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 233412000139 Multicopper oxidase; Region: Cu-oxidase; pfam00394 233412000140 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 233412000141 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 233412000142 Sialyltransferase PMO188; Region: PM0188; pfam11477 233412000143 elongation factor Tu; Reviewed; Region: PRK00049 233412000144 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 233412000145 G1 box; other site 233412000146 GEF interaction site [polypeptide binding]; other site 233412000147 GTP/Mg2+ binding site [chemical binding]; other site 233412000148 Switch I region; other site 233412000149 G2 box; other site 233412000150 G3 box; other site 233412000151 Switch II region; other site 233412000152 G4 box; other site 233412000153 G5 box; other site 233412000154 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 233412000155 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 233412000156 Antibiotic Binding Site [chemical binding]; other site 233412000157 pantothenate kinase; Provisional; Region: PRK05439 233412000158 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point...; Region: PanK; cd02025 233412000159 ATP-binding site [chemical binding]; other site 233412000160 CoA-binding site [chemical binding]; other site 233412000161 Mg2+-binding site [ion binding]; other site 233412000162 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 233412000163 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 233412000164 catalytic residues [active] 233412000165 central insert; other site 233412000166 cytochrome c-type biogenesis protein CcmH precursor, N-terminal fragment; HDp0060A 233412000167 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 233412000168 MPT binding site; other site 233412000169 trimer interface [polypeptide binding]; other site 233412000170 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 233412000171 Nitrogen regulatory protein P-II; Region: P-II; smart00938 233412000172 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 233412000173 lipoprotein signal peptidase; Provisional; Region: PRK14787 233412000174 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 233412000175 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 233412000176 Uncharacterized conserved protein [Function unknown]; Region: COG2938 233412000177 Patatin-like phospholipase; Region: Patatin; pfam01734 233412000178 active site 233412000179 nucleophile elbow; other site 233412000180 Ferritin-like domain; Region: Ferritin; pfam00210 233412000181 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 233412000182 dimerization interface [polypeptide binding]; other site 233412000183 DPS ferroxidase diiron center [ion binding]; other site 233412000184 ion pore; other site 233412000185 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 233412000186 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 233412000187 ferredoxin-type protein NapF; Region: napF; TIGR00402 233412000188 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 233412000189 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 233412000190 NapD protein; Region: NapD; pfam03927 233412000191 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 233412000192 Nitrate reductases, NapA (Nitrate-R-NapA), 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...; Region: MopB_Nitrate-R-NapA-like; cd02754 233412000193 [4Fe-4S] binding site [ion binding]; other site 233412000194 molybdopterin cofactor binding site; other site 233412000195 Nitrate reductases, NapA (Nitrate-R-NapA), 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...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 233412000196 molybdopterin cofactor binding site; other site 233412000197 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 233412000198 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 233412000199 4Fe-4S binding domain; Region: Fer4_5; pfam12801 233412000200 4Fe-4S binding domain; Region: Fer4_6; pfam12837 233412000201 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 233412000202 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 233412000203 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 233412000204 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 233412000205 FAD binding domain; Region: FAD_binding_4; pfam01565 233412000206 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 233412000207 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 233412000208 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 233412000209 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 233412000210 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 233412000211 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 233412000212 phosphate binding site [ion binding]; other site 233412000213 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 233412000214 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 233412000215 Sigma-70, region 4; Region: Sigma70_r4; pfam04545 233412000216 DNA binding residues [nucleotide binding] 233412000217 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 233412000218 non-specific DNA binding site [nucleotide binding]; other site 233412000219 Predicted transcriptional regulator [Transcription]; Region: COG2932 233412000220 salt bridge; other site 233412000221 sequence-specific DNA binding site [nucleotide binding]; other site 233412000222 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 233412000223 Catalytic site [active] 233412000224 Winged helix-turn-helix DNA-binding; Region: HTH_35; cl17423 233412000225 Mu-like prophage FluMu transposase A, N-terminal fragment; HDp0094A 233412000226 Uncharacterized ATPase, putative transposase [General function prediction only]; Region: COG2842 233412000227 Mu B transposition protein, C terminal; Region: Phage-MuB_C; pfam09077 233412000228 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 233412000229 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 233412000230 Protein of unknown function (DUF2786); Region: DUF2786; pfam10979 233412000231 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 233412000232 Mor transcription activator family; Region: Mor; cl02360 233412000233 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 233412000234 amidase catalytic site [active] 233412000235 Zn binding residues [ion binding]; other site 233412000236 substrate binding site [chemical binding]; other site 233412000237 Protein of unknown function (DUF2644); Region: DUF2644; pfam10841 233412000238 Protein of unknown function (DUF2681); Region: DUF2681; pfam10883 233412000239 phage/conjugal plasmid C-4 type zinc finger protein, TraR family; Region: C4_traR_proteo; TIGR02419 233412000240 Protein of unknown function (DUF2730); Region: DUF2730; pfam10805 233412000241 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 233412000242 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 233412000243 Terminase-like family; Region: Terminase_6; pfam03237 233412000244 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 233412000245 Protein of unknown function (DUF935); Region: DUF935; pfam06074 233412000246 Mu-like prophage FluMu F protein, N-terminal fragment; HDp0126A 233412000247 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 233412000248 Mu-like prophage FluMu I protein, N-terminal fragment; HDp0130A 233412000249 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 233412000250 HeH/LEM domain; Region: HeH; pfam12949 233412000251 Protein of unknown function (DUF1320); Region: DUF1320; cl01818 233412000252 Domain of unknown function (DUF1834); Region: DUF1834; pfam08873 233412000253 tape measure domain; Region: tape_meas_nterm; TIGR02675 233412000254 L-rhamnose isomerase; Region: rhaA; TIGR01748 233412000255 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 233412000256 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 233412000257 SseB protein; Region: SseB; cl06279 233412000258 Putative phage tail protein; Region: Phage-tail_3; pfam13550 233412000259 Putative amino acid metabolism; Region: DUF1831; pfam08866 233412000260 TfpB protein homolog, N-terminal fragment; HDp0164A 233412000261 malate:quinone oxidoreductase; Validated; Region: PRK05257 233412000262 malate:quinone-oxidoreductase; Region: mal_quin_oxido; TIGR01320 233412000263 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 233412000264 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 233412000265 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 233412000266 S-adenosylmethionine binding site [chemical binding]; other site 233412000267 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 233412000268 dimer interface [polypeptide binding]; other site 233412000269 substrate binding site [chemical binding]; other site 233412000270 metal binding sites [ion binding]; metal-binding site 233412000271 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 233412000272 putative active site [active] 233412000273 Ap4A binding site [chemical binding]; other site 233412000274 nudix motif; other site 233412000275 putative metal binding site [ion binding]; other site 233412000276 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 233412000277 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 233412000278 phosphoglycolate phosphatase; Provisional; Region: PRK13222 233412000279 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 233412000280 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 233412000281 motif II; other site 233412000282 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 233412000283 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 233412000284 active site 233412000285 HIGH motif; other site 233412000286 dimer interface [polypeptide binding]; other site 233412000287 KMSKS motif; other site 233412000288 Ter macrodomain organizer matS-binding protein; Provisional; Region: PRK05097 233412000289 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 233412000290 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 233412000291 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 233412000292 active site 1 [active] 233412000293 dimer interface [polypeptide binding]; other site 233412000294 active site 2 [active] 233412000295 Prokaryotic N-terminal methylation motif; Region: N_methyl; pfam07963 233412000296 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 233412000297 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 233412000298 protease3; Provisional; Region: PRK15101 233412000299 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 233412000300 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 233412000301 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 233412000302 chaperone protein DnaJ; Provisional; Region: PRK10767 233412000303 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 233412000304 HSP70 interaction site [polypeptide binding]; other site 233412000305 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 233412000306 substrate binding site [polypeptide binding]; other site 233412000307 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 233412000308 Zn binding sites [ion binding]; other site 233412000309 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 233412000310 dimer interface [polypeptide binding]; other site 233412000311 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 233412000312 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 233412000313 nucleotide binding site [chemical binding]; other site 233412000314 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 233412000315 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 233412000316 active site 233412000317 Zn binding site [ion binding]; other site 233412000318 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 233412000319 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 233412000320 homodimer interface [polypeptide binding]; other site 233412000321 oligonucleotide binding site [chemical binding]; other site 233412000322 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 233412000323 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1755 233412000324 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 233412000325 high-affinity zinc transporter periplasmic component; Reviewed; Region: znuA; PRK09545 233412000326 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 233412000327 metal binding site [ion binding]; metal-binding site 233412000328 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 233412000329 tetramer (dimer of dimers) interface [polypeptide binding]; other site 233412000330 active site 233412000331 dimer interface [polypeptide binding]; other site 233412000332 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 233412000333 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 233412000334 active site 233412000335 substrate binding site [chemical binding]; other site 233412000336 metal binding site [ion binding]; metal-binding site 233412000337 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK10737 233412000338 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 233412000339 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 233412000340 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 233412000341 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 233412000342 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 233412000343 EamA-like transporter family; Region: EamA; pfam00892 233412000344 EamA-like transporter family; Region: EamA; pfam00892 233412000345 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 233412000346 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 233412000347 active site 233412000348 motif I; other site 233412000349 motif II; other site 233412000350 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 233412000351 motif II; other site 233412000352 DNA utilization protein GntX; Provisional; Region: PRK11595 233412000353 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 233412000354 active site 233412000355 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 233412000356 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 233412000357 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 233412000358 S-adenosylmethionine binding site [chemical binding]; other site 233412000359 DNA polymerase III subunit psi; Validated; Region: PRK06856 233412000360 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 233412000361 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 233412000362 Coenzyme A binding pocket [chemical binding]; other site 233412000363 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 233412000364 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 233412000365 ATP binding site [chemical binding]; other site 233412000366 Mg++ binding site [ion binding]; other site 233412000367 motif III; other site 233412000368 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 233412000369 nucleotide binding region [chemical binding]; other site 233412000370 ATP-binding site [chemical binding]; other site 233412000371 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 233412000372 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 233412000373 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 233412000374 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 233412000375 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 233412000376 peptide binding site [polypeptide binding]; other site 233412000377 Uncharacterized conserved protein [Function unknown]; Region: COG2835 233412000378 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 233412000379 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 233412000380 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 233412000381 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 233412000382 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 233412000383 Walker A motif; other site 233412000384 ATP binding site [chemical binding]; other site 233412000385 Walker B motif; other site 233412000386 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 233412000387 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 233412000388 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 233412000389 oligomer interface [polypeptide binding]; other site 233412000390 active site residues [active] 233412000391 Fe-S metabolism associated domain; Region: SufE; cl00951 233412000392 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 233412000393 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 233412000394 active site 233412000395 catalytic site [active] 233412000396 substrate binding site [chemical binding]; other site 233412000397 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 233412000398 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 233412000399 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 233412000400 ABC transporter; Region: ABC_tran_2; pfam12848 233412000401 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 233412000402 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 233412000403 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 233412000404 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 233412000405 FeS/SAM binding site; other site 233412000406 TRAM domain; Region: TRAM; pfam01938 233412000407 PTS system glucose-specific transporter subunit; Provisional; Region: PRK09439 233412000408 HPr interaction site; other site 233412000409 glycerol kinase (GK) interaction site [polypeptide binding]; other site 233412000410 active site 233412000411 phosphorylation site [posttranslational modification] 233412000412 phosphoenolpyruvate-protein phosphotransferase; Provisional; Region: PRK11177 233412000413 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 233412000414 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 233412000415 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 233412000416 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 233412000417 dimerization domain swap beta strand [polypeptide binding]; other site 233412000418 regulatory protein interface [polypeptide binding]; other site 233412000419 active site 233412000420 regulatory phosphorylation site [posttranslational modification]; other site 233412000421 thiamine transporter membrane protein; Reviewed; Region: thiP; PRK09433 233412000422 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412000423 dimer interface [polypeptide binding]; other site 233412000424 conserved gate region; other site 233412000425 putative PBP binding loops; other site 233412000426 ABC-ATPase subunit interface; other site 233412000427 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 233412000428 thiamine transporter ATP-binding subunit; Provisional; Region: thiQ; PRK10771 233412000429 ATP-binding cassette domain of the thiamine transport system; Region: ABC_ThiQ_thiamine_transporter; cd03298 233412000430 Walker A/P-loop; other site 233412000431 ATP binding site [chemical binding]; other site 233412000432 Q-loop/lid; other site 233412000433 ABC transporter signature motif; other site 233412000434 Walker B; other site 233412000435 D-loop; other site 233412000436 H-loop/switch region; other site 233412000437 ornithine carbamoyltransferase; Provisional; Region: PRK01713 233412000438 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 233412000439 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 233412000440 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 233412000441 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 233412000442 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 233412000443 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 233412000444 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 233412000445 ATP-grasp domain; Region: ATP-grasp_4; cl17255 233412000446 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 233412000447 IMP binding site; other site 233412000448 dimer interface [polypeptide binding]; other site 233412000449 interdomain contacts; other site 233412000450 partial ornithine binding site; other site 233412000451 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 233412000452 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 233412000453 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 233412000454 catalytic site [active] 233412000455 subunit interface [polypeptide binding]; other site 233412000456 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 233412000457 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK12489 233412000458 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 233412000459 MraW methylase family; Region: Methyltransf_5; pfam01795 233412000460 Cell division protein FtsL; Region: FtsL; pfam04999 233412000461 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 233412000462 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 233412000463 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 233412000464 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 233412000465 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 233412000466 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 233412000467 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 233412000468 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed; Region: murF; PRK10773 233412000469 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 233412000470 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 233412000471 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 233412000472 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 233412000473 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 233412000474 Mg++ binding site [ion binding]; other site 233412000475 putative catalytic motif [active] 233412000476 putative substrate binding site [chemical binding]; other site 233412000477 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03806 233412000478 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 233412000479 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 233412000480 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 233412000481 active site 233412000482 hypothetical protein; Provisional; Region: PRK11212 233412000483 phosphoribosylaminoimidazole-succinocarboxamide synthase, N-terminal fragment; HDp0252A 233412000484 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 233412000485 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 233412000486 hinge; other site 233412000487 active site 233412000488 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 233412000489 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 233412000490 anti sigma factor interaction site; other site 233412000491 regulatory phosphorylation site [posttranslational modification]; other site 233412000492 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 233412000493 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 233412000494 mce related protein; Region: MCE; pfam02470 233412000495 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 233412000496 Permease; Region: Permease; cl00510 233412000497 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 233412000498 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 233412000499 Walker A/P-loop; other site 233412000500 ATP binding site [chemical binding]; other site 233412000501 Q-loop/lid; other site 233412000502 ABC transporter signature motif; other site 233412000503 Walker B; other site 233412000504 D-loop; other site 233412000505 H-loop/switch region; other site 233412000506 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 233412000507 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 233412000508 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 233412000509 protein binding site [polypeptide binding]; other site 233412000510 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 233412000511 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 233412000512 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 233412000513 NAD(P) binding site [chemical binding]; other site 233412000514 active site 233412000515 arginine repressor; Provisional; Region: PRK05066 233412000516 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 233412000517 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 233412000518 malate dehydrogenase; Provisional; Region: PRK05086 233412000519 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 233412000520 NAD binding site [chemical binding]; other site 233412000521 dimerization interface [polypeptide binding]; other site 233412000522 Substrate binding site [chemical binding]; other site 233412000523 Outer membrane lipoprotein [Cell envelope biogenesis, outer membrane]; Region: SlyB; COG3133 233412000524 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_4; cd07268 233412000525 putative metal binding site [ion binding]; other site 233412000526 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 233412000527 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 233412000528 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 233412000529 active site 233412000530 HIGH motif; other site 233412000531 KMSK motif region; other site 233412000532 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 233412000533 tRNA binding surface [nucleotide binding]; other site 233412000534 anticodon binding site; other site 233412000535 GTPase CgtA; Reviewed; Region: obgE; PRK12298 233412000536 GTP1/OBG; Region: GTP1_OBG; pfam01018 233412000537 Obg GTPase; Region: Obg; cd01898 233412000538 G1 box; other site 233412000539 GTP/Mg2+ binding site [chemical binding]; other site 233412000540 Switch I region; other site 233412000541 G2 box; other site 233412000542 G3 box; other site 233412000543 Switch II region; other site 233412000544 G4 box; other site 233412000545 G5 box; other site 233412000546 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 233412000547 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 233412000548 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 233412000549 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 233412000550 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 233412000551 domain interface [polypeptide binding]; other site 233412000552 putative active site [active] 233412000553 catalytic site [active] 233412000554 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 233412000555 domain interface [polypeptide binding]; other site 233412000556 putative active site [active] 233412000557 catalytic site [active] 233412000558 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 233412000559 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 233412000560 active site 233412000561 HIGH motif; other site 233412000562 nucleotide binding site [chemical binding]; other site 233412000563 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 233412000564 active site 233412000565 KMSKS motif; other site 233412000566 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 233412000567 tRNA binding surface [nucleotide binding]; other site 233412000568 anticodon binding site; other site 233412000569 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 233412000570 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 233412000571 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 233412000572 active site 233412000573 Riboflavin kinase; Region: Flavokinase; smart00904 233412000574 transcriptional regulator NadR, N-terminal fragment; HDp0275A 233412000575 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 233412000576 active site 233412000577 metal binding site [ion binding]; metal-binding site 233412000578 two-component response regulator; Provisional; Region: PRK11173 233412000579 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 233412000580 active site 233412000581 phosphorylation site [posttranslational modification] 233412000582 intermolecular recognition site; other site 233412000583 dimerization interface [polypeptide binding]; other site 233412000584 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 233412000585 DNA binding site [nucleotide binding] 233412000586 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 233412000587 negative regulator GrlR; Provisional; Region: PRK14051 233412000588 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 233412000589 Fimbrial protein; Region: Fimbrial; cl01416 233412000590 putative fimbrial outer membrane usher protein StfC; Provisional; Region: PRK15284 233412000591 PapC N-terminal domain; Region: PapC_N; pfam13954 233412000592 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 233412000593 PapC C-terminal domain; Region: PapC_C; pfam13953 233412000594 putative fimbrial chaperone protein StfD; Provisional; Region: PRK15285 233412000595 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 233412000596 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 233412000597 Fimbrial protein; Region: Fimbrial; pfam00419 233412000598 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 233412000599 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 233412000600 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 233412000601 non-specific DNA binding site [nucleotide binding]; other site 233412000602 salt bridge; other site 233412000603 sequence-specific DNA binding site [nucleotide binding]; other site 233412000604 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 233412000605 Methyltransferase domain; Region: Methyltransf_26; pfam13659 233412000606 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 233412000607 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 233412000608 This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins; Region: LNS2; smart00775 233412000609 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 233412000610 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 233412000611 active site 233412000612 motif I; other site 233412000613 motif II; other site 233412000614 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 233412000615 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 233412000616 catalytic residue [active] 233412000617 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 233412000618 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 233412000619 G1 box; other site 233412000620 putative GEF interaction site [polypeptide binding]; other site 233412000621 GTP/Mg2+ binding site [chemical binding]; other site 233412000622 Switch I region; other site 233412000623 G2 box; other site 233412000624 G3 box; other site 233412000625 Switch II region; other site 233412000626 G4 box; other site 233412000627 G5 box; other site 233412000628 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 233412000629 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly...; Region: BipA_TypA_C; cd03710 233412000630 Glutaredoxin, GrxA family; Region: GRXA; TIGR02183 233412000631 ribonuclease PH; Reviewed; Region: rph; PRK00173 233412000632 Ribonuclease PH; Region: RNase_PH_bact; cd11362 233412000633 hexamer interface [polypeptide binding]; other site 233412000634 active site 233412000635 hypothetical protein; Provisional; Region: PRK11820 233412000636 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 233412000637 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 233412000638 putative global regulator; Reviewed; Region: PRK09559 233412000639 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 233412000640 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 233412000641 transcriptional regulator NarP; Provisional; Region: PRK10403 233412000642 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 233412000643 active site 233412000644 phosphorylation site [posttranslational modification] 233412000645 intermolecular recognition site; other site 233412000646 dimerization interface [polypeptide binding]; other site 233412000647 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 233412000648 DNA binding residues [nucleotide binding] 233412000649 dimerization interface [polypeptide binding]; other site 233412000650 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 233412000651 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 233412000652 Putative RNA methylase family UPF0020; Region: UPF0020; pfam01170 233412000653 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 233412000654 putative RNA binding site [nucleotide binding]; other site 233412000655 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 233412000656 S-adenosylmethionine binding site [chemical binding]; other site 233412000657 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 233412000658 transaldolase-like protein; Provisional; Region: PTZ00411 233412000659 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 233412000660 active site 233412000661 dimer interface [polypeptide binding]; other site 233412000662 catalytic residue [active] 233412000663 rRNA operon variant 1 difference region; HDprRNA2d 233412000664 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 233412000665 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412000666 dimer interface [polypeptide binding]; other site 233412000667 conserved gate region; other site 233412000668 putative PBP binding loops; other site 233412000669 ABC-ATPase subunit interface; other site 233412000670 dipeptide transporter; Provisional; Region: PRK10913 233412000671 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 233412000672 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412000673 dimer interface [polypeptide binding]; other site 233412000674 conserved gate region; other site 233412000675 putative PBP binding loops; other site 233412000676 ABC-ATPase subunit interface; other site 233412000677 dipeptide transporter ATP-binding subunit; Provisional; Region: dppD; PRK11022 233412000678 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 233412000679 Walker A/P-loop; other site 233412000680 ATP binding site [chemical binding]; other site 233412000681 Q-loop/lid; other site 233412000682 ABC transporter signature motif; other site 233412000683 Walker B; other site 233412000684 D-loop; other site 233412000685 H-loop/switch region; other site 233412000686 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 233412000687 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 233412000688 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 233412000689 Walker A/P-loop; other site 233412000690 ATP binding site [chemical binding]; other site 233412000691 Q-loop/lid; other site 233412000692 ABC transporter signature motif; other site 233412000693 Walker B; other site 233412000694 D-loop; other site 233412000695 H-loop/switch region; other site 233412000696 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 233412000697 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 233412000698 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 233412000699 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 233412000700 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 233412000701 RNA binding site [nucleotide binding]; other site 233412000702 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 233412000703 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 233412000704 binding surface 233412000705 TPR motif; other site 233412000706 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 233412000707 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 233412000708 FeS/SAM binding site; other site 233412000709 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 233412000710 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 233412000711 HIGH motif; other site 233412000712 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 233412000713 active site 233412000714 KMSKS motif; other site 233412000715 superoxide dismutase; Provisional; Region: PRK10925 233412000716 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 233412000717 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 233412000718 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 233412000719 homotrimer interaction site [polypeptide binding]; other site 233412000720 putative active site [active] 233412000721 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 233412000722 putative GSH binding site [chemical binding]; other site 233412000723 catalytic residues [active] 233412000724 recombination protein RecR; Reviewed; Region: recR; PRK00076 233412000725 RecR protein; Region: RecR; pfam02132 233412000726 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 233412000727 putative active site [active] 233412000728 putative metal-binding site [ion binding]; other site 233412000729 tetramer interface [polypeptide binding]; other site 233412000730 hypothetical protein; Validated; Region: PRK00153 233412000731 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 233412000732 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 233412000733 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 233412000734 tonB-system energizer ExbB, group 2; Region: exbB2; TIGR02805 233412000735 GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a...; Region: GlpE_ST; cd01444 233412000736 active site residue [active] 233412000737 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 233412000738 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 233412000739 thioredoxin reductase; Provisional; Region: PRK10262 233412000740 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 233412000741 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 233412000742 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 233412000743 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 233412000744 Ligand binding site; other site 233412000745 oligomer interface; other site 233412000746 23S rRNA pseudouridine synthase E; Provisional; Region: PRK11394 233412000747 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 233412000748 active site 233412000749 phage T7 F exclusion suppressor FxsA; Reviewed; Region: fxsA; PRK11463 233412000750 SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A...; Region: SirA; cd03423 233412000751 CPxP motif; other site 233412000752 RNase E inhibitor protein; Provisional; Region: PRK11191 233412000753 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 233412000754 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 233412000755 G1 box; other site 233412000756 GTP/Mg2+ binding site [chemical binding]; other site 233412000757 Switch I region; other site 233412000758 G2 box; other site 233412000759 G3 box; other site 233412000760 Switch II region; other site 233412000761 G4 box; other site 233412000762 G5 box; other site 233412000763 Protein of unknown function (DUF805); Region: DUF805; pfam05656 233412000764 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; PRK11125 233412000765 cytochrome c nitrite reductase pentaheme subunit; Provisional; Region: PRK11659 233412000766 cytochrome c nitrite reductase, Fe-S protein; Region: cyt_nit_nrfC; TIGR03149 233412000767 Formate-dependent nitrite reductase, membrane component [Inorganic ion transport and metabolism]; Region: NrfD; COG3301 233412000768 cytochrome c nitrite reductase, NrfD subunit; Region: cyt_nit_nrfD; TIGR03148 233412000769 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 233412000770 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 233412000771 G1 box; other site 233412000772 putative GEF interaction site [polypeptide binding]; other site 233412000773 GTP/Mg2+ binding site [chemical binding]; other site 233412000774 Switch I region; other site 233412000775 G2 box; other site 233412000776 G3 box; other site 233412000777 Switch II region; other site 233412000778 G4 box; other site 233412000779 G5 box; other site 233412000780 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 233412000781 heat shock protein HtpX; Provisional; Region: PRK05457 233412000782 glutathione reductase; Validated; Region: PRK06116 233412000783 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 233412000784 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 233412000785 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 233412000786 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 233412000787 active site 233412000788 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 233412000789 Carbon starvation protein CstA; Region: CstA; pfam02554 233412000790 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 233412000791 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 233412000792 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 233412000793 phosphoserine phosphatase; Provisional; Region: serB; PRK11133 233412000794 Uncharacterized membrane protein affecting hemolysin expression [General function prediction only]; Region: AhpA; COG3726 233412000795 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 233412000796 rRNA binding site [nucleotide binding]; other site 233412000797 predicted 30S ribosome binding site; other site 233412000798 Predicted flavoproteins [General function prediction only]; Region: COG2081 233412000799 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 233412000800 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK06901 233412000801 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 233412000802 putative deacylase active site [active] 233412000803 LexA regulated protein; Provisional; Region: PRK11675 233412000804 flavodoxin FldA; Validated; Region: PRK09267 233412000805 ferric uptake regulator; Provisional; Region: fur; PRK09462 233412000806 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 233412000807 metal binding site 2 [ion binding]; metal-binding site 233412000808 putative DNA binding helix; other site 233412000809 metal binding site 1 [ion binding]; metal-binding site 233412000810 dimer interface [polypeptide binding]; other site 233412000811 structural Zn2+ binding site [ion binding]; other site 233412000812 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 233412000813 mce related protein; Region: MCE; pfam02470 233412000814 mce related protein; Region: MCE; pfam02470 233412000815 mce related protein; Region: MCE; pfam02470 233412000816 mce related protein; Region: MCE; pfam02470 233412000817 mce related protein; Region: MCE; pfam02470 233412000818 S-ribosylhomocysteinase; Provisional; Region: PRK02260 233412000819 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 233412000820 Sulfatase; Region: Sulfatase; pfam00884 233412000821 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 233412000822 active site 233412000823 homotetramer interface [polypeptide binding]; other site 233412000824 homodimer interface [polypeptide binding]; other site 233412000825 CTP synthetase; Validated; Region: pyrG; PRK05380 233412000826 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 233412000827 Catalytic site [active] 233412000828 active site 233412000829 UTP binding site [chemical binding]; other site 233412000830 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 233412000831 active site 233412000832 putative oxyanion hole; other site 233412000833 catalytic triad [active] 233412000834 Uncharacterized integral membrane protein (DUF2301); Region: DUF2301; cl02241 233412000835 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 233412000836 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 233412000837 active site 233412000838 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 233412000839 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 233412000840 FMN binding site [chemical binding]; other site 233412000841 active site 233412000842 catalytic residues [active] 233412000843 substrate binding site [chemical binding]; other site 233412000844 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 233412000845 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 233412000846 active site 233412000847 purine riboside binding site [chemical binding]; other site 233412000848 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 233412000849 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 233412000850 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 233412000851 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 233412000852 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 233412000853 E3 interaction surface; other site 233412000854 lipoyl attachment site [posttranslational modification]; other site 233412000855 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 233412000856 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 233412000857 Na(+)-translocating NADH-quinone reductase subunit C; Provisional; Region: PRK05346 233412000858 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 233412000859 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 233412000860 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 233412000861 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 233412000862 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 233412000863 FAD binding pocket [chemical binding]; other site 233412000864 FAD binding motif [chemical binding]; other site 233412000865 phosphate binding motif [ion binding]; other site 233412000866 beta-alpha-beta structure motif; other site 233412000867 NAD binding pocket [chemical binding]; other site 233412000868 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 233412000869 ApbE family; Region: ApbE; pfam02424 233412000870 Protein of unknown function (DUF539); Region: DUF539; cl01129 233412000871 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 233412000872 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 233412000873 N-terminal plug; other site 233412000874 ligand-binding site [chemical binding]; other site 233412000875 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 233412000876 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 233412000877 Ligand Binding Site [chemical binding]; other site 233412000878 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 233412000879 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 233412000880 putative substrate translocation pore; other site 233412000881 Putative exonuclease, RdgC; Region: RdgC; pfam04381 233412000882 anaerobic ribonucleoside-triphosphate reductase; Region: RNR_anaer_Bdell; TIGR02827 233412000883 Class III ribonucleotide reductase; Region: RNR_III; cd01675 233412000884 effector binding site; other site 233412000885 active site 233412000886 Zn binding site [ion binding]; other site 233412000887 glycine loop; other site 233412000888 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: RNR_activ_nrdG3; TIGR02826 233412000889 electron transport complex protein RsxA; Provisional; Region: PRK05151 233412000890 ferredoxin; Provisional; Region: PRK08764 233412000891 Putative Fe-S cluster; Region: FeS; pfam04060 233412000892 4Fe-4S binding domain; Region: Fer4; pfam00037 233412000893 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 233412000894 SLBB domain; Region: SLBB; pfam10531 233412000895 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...; Region: HCP_like; cl14655 233412000896 electron transport complex protein RnfD; Reviewed; Region: rnfD; PRK00816 233412000897 electron transport complex protein RnfG; Validated; Region: PRK01908 233412000898 electron transport complex RsxE subunit; Provisional; Region: PRK12405 233412000899 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 233412000900 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 233412000901 putative acyl-acceptor binding pocket; other site 233412000902 Domain of unknown function DUF302; Region: DUF302; cl01364 233412000903 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 233412000904 Glutamine amidotransferase class-I; Region: GATase; pfam00117 233412000905 glutamine binding [chemical binding]; other site 233412000906 catalytic triad [active] 233412000907 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 233412000908 RmuC family; Region: RmuC; pfam02646 233412000909 para-aminobenzoate synthase component I; Validated; Region: PRK07093 233412000910 hypothetical protein; Provisional; Region: PRK07101 233412000911 substrate-cofactor binding pocket; other site 233412000912 recombinase A; Provisional; Region: recA; PRK09354 233412000913 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 233412000914 hexamer interface [polypeptide binding]; other site 233412000915 Walker A motif; other site 233412000916 ATP binding site [chemical binding]; other site 233412000917 Walker B motif; other site 233412000918 recombination regulator RecX; Reviewed; Region: recX; PRK00117 233412000919 ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as...; Region: ASCH_yqfb_like; cd06552 233412000920 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 233412000921 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 233412000922 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 233412000923 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 233412000924 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 233412000925 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 233412000926 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 233412000927 shikimate binding site; other site 233412000928 NAD(P) binding site [chemical binding]; other site 233412000929 Membrane fusogenic activity; Region: BMFP; pfam04380 233412000930 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 233412000931 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 233412000932 active site 233412000933 dimer interface [polypeptide binding]; other site 233412000934 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 233412000935 dimer interface [polypeptide binding]; other site 233412000936 active site 233412000937 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 233412000938 Na2 binding site [ion binding]; other site 233412000939 putative substrate binding site 1 [chemical binding]; other site 233412000940 Na binding site 1 [ion binding]; other site 233412000941 putative substrate binding site 2 [chemical binding]; other site 233412000942 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 233412000943 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 233412000944 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 233412000945 active site 233412000946 dimer interface [polypeptide binding]; other site 233412000947 metal binding site [ion binding]; metal-binding site 233412000948 shikimate kinase; Reviewed; Region: aroK; PRK00131 233412000949 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 233412000950 ADP binding site [chemical binding]; other site 233412000951 magnesium binding site [ion binding]; other site 233412000952 putative shikimate binding site; other site 233412000953 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 233412000954 Transglycosylase; Region: Transgly; pfam00912 233412000955 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 233412000956 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 233412000957 proteasome-activating nucleotidase; Provisional; Region: PRK03992 233412000958 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 233412000959 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 233412000960 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 233412000961 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 233412000962 putative RNA binding site [nucleotide binding]; other site 233412000963 thiamine monophosphate kinase; Provisional; Region: PRK05731 233412000964 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 233412000965 ATP binding site [chemical binding]; other site 233412000966 dimerization interface [polypeptide binding]; other site 233412000967 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 233412000968 tetramer interfaces [polypeptide binding]; other site 233412000969 binuclear metal-binding site [ion binding]; other site 233412000970 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 233412000971 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 233412000972 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 233412000973 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 233412000974 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 233412000975 active site 233412000976 dimerization interface [polypeptide binding]; other site 233412000977 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 233412000978 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 233412000979 TPP-binding site; other site 233412000980 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 233412000981 PYR/PP interface [polypeptide binding]; other site 233412000982 dimer interface [polypeptide binding]; other site 233412000983 TPP binding site [chemical binding]; other site 233412000984 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 233412000985 HDp0442B; TyrA T-protein homolog, central fragment; This region contains an authentic frameshift or in-frame stop in the coding sequence and is not the result of a sequencing error 233412000986 HDp0442A; TyrA T-protein homolog, N-terminal fragment 233412000987 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 233412000988 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 233412000989 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 233412000990 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 233412000991 putative active site [active] 233412000992 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 233412000993 pyruvate kinase; Provisional; Region: PRK05826 233412000994 domain interfaces; other site 233412000995 active site 233412000996 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 233412000997 catalytic core [active] 233412000998 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 233412000999 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 233412001000 FMN binding site [chemical binding]; other site 233412001001 active site 233412001002 catalytic residues [active] 233412001003 substrate binding site [chemical binding]; other site 233412001004 Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]; Region: Fis; COG2901 233412001005 global DNA-binding transcriptional dual regulator Fis; Provisional; Region: fis; PRK00430 233412001006 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 233412001007 active site 233412001008 metal binding site [ion binding]; metal-binding site 233412001009 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 233412001010 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 233412001011 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 233412001012 catalytic site [active] 233412001013 putative active site [active] 233412001014 putative substrate binding site [chemical binding]; other site 233412001015 dimer interface [polypeptide binding]; other site 233412001016 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 233412001017 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 233412001018 active site 233412001019 (T/H)XGH motif; other site 233412001020 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 233412001021 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 233412001022 Glycosyl transferases group 1; Region: Glycos_transf_1; pfam00534 233412001023 putative protease; Provisional; Region: PRK15452 233412001024 Peptidase family U32; Region: Peptidase_U32; pfam01136 233412001025 Cytochrome b562; Region: Cytochrom_B562; cl01546 233412001026 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 233412001027 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 233412001028 amino acid carrier protein; Region: agcS; TIGR00835 233412001029 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 233412001030 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 233412001031 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 233412001032 catalytic residue [active] 233412001033 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include bacterial ATP-dependent...; Region: Bacterial_PFK; cd00763 233412001034 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 233412001035 active site 233412001036 ADP/pyrophosphate binding site [chemical binding]; other site 233412001037 dimerization interface [polypeptide binding]; other site 233412001038 allosteric effector site; other site 233412001039 fructose-1,6-bisphosphate binding site; other site 233412001040 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 233412001041 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 233412001042 active site 233412001043 YwiC-like protein; Region: YwiC; pfam14256 233412001044 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 233412001045 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 233412001046 RNA binding surface [nucleotide binding]; other site 233412001047 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 233412001048 active site 233412001049 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 233412001050 UGMP family protein; Validated; Region: PRK09604 233412001051 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 233412001052 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 233412001053 conserved human frataxin homolog, N-terminal fragment; HDp0473A 233412001054 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 233412001055 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 233412001056 ATP binding site [chemical binding]; other site 233412001057 putative Mg++ binding site [ion binding]; other site 233412001058 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 233412001059 nucleotide binding region [chemical binding]; other site 233412001060 ATP-binding site [chemical binding]; other site 233412001061 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 233412001062 HRDC domain; Region: HRDC; pfam00570 233412001063 enolase; Provisional; Region: eno; PRK00077 233412001064 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 233412001065 dimer interface [polypeptide binding]; other site 233412001066 metal binding site [ion binding]; metal-binding site 233412001067 substrate binding pocket [chemical binding]; other site 233412001068 23S rRNA methyluridine methyltransferase; Reviewed; Region: rumB; PRK03522 233412001069 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 233412001070 non-specific DNA binding site [nucleotide binding]; other site 233412001071 salt bridge; other site 233412001072 sequence-specific DNA binding site [nucleotide binding]; other site 233412001073 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; cl17220 233412001074 putative Zn2+ binding site [ion binding]; other site 233412001075 Phage transposase, N-terminal fragment; HDp0482A 233412001076 phage transposase, N-terminal fragment; HDp0485A 233412001077 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 233412001078 Protein of unknown function (DUF551); Region: DUF551; pfam04448 233412001079 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 233412001080 AntA/AntB antirepressor; Region: AntA; pfam08346 233412001081 Mor transcription activator family; Region: Mor; cl02360 233412001082 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 233412001083 amidase catalytic site [active] 233412001084 Zn binding residues [ion binding]; other site 233412001085 substrate binding site [chemical binding]; other site 233412001086 Protein of unknown function (DUF2644); Region: DUF2644; pfam10841 233412001087 Protein of unknown function (DUF2681); Region: DUF2681; pfam10883 233412001088 Protein of unknown function (DUF1804); Region: DUF1804; pfam08822 233412001089 conserved hypothetical protein, N-terminal fragment; HDp0512A 233412001090 Protein of unknown function (DUF935); Region: DUF935; pfam06074 233412001091 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 233412001092 Uncharacterized protein, homolog of phage Mu protein gp30 [Function unknown]; Region: COG2369 233412001093 Phage Mu protein F like protein; Region: Phage_Mu_F; pfam04233 233412001094 Mu-like prophage protein gpG [General function prediction only]; Region: COG5005 233412001095 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 233412001096 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; pfam10124 233412001097 Protein of unknown function (DUF1320); Region: DUF1320; pfam07030 233412001098 Phage-related minor tail protein [Function unknown]; Region: COG5281 233412001099 tape measure domain; Region: tape_meas_nterm; TIGR02675 233412001100 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 233412001101 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 233412001102 Putative phage tail protein; Region: Phage-tail_3; pfam13550 233412001103 conserved probable RNA methyltransferase, N-terminal fragment; HDp0541A 233412001104 beta-hexosaminidase; Provisional; Region: PRK05337 233412001105 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 233412001106 MutH is a 28kD endonuclease involved in methyl-directed DNA mismatch repair in gram negative bacteria. MutH is both sequence-specific and methylation-specific, introducing a nick in the unmethylated strand of a hemi-methylated d(GATC) DNA duplex. MutH...; Region: MutH_Sau3AI; cd00583 233412001107 putative DNA-binding cleft [nucleotide binding]; other site 233412001108 putative DNA clevage site; other site 233412001109 molecular lever; other site 233412001110 LexA repressor; Validated; Region: PRK00215 233412001111 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 233412001112 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 233412001113 Catalytic site [active] 233412001114 glycerol-3-phosphate O-acyltransferase; Region: plsB; TIGR03703 233412001115 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 233412001116 putative acyl-acceptor binding pocket; other site 233412001117 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 233412001118 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 233412001119 ATP-grasp domain; Region: ATP-grasp; pfam02222 233412001120 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 233412001121 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 233412001122 putative active site [active] 233412001123 putative PHP Thumb interface [polypeptide binding]; other site 233412001124 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 233412001125 generic binding surface II; other site 233412001126 generic binding surface I; other site 233412001127 lipopolysaccharide ABC transporter permease; Provisional; Region: PRK15071 233412001128 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 233412001129 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 233412001130 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 233412001131 multifunctional aminopeptidase A; Provisional; Region: PRK00913 233412001132 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 233412001133 interface (dimer of trimers) [polypeptide binding]; other site 233412001134 Substrate-binding/catalytic site; other site 233412001135 Zn-binding sites [ion binding]; other site 233412001136 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 233412001137 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 233412001138 FeS/SAM binding site; other site 233412001139 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 233412001140 active site 233412001141 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 233412001142 Ligand Binding Site [chemical binding]; other site 233412001143 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 233412001144 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 233412001145 dimerization interface [polypeptide binding]; other site 233412001146 putative ATP binding site [chemical binding]; other site 233412001147 phosphoribosylformylglycinamidine cyclo-ligase, C-terminal fragment; HDp0561A 233412001148 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 233412001149 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 233412001150 Aspartase; Region: Aspartase; cd01357 233412001151 active sites [active] 233412001152 tetramer interface [polypeptide binding]; other site 233412001153 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 233412001154 Clp amino terminal domain; Region: Clp_N; pfam02861 233412001155 Clp amino terminal domain; Region: Clp_N; pfam02861 233412001156 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 233412001157 Walker A motif; other site 233412001158 ATP binding site [chemical binding]; other site 233412001159 Walker B motif; other site 233412001160 arginine finger; other site 233412001161 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 233412001162 Walker A motif; other site 233412001163 ATP binding site [chemical binding]; other site 233412001164 Walker B motif; other site 233412001165 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 233412001166 acetylornithine deacetylase; Provisional; Region: PRK05111 233412001167 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 233412001168 metal binding site [ion binding]; metal-binding site 233412001169 putative dimer interface [polypeptide binding]; other site 233412001170 arginine-ornithine antiporter; Region: arg_ornith_anti; TIGR03810 233412001171 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 233412001172 S-adenosylmethionine synthetase; Validated; Region: PRK05250 233412001173 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 233412001174 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 233412001175 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 233412001176 active site 233412001177 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 233412001178 Part of AAA domain; Region: AAA_19; pfam13245 233412001179 Family description; Region: UvrD_C_2; pfam13538 233412001180 putrescine/spermidine ABC transporter ATPase protein; Reviewed; Region: potA; PRK09452 233412001181 ATP-binding cassette domain of the polyamine transporter; Region: ABC_PotA_N; cd03300 233412001182 Walker A/P-loop; other site 233412001183 ATP binding site [chemical binding]; other site 233412001184 Q-loop/lid; other site 233412001185 ABC transporter signature motif; other site 233412001186 Walker B; other site 233412001187 D-loop; other site 233412001188 H-loop/switch region; other site 233412001189 TOBE domain; Region: TOBE_2; pfam08402 233412001190 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412001191 dimer interface [polypeptide binding]; other site 233412001192 conserved gate region; other site 233412001193 putative PBP binding loops; other site 233412001194 ABC-ATPase subunit interface; other site 233412001195 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 233412001196 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412001197 dimer interface [polypeptide binding]; other site 233412001198 conserved gate region; other site 233412001199 putative PBP binding loops; other site 233412001200 ABC-ATPase subunit interface; other site 233412001201 peptide chain release factor 2; Validated; Region: prfB; PRK00578 233412001202 This domain is found in peptide chain release factors; Region: PCRF; smart00937 233412001203 RF-1 domain; Region: RF-1; pfam00472 233412001204 selenophosphate synthetase; Provisional; Region: PRK00943 233412001205 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 233412001206 dimerization interface [polypeptide binding]; other site 233412001207 putative ATP binding site [chemical binding]; other site 233412001208 2-octaprenyl-6-methoxyphenol 4-monoxygenase protein, N-terminal fragment; HDp0579A 233412001209 hypothetical protein; Provisional; Region: PRK11281 233412001210 putative mechanosensitive channel protein; Provisional; Region: PRK10929 233412001211 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 233412001212 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 233412001213 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 233412001214 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 233412001215 active site 233412001216 phosphorylation site [posttranslational modification] 233412001217 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 233412001218 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 233412001219 Walker A/P-loop; other site 233412001220 ATP binding site [chemical binding]; other site 233412001221 Q-loop/lid; other site 233412001222 ABC transporter signature motif; other site 233412001223 Walker B; other site 233412001224 D-loop; other site 233412001225 H-loop/switch region; other site 233412001226 OstA-like protein; Region: OstA; cl00844 233412001227 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 233412001228 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 233412001229 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 233412001230 Repair protein; Region: Repair_PSII; pfam04536 233412001231 Repair protein; Region: Repair_PSII; cl01535 233412001232 LemA family; Region: LemA; cl00742 233412001233 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 233412001234 active site 233412001235 putative DNA-binding cleft [nucleotide binding]; other site 233412001236 dimer interface [polypeptide binding]; other site 233412001237 hypothetical protein; Validated; Region: PRK00110 233412001238 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_7; cd04664 233412001239 nudix motif; other site 233412001240 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 233412001241 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 233412001242 dimer interface [polypeptide binding]; other site 233412001243 anticodon binding site; other site 233412001244 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 233412001245 homodimer interface [polypeptide binding]; other site 233412001246 motif 1; other site 233412001247 active site 233412001248 motif 2; other site 233412001249 GAD domain; Region: GAD; pfam02938 233412001250 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 233412001251 active site 233412001252 motif 3; other site 233412001253 hypothetical protein; Validated; Region: PRK06886 233412001254 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 233412001255 active site 233412001256 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 233412001257 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 233412001258 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 233412001259 poly(A) polymerase I; Provisional; Region: pcnB; PRK11623 233412001260 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 233412001261 active site 233412001262 NTP binding site [chemical binding]; other site 233412001263 metal binding triad [ion binding]; metal-binding site 233412001264 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 233412001265 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 233412001266 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 233412001267 catalytic center binding site [active] 233412001268 ATP binding site [chemical binding]; other site 233412001269 YnbE-like lipoprotein; Region: Lipoprotein_19; pfam13617 233412001270 hypothetical protein; Provisional; Region: PRK10695 233412001271 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 233412001272 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 233412001273 dimer interface [polypeptide binding]; other site 233412001274 active site 233412001275 metal binding site [ion binding]; metal-binding site 233412001276 glutathione binding site [chemical binding]; other site 233412001277 ribonuclease T; Provisional; Region: PRK05168 233412001278 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 233412001279 active site 233412001280 catalytic site [active] 233412001281 substrate binding site [chemical binding]; other site 233412001282 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 233412001283 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 233412001284 dimer interface [polypeptide binding]; other site 233412001285 active site 233412001286 adenylate cyclase; Provisional; Region: cyaA; PRK09450 233412001287 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 233412001288 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 233412001289 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 233412001290 transporter, monovalent cation:proton antiporter-2 (CPA2) family; Region: 2a37; TIGR00932 233412001291 TrkA-N domain; Region: TrkA_N; pfam02254 233412001292 cytochrome c nitrate reductase biogenesis protein NrfE; Region: cyt_nit_nrfE; TIGR03145 233412001293 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 233412001294 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 233412001295 catalytic residues [active] 233412001296 central insert; other site 233412001297 cytochrome c-type biogenesis protein, N-terminal fragment; HDp0619A 233412001298 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 233412001299 heme utilization protein HutZ; Region: heme_HutZ; TIGR04110 233412001300 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 233412001301 chorismate binding enzyme; Region: Chorismate_bind; cl10555 233412001302 primosome assembly protein PriA; Validated; Region: PRK05580 233412001303 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 233412001304 ATP binding site [chemical binding]; other site 233412001305 putative Mg++ binding site [ion binding]; other site 233412001306 helicase superfamily c-terminal domain; Region: HELICc; smart00490 233412001307 ATP-binding site [chemical binding]; other site 233412001308 alanine racemase; Reviewed; Region: alr; PRK00053 233412001309 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 233412001310 active site 233412001311 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 233412001312 substrate binding site [chemical binding]; other site 233412001313 catalytic residues [active] 233412001314 dimer interface [polypeptide binding]; other site 233412001315 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 233412001316 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 233412001317 ATP binding site [chemical binding]; other site 233412001318 putative Mg++ binding site [ion binding]; other site 233412001319 Family description; Region: UvrD_C_2; pfam13538 233412001320 rRNA operon variant 2 difference region; HDprRNA3d 233412001321 Uncharacterized paraquat-inducible protein A [Function unknown]; Region: PqiA; COG2995 233412001322 Paraquat-inducible protein A; Region: PqiA; pfam04403 233412001323 Paraquat-inducible protein A; Region: PqiA; pfam04403 233412001324 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 233412001325 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 233412001326 trimer interface [polypeptide binding]; other site 233412001327 active site 233412001328 substrate binding site [chemical binding]; other site 233412001329 CoA binding site [chemical binding]; other site 233412001330 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 233412001331 ArsC family; Region: ArsC; pfam03960 233412001332 catalytic residues [active] 233412001333 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 233412001334 Dehydroquinase class II; Region: DHquinase_II; pfam01220 233412001335 active site 233412001336 trimer interface [polypeptide binding]; other site 233412001337 dimer interface [polypeptide binding]; other site 233412001338 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 233412001339 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 233412001340 carboxyltransferase (CT) interaction site; other site 233412001341 biotinylation site [posttranslational modification]; other site 233412001342 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 233412001343 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 233412001344 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 233412001345 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 233412001346 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional; Region: PRK14489 233412001347 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 233412001348 GTP binding site; other site 233412001349 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 233412001350 Walker A motif; other site 233412001351 Protein of unknown function (DUF1040); Region: DUF1040; cl01176 233412001352 DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol...; Region: DsbA_DsbA; cd03019 233412001353 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 233412001354 catalytic residues [active] 233412001355 hinge region; other site 233412001356 alpha helical domain; other site 233412001357 cell division protein FtsN; Region: ftsN; TIGR02223 233412001358 Sporulation related domain; Region: SPOR; pfam05036 233412001359 Putative SAM-dependent methyltransferase; Region: SAM_MT; cl17517 233412001360 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: VanY; COG1876 233412001361 D-alanyl-D-alanine carboxypeptidase; Region: VanY; pfam02557 233412001362 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 233412001363 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 233412001364 metal binding site [ion binding]; metal-binding site 233412001365 dimer interface [polypeptide binding]; other site 233412001366 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 233412001367 ArsC family; Region: ArsC; pfam03960 233412001368 putative catalytic residues [active] 233412001369 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 233412001370 dihydropteroate synthase; Region: DHPS; TIGR01496 233412001371 substrate binding pocket [chemical binding]; other site 233412001372 dimer interface [polypeptide binding]; other site 233412001373 inhibitor binding site; inhibition site 233412001374 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 233412001375 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 233412001376 RNA binding surface [nucleotide binding]; other site 233412001377 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 233412001378 active site 233412001379 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 233412001380 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 (16,20)...; Region: OM_channels; cl17244 233412001381 mechanosensitive channel MscS; Provisional; Region: PRK10334 233412001382 Mechanosensitive ion channel; Region: MS_channel; pfam00924 233412001383 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 233412001384 aromatic amino acid transport protein; Region: araaP; TIGR00837 233412001385 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 233412001386 competence protein ComEA helix-hairpin-helix repeat region; Region: TIGR00426 233412001387 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 233412001388 Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]; Region: OapA; COG3061 233412001389 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 233412001390 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 233412001391 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 233412001392 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 233412001393 putative active site [active] 233412001394 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 233412001395 S17 interaction site [polypeptide binding]; other site 233412001396 S8 interaction site; other site 233412001397 16S rRNA interaction site [nucleotide binding]; other site 233412001398 streptomycin interaction site [chemical binding]; other site 233412001399 23S rRNA interaction site [nucleotide binding]; other site 233412001400 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 233412001401 30S ribosomal protein S7; Validated; Region: PRK05302 233412001402 elongation factor G; Reviewed; Region: PRK00007 233412001403 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 233412001404 G1 box; other site 233412001405 putative GEF interaction site [polypeptide binding]; other site 233412001406 GTP/Mg2+ binding site [chemical binding]; other site 233412001407 Switch I region; other site 233412001408 G2 box; other site 233412001409 G3 box; other site 233412001410 Switch II region; other site 233412001411 G4 box; other site 233412001412 G5 box; other site 233412001413 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 233412001414 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 233412001415 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 233412001416 elongation factor Tu; Reviewed; Region: PRK00049 233412001417 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 233412001418 G1 box; other site 233412001419 GEF interaction site [polypeptide binding]; other site 233412001420 GTP/Mg2+ binding site [chemical binding]; other site 233412001421 Switch I region; other site 233412001422 G2 box; other site 233412001423 G3 box; other site 233412001424 Switch II region; other site 233412001425 G4 box; other site 233412001426 G5 box; other site 233412001427 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 233412001428 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 233412001429 Antibiotic Binding Site [chemical binding]; other site 233412001430 serine acetyltransferase; Provisional; Region: cysE; PRK11132 233412001431 Serine acetyltransferase, N-terminal; Region: SATase_N; smart00971 233412001432 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 233412001433 trimer interface [polypeptide binding]; other site 233412001434 active site 233412001435 substrate binding site [chemical binding]; other site 233412001436 CoA binding site [chemical binding]; other site 233412001437 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 233412001438 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 233412001439 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 233412001440 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 233412001441 SecA binding site; other site 233412001442 Preprotein binding site; other site 233412001443 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 233412001444 active site residue [active] 233412001445 trigger factor; Provisional; Region: tig; PRK01490 233412001446 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 233412001447 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 233412001448 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 233412001449 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 233412001450 DNA polymerase III subunit chi; Validated; Region: PRK05728 233412001451 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 233412001452 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 233412001453 HIGH motif; other site 233412001454 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 233412001455 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 233412001456 active site 233412001457 KMSKS motif; other site 233412001458 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 233412001459 tRNA binding surface [nucleotide binding]; other site 233412001460 anticodon binding site; other site 233412001461 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 233412001462 Na(+)/pantothenate cotransporters: PanF of Escherichia coli and related proteins; solute binding domain; Region: SLC5sbd_PanF; cd10327 233412001463 putative transporter; Provisional; Region: PRK10484 233412001464 Na binding site [ion binding]; other site 233412001465 Protein of unknown function (DUF997); Region: DUF997; pfam06196 233412001466 Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox'...; Region: Met_repressor_MetJ; cd00490 233412001467 dimerization interface [polypeptide binding]; other site 233412001468 DNA binding site [nucleotide binding] 233412001469 corepressor binding sites; other site 233412001470 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 233412001471 Site-specific recombinase; Region: SpecificRecomb; pfam10136 233412001472 Protein of unknown function (DUF541); Region: SIMPL; cl01077 233412001473 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 233412001474 homodimer interaction site [polypeptide binding]; other site 233412001475 cofactor binding site; other site 233412001476 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 233412001477 UbiA prenyltransferase family; Region: UbiA; pfam01040 233412001478 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 233412001479 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 233412001480 ligand binding site; other site 233412001481 tetramer interface; other site 233412001482 Glycosyltransferase family 52; Region: Glyco_transf_52; pfam07922 233412001483 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 233412001484 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 233412001485 NAD binding site [chemical binding]; other site 233412001486 substrate binding site [chemical binding]; other site 233412001487 homodimer interface [polypeptide binding]; other site 233412001488 active site 233412001489 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 233412001490 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 233412001491 substrate binding site; other site 233412001492 tetramer interface; other site 233412001493 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 233412001494 DNA primase; Validated; Region: dnaG; PRK05667 233412001495 CHC2 zinc finger; Region: zf-CHC2; pfam01807 233412001496 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 233412001497 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 233412001498 active site 233412001499 metal binding site [ion binding]; metal-binding site 233412001500 interdomain interaction site; other site 233412001501 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 233412001502 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 233412001503 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 233412001504 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 233412001505 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 233412001506 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 233412001507 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 233412001508 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 233412001509 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 233412001510 DNA binding residues [nucleotide binding] 233412001511 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 233412001512 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 233412001513 active site 233412001514 HIGH motif; other site 233412001515 dimer interface [polypeptide binding]; other site 233412001516 KMSKS motif; other site 233412001517 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 233412001518 RNA binding surface [nucleotide binding]; other site 233412001519 exoribonuclease R; Provisional; Region: PRK11642 233412001520 Ribonuclease R winged-helix domain; Region: HTH_12; pfam08461 233412001521 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 233412001522 RNB domain; Region: RNB; pfam00773 233412001523 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 233412001524 RNA binding site [nucleotide binding]; other site 233412001525 TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif; Region: TlpA_like_ScsD_MtbDsbE; cd03011 233412001526 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 233412001527 catalytic residues [active] 233412001528 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 233412001529 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 233412001530 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 233412001531 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 233412001532 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 233412001533 dimerization interface [polypeptide binding]; other site 233412001534 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 233412001535 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 233412001536 catalytic triad [active] 233412001537 dimer interface [polypeptide binding]; other site 233412001538 Glutaredoxin-family domain; Region: GlrX-dom; TIGR02190 233412001539 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; Region: FBPase; cd00354 233412001540 AMP binding site [chemical binding]; other site 233412001541 metal binding site [ion binding]; metal-binding site 233412001542 active site 233412001543 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 233412001544 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 233412001545 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 233412001546 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 233412001547 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 233412001548 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 233412001549 substrate binding pocket [chemical binding]; other site 233412001550 chain length determination region; other site 233412001551 substrate-Mg2+ binding site; other site 233412001552 catalytic residues [active] 233412001553 aspartate-rich region 1; other site 233412001554 active site lid residues [active] 233412001555 aspartate-rich region 2; other site 233412001556 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 233412001557 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 233412001558 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 233412001559 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 233412001560 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 233412001561 NAD(P) binding site [chemical binding]; other site 233412001562 homotetramer interface [polypeptide binding]; other site 233412001563 homodimer interface [polypeptide binding]; other site 233412001564 active site 233412001565 3-oxoacyl-(acyl-carrier-protein) reductase, C-terminal fragment; HDp0708A 233412001566 Branched-chain amino acid permeases [Amino acid transport and metabolism]; Region: BrnQ; COG1114 233412001567 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 233412001568 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 233412001569 DNA binding site [nucleotide binding] 233412001570 catalytic residue [active] 233412001571 H2TH interface [polypeptide binding]; other site 233412001572 putative catalytic residues [active] 233412001573 turnover-facilitating residue; other site 233412001574 intercalation triad [nucleotide binding]; other site 233412001575 8OG recognition residue [nucleotide binding]; other site 233412001576 putative reading head residues; other site 233412001577 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 233412001578 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 233412001579 Predicted membrane protein [Function unknown]; Region: COG3671 233412001580 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 233412001581 sec-independent translocase; Provisional; Region: PRK01770 233412001582 twin arginine translocase protein A; Provisional; Region: tatA; PRK01833 233412001583 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 233412001584 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 233412001585 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 233412001586 SCP-2 sterol transfer family; Region: SCP2; pfam02036 233412001587 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 233412001588 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 233412001589 S-adenosylmethionine binding site [chemical binding]; other site 233412001590 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 233412001591 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 233412001592 Cl binding site [ion binding]; other site 233412001593 oligomer interface [polypeptide binding]; other site 233412001594 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 233412001595 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 233412001596 S-adenosylmethionine binding site [chemical binding]; other site 233412001597 hypothetical protein; Provisional; Region: PRK11027 233412001598 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 233412001599 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 233412001600 catalytic residue [active] 233412001601 diaminobutyrate--2-oxoglutarate aminotransferase; Provisional; Region: PRK06931 233412001602 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 233412001603 inhibitor-cofactor binding pocket; inhibition site 233412001604 pyridoxal 5'-phosphate binding site [chemical binding]; other site 233412001605 catalytic residue [active] 233412001606 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 233412001607 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 233412001608 hypothetical protein; Reviewed; Region: PRK00024 233412001609 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 233412001610 MPN+ (JAMM) motif; other site 233412001611 Zinc-binding site [ion binding]; other site 233412001612 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 233412001613 Flavoprotein; Region: Flavoprotein; pfam02441 233412001614 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 233412001615 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 233412001616 trimer interface [polypeptide binding]; other site 233412001617 active site 233412001618 division inhibitor protein; Provisional; Region: slmA; PRK09480 233412001619 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 233412001620 hypothetical protein; Provisional; Region: PRK04966 233412001621 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 233412001622 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 233412001623 ligand binding site [chemical binding]; other site 233412001624 flexible hinge region; other site 233412001625 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 233412001626 putative switch regulator; other site 233412001627 non-specific DNA interactions [nucleotide binding]; other site 233412001628 DNA binding site [nucleotide binding] 233412001629 sequence specific DNA binding site [nucleotide binding]; other site 233412001630 putative cAMP binding site [chemical binding]; other site 233412001631 GTPase HflX; Provisional; Region: PRK11058 233412001632 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 233412001633 HflX GTPase family; Region: HflX; cd01878 233412001634 G1 box; other site 233412001635 GTP/Mg2+ binding site [chemical binding]; other site 233412001636 Switch I region; other site 233412001637 G2 box; other site 233412001638 G3 box; other site 233412001639 Switch II region; other site 233412001640 G4 box; other site 233412001641 G5 box; other site 233412001642 bacterial Hfq-like; Region: Hfq; cd01716 233412001643 hexamer interface [polypeptide binding]; other site 233412001644 Sm1 motif; other site 233412001645 RNA binding site [nucleotide binding]; other site 233412001646 Sm2 motif; other site 233412001647 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 233412001648 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 233412001649 DNA mismatch repair protein MutL; Region: mutl; TIGR00585 233412001650 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 233412001651 ATP binding site [chemical binding]; other site 233412001652 Mg2+ binding site [ion binding]; other site 233412001653 G-X-G motif; other site 233412001654 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 233412001655 ATP binding site [chemical binding]; other site 233412001656 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 233412001657 hypothetical protein; Reviewed; Region: PRK01637 233412001658 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 233412001659 putative active site [active] 233412001660 dimerization interface [polypeptide binding]; other site 233412001661 putative tRNAtyr binding site [nucleotide binding]; other site 233412001662 Ricin-type beta-trefoil lectin domain; Region: Ricin_B_lectin; pfam00652 233412001663 Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific...; Region: RICIN; cd00161 233412001664 putative sugar binding sites [chemical binding]; other site 233412001665 Q-X-W motif; other site 233412001666 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09560 233412001667 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 233412001668 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 233412001669 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 233412001670 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 233412001671 active site 233412001672 metal binding site [ion binding]; metal-binding site 233412001673 hexamer interface [polypeptide binding]; other site 233412001674 glutamine synthetase; Provisional; Region: glnA; PRK09469 233412001675 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 233412001676 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 233412001677 Haemolytic domain; Region: Haemolytic; cl00506 233412001678 ribonuclease P; Reviewed; Region: rnpA; PRK01732 233412001679 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 233412001680 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 233412001681 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 233412001682 Peptidase family M23; Region: Peptidase_M23; pfam01551 233412001683 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 233412001684 Predicted membrane protein [Function unknown]; Region: COG1238 233412001685 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 233412001686 possible hydrogenase subunit, N-terminal fragment; HDp0759A 233412001687 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 233412001688 triosephosphate isomerase; Provisional; Region: PRK14567 233412001689 substrate binding site [chemical binding]; other site 233412001690 dimer interface [polypeptide binding]; other site 233412001691 catalytic triad [active] 233412001692 Alpha-Mannosidase Binding Domain of Atg19/34; Region: ABD; cl15429 233412001693 mannose-6-phosphate isomerase; Region: PLN02288 233412001694 Alpha-Mannosidase Binding Domain of Atg19/34; Region: ABD; cl15429 233412001695 PTS system mannose-specific transporter subunit IID; Provisional; Region: PRK11103 233412001696 PTS system mannose-specific transporter subunit IIC; Provisional; Region: PRK15065 233412001697 PTS system mannose-specific transporter subunits IIAB; Provisional; Region: PRK15088 233412001698 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cd00006 233412001699 active pocket/dimerization site; other site 233412001700 active site 233412001701 phosphorylation site [posttranslational modification] 233412001702 PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_man; cd00001 233412001703 active site 233412001704 phosphorylation site [posttranslational modification] 233412001705 YadA-like C-terminal region; Region: YadA; pfam03895 233412001706 hypothetical protein; Provisional; Region: PRK11573 233412001707 Domain of unknown function DUF21; Region: DUF21; pfam01595 233412001708 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 233412001709 Transporter associated domain; Region: CorC_HlyC; smart01091 233412001710 hypothetical protein; Provisional; Region: PRK11193 233412001711 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 233412001712 putative phosphate acyltransferase; Provisional; Region: PRK05331 233412001713 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 233412001714 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 233412001715 dimer interface [polypeptide binding]; other site 233412001716 active site 233412001717 CoA binding pocket [chemical binding]; other site 233412001718 tRNA (guanine-N(7)-)-methyltransferase; Reviewed; Region: trmB; PRK00121 233412001719 hypothetical protein; Provisional; Region: PRK11702 233412001720 YGGT family; Region: YGGT; pfam02325 233412001721 YGGT family; Region: YGGT; pfam02325 233412001722 hypothetical protein; Validated; Region: PRK05090 233412001723 cytochrome c peroxidase, N-terminal fragment; HDp0779A 233412001724 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 233412001725 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 233412001726 PhnA protein; Region: PhnA; pfam03831 233412001727 Na+-transporting oxaloacetate decarboxylase beta subunit; Region: OAD_beta; cl00816 233412001728 oxaloacetate decarboxylase; Provisional; Region: PRK14040 233412001729 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 233412001730 active site 233412001731 catalytic residues [active] 233412001732 metal binding site [ion binding]; metal-binding site 233412001733 homodimer binding site [polypeptide binding]; other site 233412001734 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 233412001735 carboxyltransferase (CT) interaction site; other site 233412001736 biotinylation site [posttranslational modification]; other site 233412001737 oxaloacetate decarboxylase subunit gamma; Provisional; Region: PRK02919 233412001738 rRNA operon variant 1 difference region; HDprRNA4d 233412001739 DNA replication initiation factor; Validated; Region: PRK06893 233412001740 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 233412001741 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 233412001742 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 233412001743 Walker A/P-loop; other site 233412001744 ATP binding site [chemical binding]; other site 233412001745 Q-loop/lid; other site 233412001746 ABC transporter signature motif; other site 233412001747 Walker B; other site 233412001748 D-loop; other site 233412001749 H-loop/switch region; other site 233412001750 heme exporter protein CcmB; Region: ccmB; TIGR01190 233412001751 heme exporter protein CcmC; Region: ccmC; TIGR01191 233412001752 Heme exporter protein D [Intracellular trafficking and secretion]; Region: CcmD; COG3114 233412001753 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13165 233412001754 c-type cytochrome biogenesis protein CcmF; Region: nrfE; TIGR00353 233412001755 Sulphur transport; Region: Sulf_transp; pfam04143 233412001756 putative selenium metabolism protein, YedE family; Region: seleno_YedE; TIGR04112 233412001757 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 233412001758 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 233412001759 active site residue [active] 233412001760 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 233412001761 active site residue [active] 233412001762 probable oxidoreductase, N-terminal fragment; HDp0797A 233412001763 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 233412001764 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 233412001765 substrate binding pocket [chemical binding]; other site 233412001766 membrane-bound complex binding site; other site 233412001767 hinge residues; other site 233412001768 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 233412001769 N-acetyl-D-glucosamine binding site [chemical binding]; other site 233412001770 catalytic residue [active] 233412001771 outer membrane lipoprotein; Provisional; Region: PRK11023 233412001772 BON domain; Region: BON; pfam04972 233412001773 BON domain; Region: BON; pfam04972 233412001774 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 233412001775 dimer interface [polypeptide binding]; other site 233412001776 active site 233412001777 hypothetical protein; Reviewed; Region: PRK12497 233412001778 LppC putative lipoprotein; Region: LppC; pfam04348 233412001779 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 233412001780 putative ligand binding site [chemical binding]; other site 233412001781 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional; Region: PRK14994 233412001782 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 233412001783 putative SAM binding site [chemical binding]; other site 233412001784 putative homodimer interface [polypeptide binding]; other site 233412001785 Protein of unknown function, DUF462; Region: DUF462; pfam04315 233412001786 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 233412001787 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 233412001788 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 233412001789 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 233412001790 DsbD alpha interface [polypeptide binding]; other site 233412001791 catalytic residues [active] 233412001792 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 233412001793 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 233412001794 arginine transporter ATP-binding subunit; Provisional; Region: artP; PRK11124 233412001795 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 233412001796 Walker A/P-loop; other site 233412001797 ATP binding site [chemical binding]; other site 233412001798 Q-loop/lid; other site 233412001799 ABC transporter signature motif; other site 233412001800 Walker B; other site 233412001801 D-loop; other site 233412001802 H-loop/switch region; other site 233412001803 putative ABC transporter arginine-biding protein; Provisional; Region: PRK15007 233412001804 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 233412001805 substrate binding pocket [chemical binding]; other site 233412001806 membrane-bound complex binding site; other site 233412001807 hinge residues; other site 233412001808 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 233412001809 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412001810 dimer interface [polypeptide binding]; other site 233412001811 conserved gate region; other site 233412001812 putative PBP binding loops; other site 233412001813 ABC-ATPase subunit interface; other site 233412001814 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412001815 dimer interface [polypeptide binding]; other site 233412001816 conserved gate region; other site 233412001817 putative PBP binding loops; other site 233412001818 ABC-ATPase subunit interface; other site 233412001819 recombination and repair protein; Provisional; Region: PRK10869 233412001820 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 233412001821 Walker A/P-loop; other site 233412001822 ATP binding site [chemical binding]; other site 233412001823 Q-loop/lid; other site 233412001824 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 233412001825 ABC transporter signature motif; other site 233412001826 Walker B; other site 233412001827 D-loop; other site 233412001828 H-loop/switch region; other site 233412001829 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 233412001830 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 233412001831 cell division protein FtsZ; Validated; Region: PRK09330 233412001832 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at...; Region: FtsZ_type1; cd02201 233412001833 nucleotide binding site [chemical binding]; other site 233412001834 SulA interaction site; other site 233412001835 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 233412001836 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 233412001837 nucleotide binding site [chemical binding]; other site 233412001838 SHS2 domain inserted in FTSA; Region: SHS2_FTSA; pfam02491 233412001839 Cell division protein FtsA; Region: FtsA; pfam14450 233412001840 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 233412001841 Cell division protein FtsQ; Region: FtsQ; pfam03799 233412001842 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 233412001843 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 233412001844 ATP-grasp domain; Region: ATP-grasp_4; cl17255 233412001845 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 233412001846 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 233412001847 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 233412001848 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 233412001849 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 233412001850 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 233412001851 active site 233412001852 homodimer interface [polypeptide binding]; other site 233412001853 adenylate kinase; Reviewed; Region: adk; PRK00279 233412001854 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 233412001855 AMP-binding site [chemical binding]; other site 233412001856 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 233412001857 muropeptide transporter; Reviewed; Region: ampG; PRK11902 233412001858 AmpG-like permease; Region: 2A0125; TIGR00901 233412001859 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 233412001860 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 233412001861 NAD binding site [chemical binding]; other site 233412001862 homodimer interface [polypeptide binding]; other site 233412001863 active site 233412001864 substrate binding site [chemical binding]; other site 233412001865 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 233412001866 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 233412001867 nucleotide binding pocket [chemical binding]; other site 233412001868 K-X-D-G motif; other site 233412001869 catalytic site [active] 233412001870 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 233412001871 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 233412001872 H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Region: H3TH_StructSpec-5'-nucleases; cl14815 233412001873 DNA binding site [nucleotide binding] 233412001874 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 233412001875 Dimer interface [polypeptide binding]; other site 233412001876 BRCT sequence motif; other site 233412001877 cell division protein ZipA; Provisional; Region: PRK01741 233412001878 ZipA, C-terminal FtsZ-binding domain; Region: ZipA_C; pfam04354 233412001879 FtsZ protein binding site [polypeptide binding]; other site 233412001880 putative sulfate transport protein CysZ; Validated; Region: PRK04949 233412001881 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 233412001882 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 233412001883 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 233412001884 benzoate transport; Region: 2A0115; TIGR00895 233412001885 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 233412001886 putative substrate translocation pore; other site 233412001887 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 233412001888 putative substrate translocation pore; other site 233412001889 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 233412001890 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 233412001891 putative active site [active] 233412001892 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 233412001893 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 233412001894 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 233412001895 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 233412001896 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 233412001897 active site 233412001898 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 233412001899 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 233412001900 dimer interface [polypeptide binding]; other site 233412001901 ADP-ribose binding site [chemical binding]; other site 233412001902 active site 233412001903 nudix motif; other site 233412001904 metal binding site [ion binding]; metal-binding site 233412001905 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 233412001906 RNA binding surface [nucleotide binding]; other site 233412001907 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 233412001908 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 233412001909 dimerization interface [polypeptide binding]; other site 233412001910 domain crossover interface; other site 233412001911 redox-dependent activation switch; other site 233412001912 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 233412001913 putative inner membrane peptidase; Provisional; Region: PRK11778 233412001914 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 233412001915 tandem repeat interface [polypeptide binding]; other site 233412001916 oligomer interface [polypeptide binding]; other site 233412001917 active site residues [active] 233412001918 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 233412001919 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 233412001920 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 233412001921 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 233412001922 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 233412001923 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 233412001924 E-class dimer interface [polypeptide binding]; other site 233412001925 P-class dimer interface [polypeptide binding]; other site 233412001926 active site 233412001927 Cu2+ binding site [ion binding]; other site 233412001928 Zn2+ binding site [ion binding]; other site 233412001929 recF protein; Region: recf; TIGR00611 233412001930 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 233412001931 Walker A/P-loop; other site 233412001932 ATP binding site [chemical binding]; other site 233412001933 Q-loop/lid; other site 233412001934 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 233412001935 ABC transporter signature motif; other site 233412001936 Walker B; other site 233412001937 D-loop; other site 233412001938 DNA polymerase III subunit beta; Validated; Region: PRK05643 233412001939 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cd00140 233412001940 putative DNA binding surface [nucleotide binding]; other site 233412001941 dimer interface [polypeptide binding]; other site 233412001942 beta-clamp/clamp loader binding surface; other site 233412001943 beta-clamp/translesion DNA polymerase binding surface; other site 233412001944 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 233412001945 DnaA N-terminal domain; Region: DnaA_N; pfam11638 233412001946 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 233412001947 Walker B motif; other site 233412001948 arginine finger; other site 233412001949 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 233412001950 DnaA box-binding interface [nucleotide binding]; other site 233412001951 putative metal dependent hydrolase; Provisional; Region: PRK11598 233412001952 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 233412001953 Sulfatase; Region: Sulfatase; pfam00884 233412001954 peptide chain release factor 1; Validated; Region: prfA; PRK00591 233412001955 This domain is found in peptide chain release factors; Region: PCRF; smart00937 233412001956 RF-1 domain; Region: RF-1; pfam00472 233412001957 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 233412001958 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 233412001959 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 233412001960 Tetratricopeptide repeat; Region: TPR_9; pfam13371 233412001961 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 233412001962 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 233412001963 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 233412001964 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 233412001965 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 233412001966 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 233412001967 Walker A/P-loop; other site 233412001968 ATP binding site [chemical binding]; other site 233412001969 Q-loop/lid; other site 233412001970 ABC transporter signature motif; other site 233412001971 Walker B; other site 233412001972 D-loop; other site 233412001973 H-loop/switch region; other site 233412001974 outer membrane-specific lipoprotein transporter subunit LolE; Provisional; Region: PRK11146 233412001975 FtsX-like permease family; Region: FtsX; pfam02687 233412001976 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapF; COG4167 233412001977 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 233412001978 Walker A/P-loop; other site 233412001979 ATP binding site [chemical binding]; other site 233412001980 Q-loop/lid; other site 233412001981 ABC transporter signature motif; other site 233412001982 Walker B; other site 233412001983 D-loop; other site 233412001984 H-loop/switch region; other site 233412001985 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 233412001986 Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is...; Region: FBP_aldolase_IIA; cd00946 233412001987 active site 233412001988 intersubunit interface [polypeptide binding]; other site 233412001989 zinc binding site [ion binding]; other site 233412001990 Na+ binding site [ion binding]; other site 233412001991 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 233412001992 Phosphoglycerate kinase; Region: PGK; pfam00162 233412001993 substrate binding site [chemical binding]; other site 233412001994 hinge regions; other site 233412001995 ADP binding site [chemical binding]; other site 233412001996 catalytic site [active] 233412001997 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 233412001998 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 233412001999 transmembrane helices; other site 233412002000 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 233412002001 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 233412002002 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 233412002003 ATP binding site [chemical binding]; other site 233412002004 Mg2+ binding site [ion binding]; other site 233412002005 G-X-G motif; other site 233412002006 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 233412002007 anchoring element; other site 233412002008 dimer interface [polypeptide binding]; other site 233412002009 ATP binding site [chemical binding]; other site 233412002010 TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands...; Region: TOPRIM_TopoIIA_like; cd01030 233412002011 active site 233412002012 putative metal-binding site [ion binding]; other site 233412002013 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 233412002014 copper exporting ATPase; Provisional; Region: copA; PRK10671 233412002015 bifunctional chorismate mutase/prephenate dehydratase; Provisional; Region: pheA; PRK10622 233412002016 chorismate mutase domain of proteobacterial P-protein, clade 1; Region: CM_P_1; TIGR01797 233412002017 Prephenate dehydratase; Region: PDT; pfam00800 233412002018 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 233412002019 putative L-Phe binding site [chemical binding]; other site 233412002020 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 233412002021 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 233412002022 hypothetical protein; Provisional; Region: PRK04860 233412002023 Zn-dependent metalloprotease, SprT family [General function prediction only]; Region: SprT; COG3091 233412002024 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_prok; cd01062 233412002025 B1 nucleotide binding pocket [chemical binding]; other site 233412002026 B2 nucleotide binding pocket [chemical binding]; other site 233412002027 CAS motifs; other site 233412002028 active site 233412002029 protease 4; Provisional; Region: PRK10949 233412002030 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 233412002031 tandem repeat interface [polypeptide binding]; other site 233412002032 oligomer interface [polypeptide binding]; other site 233412002033 active site residues [active] 233412002034 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 233412002035 tandem repeat interface [polypeptide binding]; other site 233412002036 oligomer interface [polypeptide binding]; other site 233412002037 active site residues [active] 233412002038 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 233412002039 putative FMN binding site [chemical binding]; other site 233412002040 short chain dehydrogenase; Provisional; Region: PRK05993 233412002041 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 233412002042 NADP binding site [chemical binding]; other site 233412002043 active site 233412002044 steroid binding site; other site 233412002045 Uncharacterized conserved protein [Function unknown]; Region: COG1434 233412002046 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 233412002047 putative active site [active] 233412002048 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 233412002049 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 233412002050 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 233412002051 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 233412002052 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 233412002053 active site 233412002054 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 233412002055 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 233412002056 active site 233412002057 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 233412002058 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 233412002059 Nucleoside recognition; Region: Gate; pfam07670 233412002060 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 233412002061 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 233412002062 intersubunit interface [polypeptide binding]; other site 233412002063 active site 233412002064 catalytic residue [active] 233412002065 purine nucleoside phosphorylase; Reviewed; Region: deoD; PRK05819 233412002066 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 233412002067 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 233412002068 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 233412002069 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 233412002070 homohexameric interface [polypeptide binding]; other site 233412002071 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed; Region: PRK12454 233412002072 nucleotide binding site [chemical binding]; other site 233412002073 N-acetyl-L-glutamate binding site [chemical binding]; other site 233412002074 acetylornithine aminotransferase; Provisional; Region: PRK02627 233412002075 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 233412002076 inhibitor-cofactor binding pocket; inhibition site 233412002077 pyridoxal 5'-phosphate binding site [chemical binding]; other site 233412002078 catalytic residue [active] 233412002079 transcription termination factor Rho; Provisional; Region: rho; PRK09376 233412002080 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 233412002081 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 233412002082 RNA binding site [nucleotide binding]; other site 233412002083 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 233412002084 multimer interface [polypeptide binding]; other site 233412002085 Walker A motif; other site 233412002086 ATP binding site [chemical binding]; other site 233412002087 Walker B motif; other site 233412002088 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 233412002089 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 233412002090 dimer interface [polypeptide binding]; other site 233412002091 pyridoxal 5'-phosphate binding site [chemical binding]; other site 233412002092 catalytic residue [active] 233412002093 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 233412002094 active site 233412002095 Int/Topo IB signature motif; other site 233412002096 catalytic residues [active] 233412002097 DNA binding site [nucleotide binding] 233412002098 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 233412002099 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 233412002100 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 233412002101 Putative helicase; Region: TraI_2; pfam07514 233412002102 Cytolethal distending toxin A/C family; Region: CDtoxinA; pfam03498 233412002103 Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific...; Region: RICIN; cl15820 233412002104 CdtB, the catalytic DNase I-like subunit of cytolethal distending toxin (CDT) protein; Region: CdtB; cd09081 233412002105 putative catalytic site [active] 233412002106 CdtC interface [polypeptide binding]; other site 233412002107 heterotrimer interface [polypeptide binding]; other site 233412002108 CdtA interface [polypeptide binding]; other site 233412002109 putative metal binding site [ion binding]; other site 233412002110 putative phosphate binding site [ion binding]; other site 233412002111 Cytolethal distending toxin A/C family; Region: CDtoxinA; pfam03498 233412002112 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 233412002113 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 233412002114 Abi-like protein; Region: Abi_2; pfam07751 233412002115 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 233412002116 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 233412002117 catalytic residues [active] 233412002118 catalytic nucleophile [active] 233412002119 Presynaptic Site I dimer interface [polypeptide binding]; other site 233412002120 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 233412002121 Synaptic Flat tetramer interface [polypeptide binding]; other site 233412002122 Synaptic Site I dimer interface [polypeptide binding]; other site 233412002123 DNA binding site [nucleotide binding] 233412002124 Homeodomain-like domain; Region: HTH_23; cl17451 233412002125 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 233412002126 HicB family; Region: HicB; pfam05534 233412002127 AAA domain; Region: AAA_17; cl17253 233412002128 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 233412002129 sequence-specific DNA binding site [nucleotide binding]; other site 233412002130 salt bridge; other site 233412002131 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 233412002132 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 233412002133 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 233412002134 Protein of unknown function (DUF1525); Region: DUF1525; cl06515 233412002135 TraU protein; Region: TraU; cl06067 233412002136 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 233412002137 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 233412002138 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 233412002139 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 233412002140 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 233412002141 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 233412002142 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 233412002143 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 233412002144 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 233412002145 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 233412002146 Protein of unknown function (DUF3438); Region: DUF3438; pfam11920 233412002147 Protein of unknown function (DUF2895); Region: DUF2895; pfam11444 233412002148 Protein of unknown function (DUF3487); Region: DUF3487; pfam11990 233412002149 Protein of unknown function (DUF2976); Region: DUF2976; pfam11190 233412002150 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 233412002151 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 233412002152 integrating conjugative element membrane protein, PFL_4697 family; Region: conj_TIGR03747 233412002153 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 233412002154 MPN+ (JAMM) motif; other site 233412002155 Zinc-binding site [ion binding]; other site 233412002156 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 233412002157 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: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 233412002158 active site 233412002159 putative interdomain interaction site [polypeptide binding]; other site 233412002160 putative metal-binding site [ion binding]; other site 233412002161 putative nucleotide binding site [chemical binding]; other site 233412002162 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cl11986 233412002163 domain I; other site 233412002164 DNA binding groove [nucleotide binding] 233412002165 phosphate binding site [ion binding]; other site 233412002166 domain II; other site 233412002167 domain III; other site 233412002168 nucleotide binding site [chemical binding]; other site 233412002169 catalytic site [active] 233412002170 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 233412002171 Protein of unknown function (DUF551); Region: DUF551; pfam04448 233412002172 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 233412002173 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 233412002174 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 233412002175 dimer interface [polypeptide binding]; other site 233412002176 ssDNA binding site [nucleotide binding]; other site 233412002177 tetramer (dimer of dimers) interface [polypeptide binding]; other site 233412002178 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 233412002179 integrating conjugative element protein, PFL_4669 family; Region: ICE_PFL4669; TIGR03761 233412002180 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 233412002181 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 233412002182 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 233412002183 replicative DNA helicase; Region: DnaB; TIGR00665 233412002184 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 233412002185 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 233412002186 Walker A motif; other site 233412002187 ATP binding site [chemical binding]; other site 233412002188 Walker B motif; other site 233412002189 DNA binding loops [nucleotide binding] 233412002190 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 233412002191 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 233412002192 P-loop; other site 233412002193 Magnesium ion binding site [ion binding]; other site 233412002194 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 233412002195 Magnesium ion binding site [ion binding]; other site 233412002196 transcription-repair coupling factor; Provisional; Region: PRK10689 233412002197 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 233412002198 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 233412002199 ATP binding site [chemical binding]; other site 233412002200 putative Mg++ binding site [ion binding]; other site 233412002201 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 233412002202 nucleotide binding region [chemical binding]; other site 233412002203 ATP-binding site [chemical binding]; other site 233412002204 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 233412002205 aminopeptidase N; Provisional; Region: pepN; PRK14015 233412002206 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 233412002207 active site 233412002208 Zn binding site [ion binding]; other site 233412002209 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 233412002210 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 233412002211 homooctamer interface [polypeptide binding]; other site 233412002212 active site 233412002213 cytidine deaminase; Provisional; Region: PRK09027 233412002214 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 233412002215 active site 233412002216 catalytic motif [active] 233412002217 Zn binding site [ion binding]; other site 233412002218 Cytidine and deoxycytidylate deaminase zinc-binding region; Region: dCMP_cyt_deam_2; pfam08211 233412002219 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 233412002220 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 233412002221 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 233412002222 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 233412002223 Walker A/P-loop; other site 233412002224 ATP binding site [chemical binding]; other site 233412002225 Q-loop/lid; other site 233412002226 ABC transporter signature motif; other site 233412002227 Walker B; other site 233412002228 D-loop; other site 233412002229 H-loop/switch region; other site 233412002230 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 233412002231 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 233412002232 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 233412002233 P loop; other site 233412002234 GTP binding site [chemical binding]; other site 233412002235 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 233412002236 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 233412002237 S-adenosylmethionine binding site [chemical binding]; other site 233412002238 dsDNA-mimic protein; Reviewed; Region: PRK05094 233412002239 4-hydroxyphenylacetate 3-monooxygenase, reductase component; Region: HpaC; TIGR02296 233412002240 oligopeptidase A; Provisional; Region: PRK10911 233412002241 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 233412002242 active site 233412002243 Zn binding site [ion binding]; other site 233412002244 pyruvate formate lyase-activating enzyme 1; Provisional; Region: pflA; PRK11145 233412002245 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 233412002246 FeS/SAM binding site; other site 233412002247 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 233412002248 Pyruvate formate lyase 1; Region: PFL1; cd01678 233412002249 coenzyme A binding site [chemical binding]; other site 233412002250 active site 233412002251 catalytic residues [active] 233412002252 glycine loop; other site 233412002253 formate transporter FocA; Region: formate_focA; TIGR04060 233412002254 Predicted membrane protein [Function unknown]; Region: COG1238 233412002255 spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed; Region: potD; PRK09501 233412002256 Bacterial extracellular solute-binding protein; Region: SBP_bac_6; pfam13343 233412002257 GTP-binding protein YchF; Reviewed; Region: PRK09601 233412002258 YchF GTPase; Region: YchF; cd01900 233412002259 G1 box; other site 233412002260 GTP/Mg2+ binding site [chemical binding]; other site 233412002261 Switch I region; other site 233412002262 G2 box; other site 233412002263 Switch II region; other site 233412002264 G3 box; other site 233412002265 G4 box; other site 233412002266 G5 box; other site 233412002267 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 233412002268 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 233412002269 putative active site [active] 233412002270 catalytic residue [active] 233412002271 uracil-xanthine permease; Region: ncs2; TIGR00801 233412002272 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 233412002273 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 233412002274 Na binding site [ion binding]; other site 233412002275 Cell division protein ZapA; Region: ZapA; cl01146 233412002276 hypothetical protein; Reviewed; Region: PRK01736 233412002277 Protein of unknown function (DUF416); Region: DUF416; cl01166 233412002278 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 233412002279 IHF dimer interface [polypeptide binding]; other site 233412002280 IHF - DNA interface [nucleotide binding]; other site 233412002281 thymidylate synthase; Reviewed; Region: thyA; PRK01827 233412002282 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 233412002283 dimerization interface [polypeptide binding]; other site 233412002284 active site 233412002285 fumarate reductase flavoprotein subunit; Validated; Region: PRK06481 233412002286 biotin synthase; Provisional; Region: PRK15108 233412002287 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 233412002288 FeS/SAM binding site; other site 233412002289 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 233412002290 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 233412002291 DNA-binding site [nucleotide binding]; DNA binding site 233412002292 RNA-binding motif; other site 233412002293 ProP expression regulator; Provisional; Region: PRK04950 233412002294 ProQ/FINO family; Region: ProQ; pfam04352 233412002295 carboxy-terminal protease; Provisional; Region: PRK11186 233412002296 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 233412002297 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 233412002298 protein binding site [polypeptide binding]; other site 233412002299 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 233412002300 Catalytic dyad [active] 233412002301 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 233412002302 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 233412002303 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 233412002304 Outer membrane protein V [Cell envelope biogenesis, outer membrane]; Region: OmpV; COG3713 233412002305 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 233412002306 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 233412002307 HlyD family secretion protein; Region: HlyD_3; pfam13437 233412002308 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 233412002309 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 233412002310 Walker A/P-loop; other site 233412002311 ATP binding site [chemical binding]; other site 233412002312 Q-loop/lid; other site 233412002313 ABC transporter signature motif; other site 233412002314 Walker B; other site 233412002315 D-loop; other site 233412002316 H-loop/switch region; other site 233412002317 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 233412002318 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 233412002319 FtsX-like permease family; Region: FtsX; pfam02687 233412002320 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 233412002321 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 233412002322 active site 233412002323 ATP binding site [chemical binding]; other site 233412002324 substrate binding site [chemical binding]; other site 233412002325 Predicted periplasmic lipoprotein [General function prediction only]; Region: COG5633 233412002326 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 233412002327 putative dimer interface [polypeptide binding]; other site 233412002328 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 233412002329 nucleotide binding site/active site [active] 233412002330 HIT family signature motif; other site 233412002331 catalytic residue [active] 233412002332 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 233412002333 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 233412002334 ABC-ATPase subunit interface; other site 233412002335 dimer interface [polypeptide binding]; other site 233412002336 putative PBP binding regions; other site 233412002337 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 233412002338 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 233412002339 ABC-ATPase subunit interface; other site 233412002340 dimer interface [polypeptide binding]; other site 233412002341 putative PBP binding regions; other site 233412002342 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 233412002343 RNA/DNA hybrid binding site [nucleotide binding]; other site 233412002344 active site 233412002345 GTPase RsgA; Reviewed; Region: PRK12288 233412002346 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 233412002347 RNA binding site [nucleotide binding]; other site 233412002348 homodimer interface [polypeptide binding]; other site 233412002349 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 233412002350 GTPase/Zn-binding domain interface [polypeptide binding]; other site 233412002351 GTP/Mg2+ binding site [chemical binding]; other site 233412002352 G4 box; other site 233412002353 G5 box; other site 233412002354 G1 box; other site 233412002355 Switch I region; other site 233412002356 G2 box; other site 233412002357 G3 box; other site 233412002358 Switch II region; other site 233412002359 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 233412002360 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 233412002361 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 233412002362 dimerization interface [polypeptide binding]; other site 233412002363 substrate binding pocket [chemical binding]; other site 233412002364 dUMP phosphatase; Provisional; Region: PRK09449 233412002365 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 233412002366 motif II; other site 233412002367 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 233412002368 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 233412002369 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 233412002370 substrate binding site [chemical binding]; other site 233412002371 dimerization interface [polypeptide binding]; other site 233412002372 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 233412002373 Part of AAA domain; Region: AAA_19; pfam13245 233412002374 Family description; Region: UvrD_C_2; pfam13538 233412002375 argininosuccinate lyase; Provisional; Region: PRK04833 233412002376 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 233412002377 active sites [active] 233412002378 tetramer interface [polypeptide binding]; other site 233412002379 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 233412002380 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 233412002381 Sulfate transporter family; Region: Sulfate_transp; pfam00916 233412002382 cytoskeletal protein RodZ; Provisional; Region: PRK10856 233412002383 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 233412002384 non-specific DNA binding site [nucleotide binding]; other site 233412002385 salt bridge; other site 233412002386 sequence-specific DNA binding site [nucleotide binding]; other site 233412002387 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 233412002388 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 233412002389 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 233412002390 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 233412002391 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 233412002392 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 233412002393 dimer interface [polypeptide binding]; other site 233412002394 motif 1; other site 233412002395 active site 233412002396 motif 2; other site 233412002397 motif 3; other site 233412002398 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 233412002399 anticodon binding site; other site 233412002400 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 233412002401 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 233412002402 Nicotinamide mononucleotide transporter [Coenzyme metabolism]; Region: PnuC; COG3201 233412002403 phosphoribosylamine--glycine ligase, N-terminal fragment; HDp1042A 233412002404 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 233412002405 primosomal replication protein N; Provisional; Region: PRK02801 233412002406 generic binding surface II; other site 233412002407 generic binding surface I; other site 233412002408 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 233412002409 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 233412002410 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 233412002411 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 233412002412 Methyltransferase domain; Region: Methyltransf_31; pfam13847 233412002413 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 233412002414 S-adenosylmethionine binding site [chemical binding]; other site 233412002415 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 233412002416 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 233412002417 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 233412002418 RNA binding surface [nucleotide binding]; other site 233412002419 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 233412002420 probable active site [active] 233412002421 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 233412002422 active site 233412002423 multimer interface [polypeptide binding]; other site 233412002424 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 233412002425 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 233412002426 active site 233412002427 HIGH motif; other site 233412002428 KMSKS motif; other site 233412002429 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 233412002430 tRNA binding surface [nucleotide binding]; other site 233412002431 anticodon binding site; other site 233412002432 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 233412002433 dimer interface [polypeptide binding]; other site 233412002434 putative tRNA-binding site [nucleotide binding]; other site 233412002435 O-succinylbenzoate synthase; Provisional; Region: PRK05105 233412002436 o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway; Region: OSBS; cd03320 233412002437 active site 233412002438 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 233412002439 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 233412002440 RNA binding surface [nucleotide binding]; other site 233412002441 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 233412002442 active site 233412002443 uracil binding [chemical binding]; other site 233412002444 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 233412002445 endonuclease IV; Provisional; Region: PRK01060 233412002446 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 233412002447 AP (apurinic/apyrimidinic) site pocket; other site 233412002448 DNA interaction; other site 233412002449 Metal-binding active site; metal-binding site 233412002450 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 233412002451 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 233412002452 autonomous glycyl radical cofactor GrcA; Provisional; Region: PRK11127 233412002453 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 233412002454 ligand binding site [chemical binding]; other site 233412002455 active site 233412002456 UGI interface [polypeptide binding]; other site 233412002457 catalytic site [active] 233412002458 ATP-dependent helicase HrpA homolog, central fragment; HDp1067B 233412002459 ATP-dependent helicase HrpA homolog, N-terminal fragment; HDp1067A 233412002460 Protein of unknown function (DUF441); Region: DUF441; cl01041 233412002461 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 233412002462 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 233412002463 dimer interface [polypeptide binding]; other site 233412002464 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 233412002465 spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed; Region: potD; PRK09501 233412002466 Bacterial extracellular solute-binding protein; Region: SBP_bac_6; pfam13343 233412002467 multidrug efflux protein; Reviewed; Region: PRK01766 233412002468 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 233412002469 cation binding site [ion binding]; other site 233412002470 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 233412002471 Part of AAA domain; Region: AAA_19; pfam13245 233412002472 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 233412002473 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 233412002474 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 233412002475 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 233412002476 DNA binding site [nucleotide binding] 233412002477 active site 233412002478 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 233412002479 Transcriptional regulator; Region: Rrf2; cl17282 233412002480 Rrf2 family protein; Region: rrf2_super; TIGR00738 233412002481 cysteine desulfurase; Provisional; Region: PRK14012 233412002482 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 233412002483 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 233412002484 catalytic residue [active] 233412002485 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 233412002486 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 233412002487 trimerization site [polypeptide binding]; other site 233412002488 active site 233412002489 iron-sulfur cluster assembly protein; Provisional; Region: iscA; PRK09502 233412002490 co-chaperone HscB; Provisional; Region: hscB; PRK01773 233412002491 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 233412002492 HSP70 interaction site [polypeptide binding]; other site 233412002493 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 233412002494 Protein of unknown function DUF2625; Region: DUF2625; pfam10946 233412002495 chaperone protein HscA; Provisional; Region: hscA; PRK05183 233412002496 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 233412002497 nucleotide binding site [chemical binding]; other site 233412002498 putative NEF/HSP70 interaction site [polypeptide binding]; other site 233412002499 SBD interface [polypeptide binding]; other site 233412002500 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 233412002501 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 233412002502 catalytic loop [active] 233412002503 iron binding site [ion binding]; other site 233412002504 Iron-sulphur cluster assembly; Region: Fe-S_assembly; pfam04384 233412002505 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 233412002506 Glycosyl transferase family 8; Region: Glyco_transf_8; pfam01501 233412002507 Ligand binding site; other site 233412002508 metal-binding site 233412002509 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 233412002510 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 233412002511 active site 233412002512 NTP binding site [chemical binding]; other site 233412002513 metal binding triad [ion binding]; metal-binding site 233412002514 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 233412002515 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 233412002516 substrate binding site [chemical binding]; other site 233412002517 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 233412002518 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 233412002519 active site 233412002520 HIGH motif; other site 233412002521 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 233412002522 KMSKS motif; other site 233412002523 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 233412002524 tRNA binding surface [nucleotide binding]; other site 233412002525 anticodon binding site; other site 233412002526 Peptidase S8 family domain in Autotransporter serine proteases; Region: Peptidases_S8_Autotransporter_serine_protease_like; cd04848 233412002527 catalytic triad [active] 233412002528 putative active site [active] 233412002529 Autotransporter beta-domain; Region: Autotransporter; cl17461 233412002530 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 233412002531 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 233412002532 non-specific DNA binding site [nucleotide binding]; other site 233412002533 salt bridge; other site 233412002534 sequence-specific DNA binding site [nucleotide binding]; other site 233412002535 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 233412002536 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 233412002537 Walker A/P-loop; other site 233412002538 ATP binding site [chemical binding]; other site 233412002539 Q-loop/lid; other site 233412002540 ABC transporter signature motif; other site 233412002541 Walker B; other site 233412002542 D-loop; other site 233412002543 H-loop/switch region; other site 233412002544 This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins; Region: NIL; smart00930 233412002545 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412002546 dimer interface [polypeptide binding]; other site 233412002547 conserved gate region; other site 233412002548 ABC-ATPase subunit interface; other site 233412002549 DL-methionine transporter substrate-binding subunit; Provisional; Region: metQ; PRK11063 233412002550 NLPA lipoprotein; Region: Lipoprotein_9; cl17547 233412002551 3-deoxy-D-manno-octulosonic-acid kinase; Reviewed; Region: PRK01723 233412002552 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 233412002553 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 233412002554 homodecamer interface [polypeptide binding]; other site 233412002555 GTP cyclohydrolase I; Provisional; Region: PLN03044 233412002556 active site 233412002557 putative catalytic site residues [active] 233412002558 zinc binding site [ion binding]; other site 233412002559 GTP-CH-I/GFRP interaction surface; other site 233412002560 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 233412002561 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 233412002562 dimerization interface 3.5A [polypeptide binding]; other site 233412002563 active site 233412002564 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...; Region: RaiA; cd00552 233412002565 30S subunit binding site; other site 233412002566 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 233412002567 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 233412002568 putative acyl-acceptor binding pocket; other site 233412002569 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 233412002570 dihydrodipicolinate synthase; Region: dapA; TIGR00674 233412002571 dimer interface [polypeptide binding]; other site 233412002572 active site 233412002573 catalytic residue [active] 233412002574 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 233412002575 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 233412002576 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 233412002577 homodimer interface [polypeptide binding]; other site 233412002578 NADP binding site [chemical binding]; other site 233412002579 substrate binding site [chemical binding]; other site 233412002580 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 233412002581 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 233412002582 putative substrate translocation pore; other site 233412002583 formate dehydrogenase accessory protein FdhE; Provisional; Region: PRK03564 233412002584 formate dehydrogenase accessory protein FdhE; Region: FdhE; TIGR01562 233412002585 Cytochrome b subunit of formate dehydrogenase [Energy production and conversion]; Region: FdnI; COG2864 233412002586 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 233412002587 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 233412002588 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 233412002589 endonuclease III; Provisional; Region: PRK10702 233412002590 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 233412002591 minor groove reading motif; other site 233412002592 helix-hairpin-helix signature motif; other site 233412002593 substrate binding pocket [chemical binding]; other site 233412002594 active site 233412002595 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 233412002596 hypothetical protein; Provisional; Region: PRK10621 233412002597 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 233412002598 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 233412002599 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 233412002600 folate binding site [chemical binding]; other site 233412002601 NADP+ binding site [chemical binding]; other site 233412002602 DNA repair protein RadA; Provisional; Region: PRK11823 233412002603 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 233412002604 Walker A motif/ATP binding site; other site 233412002605 ATP binding site [chemical binding]; other site 233412002606 Walker B motif; other site 233412002607 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 233412002608 putative major pilin subunit; Provisional; Region: PRK10574 233412002609 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 233412002610 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 233412002611 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 233412002612 Walker A motif; other site 233412002613 ATP binding site [chemical binding]; other site 233412002614 Walker B motif; other site 233412002615 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 233412002616 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 233412002617 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 233412002618 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 233412002619 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 233412002620 CoA-binding site [chemical binding]; other site 233412002621 ATP-binding [chemical binding]; other site 233412002622 Domain of unknown function (DUF329); Region: DUF329; pfam03884 233412002623 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 233412002624 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 233412002625 Lipopolysaccharide-assembly; Region: LptE; cl01125 233412002626 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 233412002627 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 233412002628 HIGH motif; other site 233412002629 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 233412002630 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 233412002631 active site 233412002632 KMSKS motif; other site 233412002633 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 233412002634 tRNA binding surface [nucleotide binding]; other site 233412002635 seryl-tRNA synthetase; Provisional; Region: PRK05431 233412002636 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 233412002637 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 233412002638 dimer interface [polypeptide binding]; other site 233412002639 active site 233412002640 motif 1; other site 233412002641 motif 2; other site 233412002642 motif 3; other site 233412002643 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 233412002644 SmpB-tmRNA interface; other site 233412002645 YcjX-like family, DUF463; Region: DUF463; pfam04317 233412002646 Uncharacterized protein family (UPF0181); Region: UPF0181; pfam03701 233412002647 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 233412002648 tRNA pseudouridine isomerase C; Region: PseudoU_synth_TruC; cd02563 233412002649 probable active site [active] 233412002650 tRNA pseudouridine synthase C; Region: DUF446; pfam04287 233412002651 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 233412002652 Uncharacterized conserved protein [Function unknown]; Region: COG4121 233412002653 hydroxyglutarate oxidase; Provisional; Region: PRK11728 233412002654 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 233412002655 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 233412002656 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 233412002657 serine transporter; Region: stp; TIGR00814 233412002658 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 233412002659 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 233412002660 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 233412002661 putative active site [active] 233412002662 catalytic triad [active] 233412002663 putative dimer interface [polypeptide binding]; other site 233412002664 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 233412002665 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 233412002666 Transporter associated domain; Region: CorC_HlyC; smart01091 233412002667 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 233412002668 amphipathic channel; other site 233412002669 Asn-Pro-Ala signature motifs; other site 233412002670 glycerol kinase, N-terminal fragment; HDp1148A 233412002671 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 233412002672 Found in ATP-dependent protease La (LON); Region: LON; smart00464 233412002673 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 233412002674 Walker A motif; other site 233412002675 ATP binding site [chemical binding]; other site 233412002676 Walker B motif; other site 233412002677 arginine finger; other site 233412002678 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 233412002679 glycerol-3-phosphate transporter; Region: glpT; TIGR00712 233412002680 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 233412002681 putative substrate translocation pore; other site 233412002682 glycerophosphoryl diester phosphodiesterase; Protein D, central fragment; HDp1152B 233412002683 glycerophosphoryl diester phosphodiesterase; Protein D, N-terminal fragment; HDp1152A 233412002684 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 233412002685 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 233412002686 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 233412002687 haemagglutination activity domain; Region: Haemagg_act; pfam05860 233412002688 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 233412002689 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 233412002690 Yersinia/Haemophilus virulence surface antigen; Region: Peptidase_C58; pfam03543 233412002691 sn-glycerol-3-phosphate dehydrogenase subunit A; Provisional; Region: glpA; PRK11101 233412002692 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 233412002693 anaerobic glycerol-3-phosphate dehydrogenase subunit B; Validated; Region: PRK05329 233412002694 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 233412002695 glycerol-3-phosphate dehydrogenase, anaerobic, C subunit; Region: glycerol3P_GlpC; TIGR03379 233412002696 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...; Region: HCP_like; cl14655 233412002697 Cysteine-rich domain; Region: CCG; pfam02754 233412002698 Cysteine-rich domain; Region: CCG; pfam02754 233412002699 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 233412002700 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 233412002701 catalytic motif [active] 233412002702 Zn binding site [ion binding]; other site 233412002703 RibD C-terminal domain; Region: RibD_C; cl17279 233412002704 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 233412002705 Lumazine binding domain; Region: Lum_binding; pfam00677 233412002706 Lumazine binding domain; Region: Lum_binding; pfam00677 233412002707 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 233412002708 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 233412002709 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 233412002710 dimerization interface [polypeptide binding]; other site 233412002711 active site 233412002712 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 233412002713 homopentamer interface [polypeptide binding]; other site 233412002714 active site 233412002715 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 233412002716 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 233412002717 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 233412002718 KpsF/GutQ family protein; Region: kpsF; TIGR00393 233412002719 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 233412002720 putative active site [active] 233412002721 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 233412002722 aminopeptidase B; Provisional; Region: PRK05015 233412002723 Peptidase; Region: DUF3663; pfam12404 233412002724 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 233412002725 interface (dimer of trimers) [polypeptide binding]; other site 233412002726 Substrate-binding/catalytic site; other site 233412002727 Zn-binding sites [ion binding]; other site 233412002728 Predicted secreted acid phosphatase [General function prediction only]; Region: COG2503 233412002729 putative hydrolase; Provisional; Region: PRK10976 233412002730 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 233412002731 active site 233412002732 motif I; other site 233412002733 motif II; other site 233412002734 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 233412002735 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 233412002736 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 233412002737 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 233412002738 DNA binding residues [nucleotide binding] 233412002739 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseA; COG3073 233412002740 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 233412002741 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 233412002742 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 233412002743 long-chain-fatty-acid--CoA ligase, N-terminal fragment; HDp1177A 233412002744 long-chain-fatty-acid--CoA ligase, central fragment; HDp1177B 233412002745 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 233412002746 active site 233412002747 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 233412002748 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 233412002749 S-adenosylmethionine binding site [chemical binding]; other site 233412002750 SurA N-terminal domain; Region: SurA_N; pfam09312 233412002751 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 233412002752 Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Region: PyrR; COG2065 233412002753 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 233412002754 active site 233412002755 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 233412002756 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 233412002757 putative ribose interaction site [chemical binding]; other site 233412002758 putative ADP binding site [chemical binding]; other site 233412002759 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 233412002760 active site 233412002761 HIGH motif; other site 233412002762 nucleotide binding site [chemical binding]; other site 233412002763 GTP-binding protein Der; Reviewed; Region: PRK00093 233412002764 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 233412002765 G1 box; other site 233412002766 GTP/Mg2+ binding site [chemical binding]; other site 233412002767 Switch I region; other site 233412002768 G2 box; other site 233412002769 Switch II region; other site 233412002770 G3 box; other site 233412002771 G4 box; other site 233412002772 G5 box; other site 233412002773 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 233412002774 G1 box; other site 233412002775 GTP/Mg2+ binding site [chemical binding]; other site 233412002776 Switch I region; other site 233412002777 G2 box; other site 233412002778 G3 box; other site 233412002779 Switch II region; other site 233412002780 G4 box; other site 233412002781 G5 box; other site 233412002782 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 233412002783 HD domain; Region: HD_4; pfam13328 233412002784 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 233412002785 synthetase active site [active] 233412002786 NTP binding site [chemical binding]; other site 233412002787 metal binding site [ion binding]; metal-binding site 233412002788 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 233412002789 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 233412002790 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 233412002791 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 233412002792 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 233412002793 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 233412002794 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 233412002795 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 233412002796 active site 233412002797 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 233412002798 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 233412002799 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 233412002800 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 233412002801 trimer interface [polypeptide binding]; other site 233412002802 active site 233412002803 UDP-GlcNAc binding site [chemical binding]; other site 233412002804 lipid binding site [chemical binding]; lipid-binding site 233412002805 periplasmic chaperone; Provisional; Region: PRK10780 233412002806 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 233412002807 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 233412002808 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 233412002809 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 233412002810 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 233412002811 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 233412002812 Surface antigen; Region: Bac_surface_Ag; pfam01103 233412002813 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 233412002814 zinc metallopeptidase RseP; Provisional; Region: PRK10779 233412002815 active site 233412002816 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 233412002817 protein binding site [polypeptide binding]; other site 233412002818 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 233412002819 protein binding site [polypeptide binding]; other site 233412002820 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 233412002821 putative substrate binding region [chemical binding]; other site 233412002822 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 233412002823 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 233412002824 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 233412002825 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 233412002826 catalytic residue [active] 233412002827 putative FPP diphosphate binding site; other site 233412002828 putative FPP binding hydrophobic cleft; other site 233412002829 dimer interface [polypeptide binding]; other site 233412002830 putative IPP diphosphate binding site; other site 233412002831 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 233412002832 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 233412002833 active site 233412002834 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 233412002835 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 233412002836 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 233412002837 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 233412002838 putative metal binding site; other site 233412002839 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 233412002840 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 233412002841 putative active site [active] 233412002842 argininosuccinate synthase; Validated; Region: PRK05370 233412002843 argininosuccinate synthase; Provisional; Region: PRK13820 233412002844 Protein of unknown function (DUF535); Region: DUF535; cl01128 233412002845 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 233412002846 RNA/DNA hybrid binding site [nucleotide binding]; other site 233412002847 active site 233412002848 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 233412002849 Colicin V production protein; Region: Colicin_V; cl00567 233412002850 amidophosphoribosyltransferase; glutaminephosphoribosyltransferase amidotransferase, N-terminal fragment; HDp1210A 233412002851 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 233412002852 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 233412002853 37 KD nucleoid-associated protein homolog, central fragment; HDp1213B 233412002854 37 KD nucleoid-associated protein homolog, N-terminal fragment; HDp1213A 233412002855 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 233412002856 homotrimer interaction site [polypeptide binding]; other site 233412002857 putative active site [active] 233412002858 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 233412002859 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 233412002860 lysozyme inhibitor; Provisional; Region: PRK13791 233412002861 Uncharacterized conserved protein [Function unknown]; Region: COG1556 233412002862 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 233412002863 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 233412002864 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...; Region: HCP_like; cl14655 233412002865 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 233412002866 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 233412002867 Cysteine-rich domain; Region: CCG; pfam02754 233412002868 Cysteine-rich domain; Region: CCG; pfam02754 233412002869 possible lactate permease, N-terminal fragment; HDp1222A 233412002870 DNA-binding protein H-NS, N-terminal fragment; HDp1226A 233412002871 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 233412002872 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 233412002873 dimer interface [polypeptide binding]; other site 233412002874 active site 233412002875 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 233412002876 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 233412002877 Walker A motif; other site 233412002878 ATP binding site [chemical binding]; other site 233412002879 Walker B motif; other site 233412002880 arginine finger; other site 233412002881 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 233412002882 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 233412002883 peptide binding site [polypeptide binding]; other site 233412002884 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapB; COG4168 233412002885 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412002886 dimer interface [polypeptide binding]; other site 233412002887 conserved gate region; other site 233412002888 putative PBP binding loops; other site 233412002889 ABC-ATPase subunit interface; other site 233412002890 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapC; COG4171 233412002891 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412002892 putative PBP binding loops; other site 233412002893 ABC-ATPase subunit interface; other site 233412002894 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapD; COG4170 233412002895 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 233412002896 Walker A/P-loop; other site 233412002897 ATP binding site [chemical binding]; other site 233412002898 Q-loop/lid; other site 233412002899 ABC transporter signature motif; other site 233412002900 Walker B; other site 233412002901 D-loop; other site 233412002902 H-loop/switch region; other site 233412002903 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 233412002904 DNA polymerase I; Provisional; Region: PRK05755 233412002905 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 233412002906 active site 233412002907 metal binding site 1 [ion binding]; metal-binding site 233412002908 putative 5' ssDNA interaction site; other site 233412002909 metal binding site 3; metal-binding site 233412002910 metal binding site 2 [ion binding]; metal-binding site 233412002911 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 233412002912 putative DNA binding site [nucleotide binding]; other site 233412002913 putative metal binding site [ion binding]; other site 233412002914 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 233412002915 active site 233412002916 catalytic site [active] 233412002917 substrate binding site [chemical binding]; other site 233412002918 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 233412002919 active site 233412002920 DNA binding site [nucleotide binding] 233412002921 catalytic site [active] 233412002922 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 233412002923 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 233412002924 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 233412002925 ATP-grasp domain; Region: ATP-grasp_4; cl17255 233412002926 Uncharacterized conserved protein [Function unknown]; Region: COG1434 233412002927 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 233412002928 putative active site [active] 233412002929 Citrate lyase synthetase [Energy production and conversion]; Region: CitC; COG3053 233412002930 Citrate lyase ligase; Region: Citrate_lyase_ligase; cd02169 233412002931 putative active site [active] 233412002932 (T/H)XGH motif; other site 233412002933 citrate lyase subunit gamma; Provisional; Region: PRK13253 233412002934 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 233412002935 Citrate lyase, alpha subunit [Energy production and conversion]; Region: CitF; COG3051 233412002936 holo-ACP synthase CitX; Region: citrate_citX; TIGR03124 233412002937 triphosphoribosyl-dephospho-CoA synthase CitG; Region: citrate_citG; TIGR03125 233412002938 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 233412002939 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; cd00625 233412002940 transmembrane helices; other site 233412002941 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 233412002942 Malic enzyme, N-terminal domain; Region: malic; pfam00390 233412002943 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 233412002944 putative NAD(P) binding site [chemical binding]; other site 233412002945 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 233412002946 5S rRNA interface [nucleotide binding]; other site 233412002947 CTC domain interface [polypeptide binding]; other site 233412002948 L16 interface [polypeptide binding]; other site 233412002949 UDP-sugar hydrolase, 5'nucleotidase, N-terminal fragment; HDp1250A 233412002950 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 233412002951 serine/threonine transporter SstT; Provisional; Region: PRK13628 233412002952 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 233412002953 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 233412002954 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 233412002955 Competence protein; Region: Competence; pfam03772 233412002956 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 233412002957 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 233412002958 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 233412002959 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 233412002960 Domain of unknown function DUF20; Region: UPF0118; pfam01594 233412002961 conserved hypothetical protein, N-terminal fragment; HDp1259A 233412002962 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 233412002963 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 233412002964 active site 233412002965 metal binding site [ion binding]; metal-binding site 233412002966 exoribonuclease II; Provisional; Region: PRK05054 233412002967 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 233412002968 RNB domain; Region: RNB; pfam00773 233412002969 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 233412002970 RNA binding site [nucleotide binding]; other site 233412002971 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 233412002972 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 233412002973 NAD binding site [chemical binding]; other site 233412002974 homotetramer interface [polypeptide binding]; other site 233412002975 homodimer interface [polypeptide binding]; other site 233412002976 substrate binding site [chemical binding]; other site 233412002977 active site 233412002978 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 233412002979 S-adenosylmethionine binding site [chemical binding]; other site 233412002980 acyl-CoA esterase; Provisional; Region: PRK10673 233412002981 PGAP1-like protein; Region: PGAP1; pfam07819 233412002982 replication initiation regulator SeqA; Provisional; Region: PRK11187 233412002983 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK09029 233412002984 O-succinylbenzoate-CoA ligase (also known as O-succinylbenzoate-CoA synthase, OSB-CoA synthetase, or MenE); Region: OSB_CoA_lg; cd05912 233412002985 acyl-activating enzyme (AAE) consensus motif; other site 233412002986 putative AMP binding site [chemical binding]; other site 233412002987 putative active site [active] 233412002988 putative CoA binding site [chemical binding]; other site 233412002989 conserved hypothetical protein, N-terminal fragment; HDp1273A 233412002990 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 233412002991 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 233412002992 Tetramer interface [polypeptide binding]; other site 233412002993 active site 233412002994 FMN-binding site [chemical binding]; other site 233412002995 penicillin-insensitive murein endopeptidase; Reviewed; Region: mepA; PRK09429 233412002996 Murein endopeptidase [Cell envelope biogenesis, outer membrane]; Region: MepA; COG3770 233412002997 DNA topoisomerase III; Provisional; Region: PRK07726 233412002998 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: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 233412002999 active site 233412003000 putative interdomain interaction site [polypeptide binding]; other site 233412003001 putative metal-binding site [ion binding]; other site 233412003002 putative nucleotide binding site [chemical binding]; other site 233412003003 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 233412003004 domain I; other site 233412003005 DNA binding groove [nucleotide binding] 233412003006 phosphate binding site [ion binding]; other site 233412003007 domain II; other site 233412003008 domain III; other site 233412003009 nucleotide binding site [chemical binding]; other site 233412003010 catalytic site [active] 233412003011 domain IV; other site 233412003012 preprotein translocase subunit SecG; Reviewed; Region: secG; PRK06870 233412003013 Peptidase S8 family domain in Autotransporter serine proteases; Region: Peptidases_S8_Autotransporter_serine_protease_like; cd04848 233412003014 catalytic triad [active] 233412003015 putative active site [active] 233412003016 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 233412003017 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; pfam12951 233412003018 Autotransporter beta-domain; Region: Autotransporter; pfam03797 233412003019 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 233412003020 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 233412003021 Potassium binding sites [ion binding]; other site 233412003022 Cesium cation binding sites [ion binding]; other site 233412003023 hypothetical protein; Provisional; Region: PRK05170 233412003024 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 233412003025 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 233412003026 dimer interface [polypeptide binding]; other site 233412003027 ssDNA binding site [nucleotide binding]; other site 233412003028 tetramer (dimer of dimers) interface [polypeptide binding]; other site 233412003029 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 233412003030 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 233412003031 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 233412003032 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 233412003033 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 233412003034 DEAD/DEAH box helicase; Region: DEAD; pfam00270 233412003035 Protein of unknown function (DUF2408); Region: DUF2408; pfam10303 233412003036 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 233412003037 LrgA family; Region: LrgA; pfam03788 233412003038 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 233412003039 methionine sulfoxide reductase B; Provisional; Region: PRK00222 233412003040 SelR domain; Region: SelR; pfam01641 233412003041 glyceraldehyde-3-phosphate dehydrogenase A; Provisional; Region: gapA; PRK15425 233412003042 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 233412003043 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 233412003044 rod shape-determining protein MreB; Provisional; Region: PRK13927 233412003045 MreB and similar proteins; Region: MreB_like; cd10225 233412003046 nucleotide binding site [chemical binding]; other site 233412003047 Mg binding site [ion binding]; other site 233412003048 putative protofilament interaction site [polypeptide binding]; other site 233412003049 RodZ interaction site [polypeptide binding]; other site 233412003050 rod shape-determining protein MreC; Region: mreC; TIGR00219 233412003051 rod shape-determining protein MreC; Region: MreC; pfam04085 233412003052 rod shape-determining protein MreD; Region: MreD; cl01087 233412003053 recombination factor protein RarA; Reviewed; Region: PRK13342 233412003054 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 233412003055 Walker A motif; other site 233412003056 ATP binding site [chemical binding]; other site 233412003057 Walker B motif; other site 233412003058 arginine finger; other site 233412003059 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 233412003060 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 233412003061 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 233412003062 ABC-ATPase subunit interface; other site 233412003063 dimer interface [polypeptide binding]; other site 233412003064 putative PBP binding regions; other site 233412003065 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 233412003066 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 233412003067 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 233412003068 TadE-like protein; Region: TadE; pfam07811 233412003069 Anaphase-promoting complex, cyclosome, subunit 3; Region: Apc3; pfam12895 233412003070 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 233412003071 binding surface 233412003072 TPR motif; other site 233412003073 Tetratricopeptide repeat; Region: TPR_16; pfam13432 233412003074 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 233412003075 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 233412003076 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 233412003077 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 233412003078 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 233412003079 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 233412003080 ATP binding site [chemical binding]; other site 233412003081 Walker A motif; other site 233412003082 hexamer interface [polypeptide binding]; other site 233412003083 Walker B motif; other site 233412003084 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 233412003085 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 233412003086 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 233412003087 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 233412003088 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 233412003089 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 233412003090 Flp/Fap pilin component; Region: Flp_Fap; cl01585 233412003091 Flp/Fap pilin component; Region: Flp_Fap; pfam04964 233412003092 Flp/Fap pilin component; Region: Flp_Fap; pfam04964 233412003093 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 233412003094 putative active site [active] 233412003095 Protein of unknown function (DUF1375); Region: DUF1375; pfam07119 233412003096 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 233412003097 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 233412003098 dimer interface [polypeptide binding]; other site 233412003099 putative anticodon binding site; other site 233412003100 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 233412003101 motif 1; other site 233412003102 active site 233412003103 motif 2; other site 233412003104 motif 3; other site 233412003105 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 233412003106 spermidine synthase; Provisional; Region: PRK03612 233412003107 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 233412003108 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 233412003109 substrate binding pocket [chemical binding]; other site 233412003110 chain length determination region; other site 233412003111 substrate-Mg2+ binding site; other site 233412003112 catalytic residues [active] 233412003113 aspartate-rich region 1; other site 233412003114 active site lid residues [active] 233412003115 aspartate-rich region 2; other site 233412003116 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 233412003117 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 233412003118 Sulfatase; Region: Sulfatase; pfam00884 233412003119 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 233412003120 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 233412003121 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 233412003122 haemagglutination activity domain; Region: Haemagg_act; pfam05860 233412003123 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 233412003124 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 233412003125 homotrimer interaction site [polypeptide binding]; other site 233412003126 zinc binding site [ion binding]; other site 233412003127 CDP-binding sites; other site 233412003128 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 233412003129 substrate binding site; other site 233412003130 dimer interface; other site 233412003131 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 233412003132 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 233412003133 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 233412003134 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 233412003135 active site 233412003136 substrate-binding site [chemical binding]; other site 233412003137 metal-binding site [ion binding] 233412003138 ATP binding site [chemical binding]; other site 233412003139 Protein of unknown function (DUF535); Region: DUF535; pfam04393 233412003140 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 233412003141 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 233412003142 E3 interaction surface; other site 233412003143 lipoyl attachment site [posttranslational modification]; other site 233412003144 e3 binding domain; Region: E3_binding; pfam02817 233412003145 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 233412003146 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 233412003147 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 233412003148 TPP-binding site [chemical binding]; other site 233412003149 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 233412003150 dimer interface [polypeptide binding]; other site 233412003151 PYR/PP interface [polypeptide binding]; other site 233412003152 TPP binding site [chemical binding]; other site 233412003153 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 233412003154 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 233412003155 putative peptidase; Provisional; Region: PRK11649 233412003156 Peptidase family M23; Region: Peptidase_M23; pfam01551 233412003157 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 233412003158 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 233412003159 dimerization domain [polypeptide binding]; other site 233412003160 dimer interface [polypeptide binding]; other site 233412003161 catalytic residues [active] 233412003162 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 233412003163 DHH family; Region: DHH; pfam01368 233412003164 DHHA1 domain; Region: DHHA1; pfam02272 233412003165 pyridoxal phosphate (PLP) phosphatase; Provisional; Region: PRK10530 233412003166 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 233412003167 active site 233412003168 motif I; other site 233412003169 motif II; other site 233412003170 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 233412003171 nitrate/nitrite sensor protein, N-terminal fragment; HDp1346A 233412003172 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 233412003173 active site 233412003174 dimerization interface [polypeptide binding]; other site 233412003175 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 233412003176 serine endoprotease; Provisional; Region: PRK10898 233412003177 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 233412003178 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 233412003179 cytidylate kinase; Provisional; Region: cmk; PRK00023 233412003180 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 233412003181 CMP-binding site; other site 233412003182 The sites determining sugar specificity; other site 233412003183 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 233412003184 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 233412003185 RNA binding site [nucleotide binding]; other site 233412003186 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 233412003187 RNA binding site [nucleotide binding]; other site 233412003188 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 233412003189 RNA binding site [nucleotide binding]; other site 233412003190 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 233412003191 RNA binding site [nucleotide binding]; other site 233412003192 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...; Region: S1_RPS1_repeat_ec5; cd05690 233412003193 RNA binding site [nucleotide binding]; other site 233412003194 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 233412003195 RNA binding site [nucleotide binding]; other site 233412003196 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 233412003197 IHF dimer interface [polypeptide binding]; other site 233412003198 IHF - DNA interface [nucleotide binding]; other site 233412003199 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 233412003200 tetratricopeptide repeat protein; Provisional; Region: PRK11788 233412003201 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 233412003202 binding surface 233412003203 TPR motif; other site 233412003204 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 233412003205 active site 233412003206 dimer interface [polypeptide binding]; other site 233412003207 translation initiation factor Sui1; Validated; Region: PRK06824 233412003208 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 233412003209 putative rRNA binding site [nucleotide binding]; other site 233412003210 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3787; cl17897 233412003211 aromatic acid decarboxylase; Validated; Region: PRK05920 233412003212 Flavoprotein; Region: Flavoprotein; pfam02441 233412003213 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 233412003214 hypothetical protein; Provisional; Region: PRK05255 233412003215 peptidase PmbA; Provisional; Region: PRK11040 233412003216 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 233412003217 active site clefts [active] 233412003218 zinc binding site [ion binding]; other site 233412003219 dimer interface [polypeptide binding]; other site 233412003220 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 233412003221 DNA-binding site [nucleotide binding]; DNA binding site 233412003222 RNA-binding motif; other site 233412003223 Protein of unknown function (DUF1439); Region: DUF1439; pfam07273 233412003224 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 233412003225 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 233412003226 SH3 domain protein [Signal transduction mechanisms]; Region: COG3103 233412003227 Bacterial SH3 domain homologues; Region: SH3b; smart00287 233412003228 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 233412003229 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 233412003230 Protein of unknown function DUF47; Region: PhoU_div; pfam01865 233412003231 replicative DNA helicase; Validated; Region: PRK06904 233412003232 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 233412003233 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 233412003234 Walker A motif; other site 233412003235 ATP binding site [chemical binding]; other site 233412003236 Walker B motif; other site 233412003237 DNA binding loops [nucleotide binding] 233412003238 YcgL domain; Region: YcgL; pfam05166 233412003239 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 233412003240 ATP cone domain; Region: ATP-cone; pfam03477 233412003241 aspartate kinase III; Validated; Region: PRK09084 233412003242 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 233412003243 nucleotide binding site [chemical binding]; other site 233412003244 substrate binding site [chemical binding]; other site 233412003245 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_1; cd04932 233412003246 lysine allosteric regulatory site; other site 233412003247 dimer interface [polypeptide binding]; other site 233412003248 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 233412003249 dimer interface [polypeptide binding]; other site 233412003250 hypothetical protein; Provisional; Region: PRK05423 233412003251 exopolyphosphatase; Provisional; Region: PRK10854 233412003252 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 233412003253 nucleotide binding site [chemical binding]; other site 233412003254 Domain of unknown function (DUF386); Region: DUF386; cl01047 233412003255 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 233412003256 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 233412003257 Protein of unknown function (DUF592); Region: DUF592; pfam04574 233412003258 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 233412003259 putative active site [active] 233412003260 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 233412003261 homodimer interface [polypeptide binding]; other site 233412003262 substrate-cofactor binding pocket; other site 233412003263 pyridoxal 5'-phosphate binding site [chemical binding]; other site 233412003264 catalytic residue [active] 233412003265 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 233412003266 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 233412003267 hinge; other site 233412003268 active site 233412003269 N-acetylglutamate synthase; Validated; Region: PRK05279 233412003270 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...; Region: AAK_NAGS-ABP; cd04237 233412003271 putative feedback inhibition sensing region; other site 233412003272 putative nucleotide binding site [chemical binding]; other site 233412003273 putative substrate binding site [chemical binding]; other site 233412003274 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 233412003275 Coenzyme A binding pocket [chemical binding]; other site 233412003276 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 233412003277 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 233412003278 active site 233412003279 interdomain interaction site; other site 233412003280 putative metal-binding site [ion binding]; other site 233412003281 nucleotide binding site [chemical binding]; other site 233412003282 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 233412003283 domain I; other site 233412003284 DNA binding groove [nucleotide binding] 233412003285 phosphate binding site [ion binding]; other site 233412003286 domain II; other site 233412003287 domain III; other site 233412003288 nucleotide binding site [chemical binding]; other site 233412003289 catalytic site [active] 233412003290 domain IV; other site 233412003291 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 233412003292 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 233412003293 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 233412003294 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 233412003295 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]; Region: COG1444 233412003296 Helicase; Region: Helicase_RecD; pfam05127 233412003297 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 233412003298 Coenzyme A binding pocket [chemical binding]; other site 233412003299 Possible tRNA binding domain; Region: tRNA_bind_2; pfam13725 233412003300 metal-binding heat shock protein; Provisional; Region: PRK00016 233412003301 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 233412003302 MoaE homodimer interface [polypeptide binding]; other site 233412003303 MoaD interaction [polypeptide binding]; other site 233412003304 active site residues [active] 233412003305 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 233412003306 MoaE interaction surface [polypeptide binding]; other site 233412003307 MoeB interaction surface [polypeptide binding]; other site 233412003308 thiocarboxylated glycine; other site 233412003309 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 guanosine...; Region: MoaC_PE; cd01420 233412003310 trimer interface [polypeptide binding]; other site 233412003311 dimer interface [polypeptide binding]; other site 233412003312 putative active site [active] 233412003313 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 233412003314 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 233412003315 FeS/SAM binding site; other site 233412003316 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 233412003317 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 233412003318 trimethylamine-N-oxide reductase c-type cytochrome TorC; Region: torC; TIGR02162 233412003319 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 233412003320 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 233412003321 molybdopterin cofactor binding site [chemical binding]; other site 233412003322 substrate binding site [chemical binding]; other site 233412003323 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-BSOR-TMAOR; cd02793 233412003324 molybdopterin cofactor binding site; other site 233412003325 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 233412003326 FtsJ-like methyltransferase; Region: FtsJ; cl17430 233412003327 conserved hypothetical protein, C-terminal fragment; HDp1396A 233412003328 Dihydrodipicolinate reductase [Amino acid transport and metabolism]; Region: DapB; COG0289 233412003329 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 233412003330 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 233412003331 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 233412003332 active site 233412003333 lytic murein transglycosylase; Provisional; Region: PRK11619 233412003334 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 233412003335 N-acetyl-D-glucosamine binding site [chemical binding]; other site 233412003336 catalytic residue [active] 233412003337 conserved transport protein, N-terminal fragment; HDp1403A 233412003338 conserved transport protein, central fragment; HDp1403B 233412003339 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 233412003340 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 233412003341 active site 233412003342 HIGH motif; other site 233412003343 nucleotide binding site [chemical binding]; other site 233412003344 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 233412003345 KMSKS motif; other site 233412003346 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 233412003347 elongation factor P; Validated; Region: PRK00529 233412003348 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 233412003349 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 233412003350 RNA binding site [nucleotide binding]; other site 233412003351 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 233412003352 RNA binding site [nucleotide binding]; other site 233412003353 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 233412003354 FeS/SAM binding site; other site 233412003355 Radical SAM superfamily; Region: Radical_SAM; pfam04055 233412003356 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 233412003357 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB...; Region: EcAsnRS_like_N; cd04318 233412003358 putative dimer interface [polypeptide binding]; other site 233412003359 putative anticodon binding site; other site 233412003360 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 233412003361 homodimer interface [polypeptide binding]; other site 233412003362 motif 1; other site 233412003363 motif 2; other site 233412003364 active site 233412003365 motif 3; other site 233412003366 exonuclease I; Provisional; Region: sbcB; PRK11779 233412003367 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 233412003368 active site 233412003369 catalytic site [active] 233412003370 substrate binding site [chemical binding]; other site 233412003371 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 233412003372 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 233412003373 putative active site [active] 233412003374 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 233412003375 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 233412003376 active site 233412003377 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 233412003378 excinuclease ABC subunit B; Provisional; Region: PRK05298 233412003379 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 233412003380 ATP binding site [chemical binding]; other site 233412003381 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 233412003382 nucleotide binding region [chemical binding]; other site 233412003383 ATP-binding site [chemical binding]; other site 233412003384 Ultra-violet resistance protein B; Region: UvrB; pfam12344 233412003385 UvrB/uvrC motif; Region: UVR; pfam02151 233412003386 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 233412003387 proline aminopeptidase P II; Provisional; Region: PRK10879 233412003388 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 on...; Region: Prolidase; cd01087 233412003389 active site 233412003390 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 233412003391 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 233412003392 pyridoxal 5'-phosphate binding site [chemical binding]; other site 233412003393 homodimer interface [polypeptide binding]; other site 233412003394 catalytic residue [active] 233412003395 ATP-grasp domain; Region: ATP-grasp_4; cl17255 233412003396 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 233412003397 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 233412003398 stringent starvation protein A; Provisional; Region: sspA; PRK09481 233412003399 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 233412003400 C-terminal domain interface [polypeptide binding]; other site 233412003401 putative GSH binding site (G-site) [chemical binding]; other site 233412003402 dimer interface [polypeptide binding]; other site 233412003403 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 233412003404 dimer interface [polypeptide binding]; other site 233412003405 N-terminal domain interface [polypeptide binding]; other site 233412003406 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 233412003407 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 233412003408 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 233412003409 ligand binding site [chemical binding]; other site 233412003410 flexible hinge region; other site 233412003411 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 233412003412 putative switch regulator; other site 233412003413 non-specific DNA interactions [nucleotide binding]; other site 233412003414 DNA binding site [nucleotide binding] 233412003415 sequence specific DNA binding site [nucleotide binding]; other site 233412003416 putative cAMP binding site [chemical binding]; other site 233412003417 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 233412003418 Ligand Binding Site [chemical binding]; other site 233412003419 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 233412003420 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 233412003421 motif 1; other site 233412003422 active site 233412003423 motif 2; other site 233412003424 motif 3; other site 233412003425 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 233412003426 DHHA1 domain; Region: DHHA1; pfam02272 233412003427 carbon storage regulator; Provisional; Region: PRK01712 233412003428 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 233412003429 active site 233412003430 tetramer interface; other site 233412003431 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 233412003432 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 233412003433 eyelet of channel; other site 233412003434 trimer interface [polypeptide binding]; other site 233412003435 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 233412003436 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 233412003437 trimer interface [polypeptide binding]; other site 233412003438 eyelet of channel; other site 233412003439 Zonular occludens toxin (Zot); Region: Zot; cl17485 233412003440 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 233412003441 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 233412003442 plasmid pNAD1A; HDppNAD1A 233412003443 Phage replication protein CRI; Region: Phage_CRI; pfam05144 233412003444 Phage X family; Region: Phage_X; pfam05155 233412003445 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 233412003446 Tryptophan halogenase; Region: Trp_halogenase; pfam04820 233412003447 putative nicotinate phosphoribosyltransferase; Provisional; Region: PRK09198 233412003448 pre-B-cell colony-enhancing factor (PBEF)-like. The mammalian members of this group of nicotinate phosphoribosyltransferases (NAPRTases) were originally identified as genes whose expression is upregulated upon activation in lymphoid cells. In general; Region: PBEF_like; cd01569 233412003449 active site 233412003450 N-terminal fragment duplicates N-terminal of acetate kinase HD1456.; HDp1448A 233412003451 plasmid pNAD1B; HDppNAD1B 233412003452 N-terminal fragment duplicates N-terminal of hypothetical protein HD1439.; HDp1448B 233412003453 Phage replication protein CRI; Region: Phage_CRI; pfam05144 233412003454 Phage X family; Region: Phage_X; pfam05155 233412003455 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 233412003456 Tryptophan halogenase; Region: Trp_halogenase; pfam04820 233412003457 putative nicotinate phosphoribosyltransferase; Provisional; Region: PRK09198 233412003458 pre-B-cell colony-enhancing factor (PBEF)-like. The mammalian members of this group of nicotinate phosphoribosyltransferases (NAPRTases) were originally identified as genes whose expression is upregulated upon activation in lymphoid cells. In general; Region: PBEF_like; cd01569 233412003459 active site 233412003460 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 233412003461 propionate/acetate kinase; Provisional; Region: PRK12379 233412003462 phosphate acetyltransferase; Reviewed; Region: PRK05632 233412003463 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 233412003464 DRTGG domain; Region: DRTGG; pfam07085 233412003465 phosphate acetyltransferase; Region: pta; TIGR00651 233412003466 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 233412003467 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 233412003468 RNA binding site [nucleotide binding]; other site 233412003469 active site 233412003470 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 233412003471 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 233412003472 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 233412003473 translation initiation factor IF-2; Validated; Region: infB; PRK05306 233412003474 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 233412003475 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 233412003476 G1 box; other site 233412003477 putative GEF interaction site [polypeptide binding]; other site 233412003478 GTP/Mg2+ binding site [chemical binding]; other site 233412003479 Switch I region; other site 233412003480 G2 box; other site 233412003481 G3 box; other site 233412003482 Switch II region; other site 233412003483 G4 box; other site 233412003484 G5 box; other site 233412003485 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell; Region: IF2_mtIF2_II; cd03702 233412003486 Translation-initiation factor 2; Region: IF-2; pfam11987 233412003487 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor...; Region: mtIF2_IVc; cd03692 233412003488 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 233412003489 NusA N-terminal domain; Region: NusA_N; pfam08529 233412003490 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 233412003491 RNA binding site [nucleotide binding]; other site 233412003492 homodimer interface [polypeptide binding]; other site 233412003493 NusA-like KH domain; Region: KH_5; pfam13184 233412003494 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 233412003495 G-X-X-G motif; other site 233412003496 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 233412003497 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 233412003498 ribosome maturation protein RimP; Reviewed; Region: PRK00092 233412003499 Sm and related proteins; Region: Sm_like; cl00259 233412003500 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 233412003501 putative oligomer interface [polypeptide binding]; other site 233412003502 putative RNA binding site [nucleotide binding]; other site 233412003503 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 233412003504 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 233412003505 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 233412003506 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 233412003507 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 233412003508 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 233412003509 homodimer interface [polypeptide binding]; other site 233412003510 metal binding site [ion binding]; metal-binding site 233412003511 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 233412003512 homodimer interface [polypeptide binding]; other site 233412003513 active site 233412003514 putative chemical substrate binding site [chemical binding]; other site 233412003515 metal binding site [ion binding]; metal-binding site 233412003516 DNA-binding response regulator CreB; Provisional; Region: PRK11083 233412003517 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 233412003518 active site 233412003519 phosphorylation site [posttranslational modification] 233412003520 intermolecular recognition site; other site 233412003521 dimerization interface [polypeptide binding]; other site 233412003522 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 233412003523 DNA binding site [nucleotide binding] 233412003524 two-component sensor protein; Provisional; Region: cpxA; PRK09470 233412003525 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 233412003526 dimerization interface [polypeptide binding]; other site 233412003527 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 233412003528 dimer interface [polypeptide binding]; other site 233412003529 phosphorylation site [posttranslational modification] 233412003530 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 233412003531 ATP binding site [chemical binding]; other site 233412003532 Mg2+ binding site [ion binding]; other site 233412003533 G-X-G motif; other site 233412003534 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 233412003535 Uncharacterized conserved protein [Function unknown]; Region: COG0327 233412003536 Protein of unknown function (DUF904); Region: DUF904; cl11531 233412003537 thymidine kinase; Provisional; Region: PRK04296 233412003538 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 233412003539 Glycoprotease family; Region: Peptidase_M22; pfam00814 233412003540 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 233412003541 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 233412003542 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 233412003543 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 233412003544 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 233412003545 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 233412003546 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 233412003547 dimerization interface [polypeptide binding]; other site 233412003548 putative DNA binding site [nucleotide binding]; other site 233412003549 putative Zn2+ binding site [ion binding]; other site 233412003550 AsnC family; Region: AsnC_trans_reg; pfam01037 233412003551 ribonuclease D; Provisional; Region: PRK10829 233412003552 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 233412003553 catalytic site [active] 233412003554 putative active site [active] 233412003555 putative substrate binding site [chemical binding]; other site 233412003556 HRDC domain; Region: HRDC; pfam00570 233412003557 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 233412003558 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 233412003559 AAA domain; Region: AAA_26; pfam13500 233412003560 outer membrane lipoprotein; Provisional; Region: spr; PRK10838 233412003561 NlpC/P60 family; Region: NLPC_P60; pfam00877 233412003562 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 233412003563 IHF dimer interface [polypeptide binding]; other site 233412003564 IHF - DNA interface [nucleotide binding]; other site 233412003565 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 233412003566 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 233412003567 putative tRNA-binding site [nucleotide binding]; other site 233412003568 B3/4 domain; Region: B3_4; pfam03483 233412003569 tRNA synthetase B5 domain; Region: B5; smart00874 233412003570 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 233412003571 dimer interface [polypeptide binding]; other site 233412003572 motif 1; other site 233412003573 motif 3; other site 233412003574 motif 2; other site 233412003575 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 233412003576 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 233412003577 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 233412003578 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 233412003579 dimer interface [polypeptide binding]; other site 233412003580 motif 1; other site 233412003581 active site 233412003582 motif 2; other site 233412003583 motif 3; other site 233412003584 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 233412003585 dimer interface [polypeptide binding]; other site 233412003586 FMN binding site [chemical binding]; other site 233412003587 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; pfam10071 233412003588 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 233412003589 Cation efflux family; Region: Cation_efflux; cl00316 233412003590 conserved hypothetical protein, N-terminal fragment; HDp1491A 233412003591 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 233412003592 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 233412003593 23S rRNA interface [nucleotide binding]; other site 233412003594 L3 interface [polypeptide binding]; other site 233412003595 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3105 233412003596 Protein of unknown function (DUF1043); Region: DUF1043; cl11473 233412003597 Protein-PII uridylyltransferase, N-terminal fragment; HDp1496A 233412003598 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 233412003599 aromatic amino acid transport protein; Region: araaP; TIGR00837 233412003600 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 233412003601 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 233412003602 Walker A motif; other site 233412003603 ATP binding site [chemical binding]; other site 233412003604 Walker B motif; other site 233412003605 arginine finger; other site 233412003606 Peptidase family M41; Region: Peptidase_M41; pfam01434 233412003607 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 233412003608 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 233412003609 S-adenosylmethionine binding site [chemical binding]; other site 233412003610 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 233412003611 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 233412003612 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 233412003613 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 233412003614 active site 233412003615 GMP synthase; Reviewed; Region: guaA; PRK00074 233412003616 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 233412003617 AMP/PPi binding site [chemical binding]; other site 233412003618 candidate oxyanion hole; other site 233412003619 catalytic triad [active] 233412003620 potential glutamine specificity residues [chemical binding]; other site 233412003621 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 233412003622 ATP Binding subdomain [chemical binding]; other site 233412003623 Ligand Binding sites [chemical binding]; other site 233412003624 Dimerization subdomain; other site 233412003625 haemagglutination activity domain; Region: Haemagg_act; pfam05860 233412003626 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 233412003627 Yersinia/Haemophilus virulence surface antigen; Region: Peptidase_C58; pfam03543 233412003628 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 233412003629 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and...; Region: PGM2; cd05799 233412003630 active site 233412003631 substrate binding site [chemical binding]; other site 233412003632 metal binding site [ion binding]; metal-binding site 233412003633 conserved hypothetical protein, N-terminal fragment; HDp1509A 233412003634 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 233412003635 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 233412003636 Substrate binding site; other site 233412003637 Mg++ binding site; other site 233412003638 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 233412003639 active site 233412003640 substrate binding site [chemical binding]; other site 233412003641 CoA binding site [chemical binding]; other site 233412003642 multidrug efflux protein; Reviewed; Region: PRK09579 233412003643 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 233412003644 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 233412003645 HlyD family secretion protein; Region: HlyD_3; pfam13437 233412003646 hypothetical protein; Provisional; Region: PRK13689 233412003647 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 233412003648 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 233412003649 Mor transcription activator family; Region: Mor; pfam08765 233412003650 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 233412003651 Bacteriophage Mu Gam like protein; Region: Phage_Mu_Gam; cl01825 233412003652 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 233412003653 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 233412003654 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 233412003655 Walker A/P-loop; other site 233412003656 ATP binding site [chemical binding]; other site 233412003657 Integrase core domain; Region: rve; pfam00665 233412003658 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 233412003659 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 233412003660 SlyX; Region: SlyX; cl01090 233412003661 phage-associated protein, BcepMu gp16 family; Region: BcepMu_gp16; TIGR04111 233412003662 Bacteriophage CI repressor helix-turn-helix domain; Region: Phage_CI_repr; pfam07022 233412003663 RIP homotypic interaction motif; Region: RHIM; pfam12721 233412003664 Phage protein (N4 Gp49/phage Sf6 gene 66) family; Region: Phage_gp49_66; pfam13876 233412003665 Protein of unknown function (DUF4063); Region: DUF4063; pfam13272 233412003666 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 233412003667 N-acetyl-D-glucosamine binding site [chemical binding]; other site 233412003668 catalytic residue [active] 233412003669 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 233412003670 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 233412003671 Terminase-like family; Region: Terminase_6; pfam03237 233412003672 Protein of unknown function (DUF935); Region: DUF935; pfam06074 233412003673 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 233412003674 Phage virion morphogenesis family; Region: Phage_tail_S; pfam05069 233412003675 Protein of unknown function (DUF1320); Region: DUF1320; pfam07030 233412003676 Phage-related minor tail protein [Function unknown]; Region: COG5281 233412003677 tape measure domain; Region: tape_meas_nterm; TIGR02675 233412003678 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 233412003679 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 233412003680 Putative phage tail protein; Region: Phage-tail_3; pfam13550 233412003681 cell division protein MukB; Provisional; Region: mukB; PRK04863 233412003682 P-loop containing region of AAA domain; Region: AAA_29; cl17516 233412003683 Putative exonuclease SbcCD, C subunit; Region: SbcCD_C; pfam13558 233412003684 condesin subunit E; Provisional; Region: PRK05256 233412003685 condesin subunit F; Provisional; Region: PRK05260 233412003686 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 233412003687 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 233412003688 CAP-like domain; other site 233412003689 active site 233412003690 primary dimer interface [polypeptide binding]; other site 233412003691 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 233412003692 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 233412003693 RNase E interface [polypeptide binding]; other site 233412003694 trimer interface [polypeptide binding]; other site 233412003695 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 233412003696 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 233412003697 RNase E interface [polypeptide binding]; other site 233412003698 trimer interface [polypeptide binding]; other site 233412003699 active site 233412003700 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 233412003701 putative nucleic acid binding region [nucleotide binding]; other site 233412003702 G-X-X-G motif; other site 233412003703 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 233412003704 RNA binding site [nucleotide binding]; other site 233412003705 domain interface; other site 233412003706 lipoprotein NlpI; Provisional; Region: PRK11189 233412003707 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 233412003708 binding surface 233412003709 TPR motif; other site 233412003710 ATP-dependent RNA helicase DeaD; Provisional; Region: PRK11634 233412003711 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 233412003712 ATP binding site [chemical binding]; other site 233412003713 Mg++ binding site [ion binding]; other site 233412003714 motif III; other site 233412003715 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 233412003716 nucleotide binding region [chemical binding]; other site 233412003717 ATP-binding site [chemical binding]; other site 233412003718 RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; Region: RRM_EcCsdA_like; cd12499 233412003719 putative RNA binding site [nucleotide binding]; other site 233412003720 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 233412003721 nucleoside/Zn binding site; other site 233412003722 dimer interface [polypeptide binding]; other site 233412003723 catalytic motif [active] 233412003724 Glutamine Amidotransferase (GATase_I) involved in pyridoxine biosynthesis; Region: GATase1_PB; cd01749 233412003725 predicted active site [active] 233412003726 catalytic triad [active] 233412003727 pyridoxal 5'-phosphate synthase, synthase subunit Pdx1; Region: TIGR00343 233412003728 PdxS is a subunit of the pyridoxal 5'-phosphate (PLP) synthase, an important enzyme in deoxyxylulose 5-phosphate (DXP)-independent pathway for de novo biosynthesis of PLP, present in some eubacteria, in archaea, fungi, plants, plasmodia, and some...; Region: pdxS; cd04727 233412003729 active site 233412003730 multimer interface [polypeptide binding]; other site 233412003731 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 233412003732 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 233412003733 DNA-binding site [nucleotide binding]; DNA binding site 233412003734 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 233412003735 pyridoxal 5'-phosphate binding site [chemical binding]; other site 233412003736 homodimer interface [polypeptide binding]; other site 233412003737 catalytic residue [active] 233412003738 ribosome recycling factor; Reviewed; Region: frr; PRK00083 233412003739 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 233412003740 hinge region; other site 233412003741 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 233412003742 putative nucleotide binding site [chemical binding]; other site 233412003743 uridine monophosphate binding site [chemical binding]; other site 233412003744 homohexameric interface [polypeptide binding]; other site 233412003745 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 233412003746 Sulfatase; Region: Sulfatase; cl17466 233412003747 elongation factor Ts; Provisional; Region: tsf; PRK09377 233412003748 UBA/TS-N domain; Region: UBA; pfam00627 233412003749 Elongation factor TS; Region: EF_TS; pfam00889 233412003750 Elongation factor TS; Region: EF_TS; pfam00889 233412003751 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 233412003752 rRNA interaction site [nucleotide binding]; other site 233412003753 S8 interaction site; other site 233412003754 putative laminin-1 binding site; other site 233412003755 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 233412003756 Domain of unknown function DUF87; Region: DUF87; pfam01935 233412003757 Zonular occludens toxin (Zot); Region: Zot; cl17485 233412003758 ATP-dependent RNA helicase, N-terminal fragment; HDp1602A 233412003759 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 233412003760 Recombination protein O N terminal; Region: RecO_N; pfam11967 233412003761 Recombination protein O C terminal; Region: RecO_C; pfam02565 233412003762 GTPase Era; Reviewed; Region: era; PRK00089 233412003763 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 233412003764 G1 box; other site 233412003765 GTP/Mg2+ binding site [chemical binding]; other site 233412003766 Switch I region; other site 233412003767 G2 box; other site 233412003768 Switch II region; other site 233412003769 G3 box; other site 233412003770 G4 box; other site 233412003771 G5 box; other site 233412003772 KH domain; Region: KH_2; pfam07650 233412003773 ribonuclease III; Reviewed; Region: rnc; PRK00102 233412003774 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 233412003775 dimerization interface [polypeptide binding]; other site 233412003776 active site 233412003777 metal binding site [ion binding]; metal-binding site 233412003778 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III; Region: DSRM; cd00048 233412003779 dsRNA binding site [nucleotide binding]; other site 233412003780 signal peptidase I; Provisional; Region: PRK10861 233412003781 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 233412003782 Catalytic site [active] 233412003783 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 233412003784 GTP-binding protein LepA; Provisional; Region: PRK05433 233412003785 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 233412003786 G1 box; other site 233412003787 putative GEF interaction site [polypeptide binding]; other site 233412003788 GTP/Mg2+ binding site [chemical binding]; other site 233412003789 Switch I region; other site 233412003790 G2 box; other site 233412003791 G3 box; other site 233412003792 Switch II region; other site 233412003793 G4 box; other site 233412003794 G5 box; other site 233412003795 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 233412003796 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 233412003797 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 233412003798 AAA domain; Region: AAA_27; pfam13514 233412003799 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 233412003800 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 233412003801 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 233412003802 non-specific DNA binding site [nucleotide binding]; other site 233412003803 salt bridge; other site 233412003804 sequence-specific DNA binding site [nucleotide binding]; other site 233412003805 Protein of unknown function (DUF4065); Region: DUF4065; pfam13274 233412003806 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 233412003807 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 233412003808 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 233412003809 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 233412003810 Sodium:alanine symporter family; Region: Na_Ala_symp; pfam01235 233412003811 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG2215 233412003812 Protein of unknown function (DUF1007); Region: DUF1007; pfam06226 233412003813 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 233412003814 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 233412003815 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 233412003816 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 233412003817 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 233412003818 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 233412003819 E3 interaction surface; other site 233412003820 lipoyl attachment site [posttranslational modification]; other site 233412003821 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 233412003822 E3 interaction surface; other site 233412003823 lipoyl attachment site [posttranslational modification]; other site 233412003824 e3 binding domain; Region: E3_binding; pfam02817 233412003825 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 233412003826 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 233412003827 Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative...; Region: TPP_E1_EcPDC_like; cd02017 233412003828 dimer interface [polypeptide binding]; other site 233412003829 TPP-binding site [chemical binding]; other site 233412003830 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 233412003831 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 233412003832 quinone interaction residues [chemical binding]; other site 233412003833 active site 233412003834 catalytic residues [active] 233412003835 FMN binding site [chemical binding]; other site 233412003836 substrate binding site [chemical binding]; other site 233412003837 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 233412003838 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 233412003839 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 233412003840 active site 233412003841 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 233412003842 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 233412003843 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 233412003844 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 233412003845 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 233412003846 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 233412003847 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 233412003848 Walker A/P-loop; other site 233412003849 ATP binding site [chemical binding]; other site 233412003850 Q-loop/lid; other site 233412003851 ABC transporter signature motif; other site 233412003852 Walker B; other site 233412003853 D-loop; other site 233412003854 H-loop/switch region; other site 233412003855 ribonuclease G; Provisional; Region: PRK11712 233412003856 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 233412003857 homodimer interface [polypeptide binding]; other site 233412003858 oligonucleotide binding site [chemical binding]; other site 233412003859 Methyltransferase domain; Region: Methyltransf_23; pfam13489 233412003860 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 233412003861 S-adenosylmethionine binding site [chemical binding]; other site 233412003862 murein transglycosylase A; Provisional; Region: mltA; PRK11162 233412003863 MltA specific insert domain; Region: MltA; smart00925 233412003864 3D domain; Region: 3D; pfam06725 233412003865 exodeoxyribonuclease VII large subunit, N-terminal fragment; HDp1638A 233412003866 Major Facilitator Superfamily; Region: MFS_1; pfam07690 233412003867 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 233412003868 putative substrate translocation pore; other site 233412003869 Mycoplasma MFS transporter; Region: MFS_Mycoplasma; pfam07672 233412003870 DNA-binding transcriptional repressor PurR; Provisional; Region: PRK10703 233412003871 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 233412003872 DNA binding site [nucleotide binding] 233412003873 domain linker motif; other site 233412003874 Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Region: PBP1_PurR; cd06275 233412003875 dimerization interface [polypeptide binding]; other site 233412003876 ligand binding site [chemical binding]; other site 233412003877 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 233412003878 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 233412003879 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 233412003880 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 233412003881 Mg2+ binding site [ion binding]; other site 233412003882 G-X-G motif; other site 233412003883 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 233412003884 anchoring element; other site 233412003885 dimer interface [polypeptide binding]; other site 233412003886 ATP binding site [chemical binding]; other site 233412003887 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 233412003888 active site 233412003889 putative metal-binding site [ion binding]; other site 233412003890 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 233412003891 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 233412003892 UbiA prenyltransferase family; Region: UbiA; pfam01040 233412003893 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 233412003894 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; pfam08220 233412003895 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 233412003896 adenylosuccinate lyase; Provisional; Region: PRK09285 233412003897 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 233412003898 tetramer interface [polypeptide binding]; other site 233412003899 active site 233412003900 putative lysogenization regulator; Reviewed; Region: PRK00218 233412003901 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 233412003902 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 233412003903 Walker A/P-loop; other site 233412003904 ATP binding site [chemical binding]; other site 233412003905 Q-loop/lid; other site 233412003906 ABC transporter signature motif; other site 233412003907 Walker B; other site 233412003908 D-loop; other site 233412003909 H-loop/switch region; other site 233412003910 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 233412003911 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 233412003912 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 233412003913 Walker A/P-loop; other site 233412003914 ATP binding site [chemical binding]; other site 233412003915 Q-loop/lid; other site 233412003916 ABC transporter signature motif; other site 233412003917 Walker B; other site 233412003918 D-loop; other site 233412003919 H-loop/switch region; other site 233412003920 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 233412003921 Family of unknown function (DUF490); Region: DUF490; pfam04357 233412003922 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 233412003923 Surface antigen; Region: Bac_surface_Ag; pfam01103 233412003924 conserved hypothetical protein, N-terminal fragment; HDp1656A 233412003925 AmiB activator; Provisional; Region: PRK11637 233412003926 Peptidase family M23; Region: Peptidase_M23; pfam01551 233412003927 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 233412003928 catalytic core [active] 233412003929 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 233412003930 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 233412003931 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 233412003932 Sugar specificity; other site 233412003933 Pyrimidine base specificity; other site 233412003934 ATP-binding site [chemical binding]; other site 233412003935 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 233412003936 trimer interface [polypeptide binding]; other site 233412003937 active site 233412003938 pyridine nucleotide transhydrogenase; Provisional; Region: pntB; PRK09444 233412003939 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 233412003940 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 233412003941 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 233412003942 ligand binding site [chemical binding]; other site 233412003943 homodimer interface [polypeptide binding]; other site 233412003944 NAD(P) binding site [chemical binding]; other site 233412003945 trimer interface B [polypeptide binding]; other site 233412003946 trimer interface A [polypeptide binding]; other site 233412003947 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 233412003948 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 233412003949 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 233412003950 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 233412003951 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 233412003952 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 233412003953 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 233412003954 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 233412003955 active site 233412003956 motif I; other site 233412003957 motif II; other site 233412003958 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 233412003959 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 233412003960 catalytic triad [active] 233412003961 HemN family oxidoreductase; Provisional; Region: PRK05660 233412003962 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 233412003963 FeS/SAM binding site; other site 233412003964 HemN C-terminal domain; Region: HemN_C; pfam06969 233412003965 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 233412003966 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cd00995 233412003967 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 233412003968 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412003969 dimer interface [polypeptide binding]; other site 233412003970 conserved gate region; other site 233412003971 putative PBP binding loops; other site 233412003972 ABC-ATPase subunit interface; other site 233412003973 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 233412003974 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412003975 dimer interface [polypeptide binding]; other site 233412003976 conserved gate region; other site 233412003977 putative PBP binding loops; other site 233412003978 ABC-ATPase subunit interface; other site 233412003979 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 233412003980 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 233412003981 Walker A/P-loop; other site 233412003982 ATP binding site [chemical binding]; other site 233412003983 Q-loop/lid; other site 233412003984 ABC transporter signature motif; other site 233412003985 Walker B; other site 233412003986 D-loop; other site 233412003987 H-loop/switch region; other site 233412003988 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 233412003989 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 233412003990 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 233412003991 Walker A/P-loop; other site 233412003992 ATP binding site [chemical binding]; other site 233412003993 Q-loop/lid; other site 233412003994 ABC transporter signature motif; other site 233412003995 Walker B; other site 233412003996 D-loop; other site 233412003997 H-loop/switch region; other site 233412003998 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 233412003999 aerobic respiration control sensor protein, central fragment; HDp1674B 233412004000 aerobic respiration control sensor protein, N-terminal fragment; HDp1674A 233412004001 hypothetical protein; Provisional; Region: PRK04946 233412004002 Smr domain; Region: Smr; pfam01713 233412004003 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 233412004004 AAA domain; Region: AAA_26; pfam13500 233412004005 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 233412004006 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 233412004007 S-adenosylmethionine binding site [chemical binding]; other site 233412004008 Protein of unknown function (DUF452); Region: DUF452; cl01062 233412004009 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 233412004010 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 233412004011 substrate-cofactor binding pocket; other site 233412004012 pyridoxal 5'-phosphate binding site [chemical binding]; other site 233412004013 catalytic residue [active] 233412004014 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06173 233412004015 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 233412004016 inhibitor-cofactor binding pocket; inhibition site 233412004017 pyridoxal 5'-phosphate binding site [chemical binding]; other site 233412004018 catalytic residue [active] 233412004019 HemK family putative methylases; Region: hemK_fam; TIGR00536 233412004020 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 233412004021 S-adenosylmethionine binding site [chemical binding]; other site 233412004022 This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins; Region: LNS2; smart00775 233412004023 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 233412004024 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 233412004025 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 233412004026 Restriction endonuclease [Defense mechanisms]; Region: COG3587 233412004027 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 233412004028 ATP binding site [chemical binding]; other site 233412004029 putative Mg++ binding site [ion binding]; other site 233412004030 type III restriction-modification system methyltransferase, central fragment; HDp1691B 233412004031 type III restriction-modification system methyltransferase, N-terminal fragment; HDp1691A 233412004032 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 233412004033 non-specific DNA binding site [nucleotide binding]; other site 233412004034 salt bridge; other site 233412004035 sequence-specific DNA binding site [nucleotide binding]; other site 233412004036 Transposase zinc-ribbon domain; Region: Zn_Tnp_IS1595; pfam12760 233412004037 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; pfam12762 233412004038 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 233412004039 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 233412004040 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 233412004041 penicillin-binding protein 4, N-terminal fragment; HDp1701A 233412004042 bifunctional purine biosynthesis protein PurH, N-terminal fragment; HDp1703A 233412004043 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 233412004044 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 233412004045 dimer interface [polypeptide binding]; other site 233412004046 putative catalytic residues [active] 233412004047 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 233412004048 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 233412004049 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 233412004050 OstA-like protein; Region: OstA; pfam03968 233412004051 Organic solvent tolerance protein; Region: OstA_C; pfam04453 233412004052 Protein of unknown function (DUF2489); Region: DUF2489; pfam10675 233412004053 Der GTPase activator (YihI); Region: YihI; pfam04220 233412004054 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 233412004055 hypothetical protein; Provisional; Region: PRK05248 233412004056 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 233412004057 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 233412004058 metal binding triad; other site 233412004059 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 233412004060 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 233412004061 metal binding triad; other site 233412004062 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 233412004063 YciI-like protein; Reviewed; Region: PRK11370 233412004064 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 233412004065 intracellular septation protein A; Reviewed; Region: PRK00259 233412004066 Protein of unknown function, DUF412; Region: DUF412; pfam04217 233412004067 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 233412004068 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 233412004069 Ligand Binding Site [chemical binding]; other site 233412004070 Predicted permease [General function prediction only]; Region: COG2056 233412004071 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 233412004072 Predicted membrane protein [Function unknown]; Region: COG1288; cl17886 233412004073 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 233412004074 putative catalytic site [active] 233412004075 putative phosphate binding site [ion binding]; other site 233412004076 active site 233412004077 metal binding site A [ion binding]; metal-binding site 233412004078 DNA binding site [nucleotide binding] 233412004079 putative AP binding site [nucleotide binding]; other site 233412004080 putative metal binding site B [ion binding]; other site 233412004081 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 233412004082 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 233412004083 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 233412004084 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 233412004085 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 233412004086 transketolase; Reviewed; Region: PRK12753 233412004087 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 233412004088 TPP-binding site [chemical binding]; other site 233412004089 dimer interface [polypeptide binding]; other site 233412004090 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 233412004091 PYR/PP interface [polypeptide binding]; other site 233412004092 dimer interface [polypeptide binding]; other site 233412004093 TPP binding site [chemical binding]; other site 233412004094 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 233412004095 ATP-binding PhoH protein homolog, N-terminal fragment; HDp1724A 233412004096 fatty acid metabolism regulator; Provisional; Region: PRK04984 233412004097 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 233412004098 DNA-binding site [nucleotide binding]; DNA binding site 233412004099 FadR C-terminal domain; Region: FadR_C; pfam07840 233412004100 sodium/proton antiporter; Reviewed; Region: nhaB; PRK09547 233412004101 disulfide bond formation protein B; Provisional; Region: PRK01749 233412004102 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 233412004103 ATP cone domain; Region: ATP-cone; pfam03477 233412004104 Class I ribonucleotide reductase; Region: RNR_I; cd01679 233412004105 active site 233412004106 dimer interface [polypeptide binding]; other site 233412004107 catalytic residues [active] 233412004108 effector binding site; other site 233412004109 R2 peptide binding site; other site 233412004110 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 233412004111 dimer interface [polypeptide binding]; other site 233412004112 putative radical transfer pathway; other site 233412004113 diiron center [ion binding]; other site 233412004114 tyrosyl radical; other site 233412004115 antiporter inner membrane protein; Provisional; Region: PRK11670 233412004116 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 233412004117 Walker A motif; other site 233412004118 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 233412004119 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 233412004120 peptide binding site [polypeptide binding]; other site 233412004121 hypothetical protein; Provisional; Region: PRK11111 233412004122 periplasmic folding chaperone; Provisional; Region: PRK10788 233412004123 SurA N-terminal domain; Region: SurA_N_3; cl07813 233412004124 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 233412004125 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome; Region: Ribosomal_S15p_S13e; cd00353 233412004126 16S/18S rRNA binding site [nucleotide binding]; other site 233412004127 S13e-L30e interaction site [polypeptide binding]; other site 233412004128 25S rRNA binding site [nucleotide binding]; other site 233412004129 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 233412004130 HemY protein N-terminus; Region: HemY_N; pfam07219 233412004131 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 233412004132 TPR motif; other site 233412004133 binding surface 233412004134 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 233412004135 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 233412004136 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 233412004137 active site 233412004138 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 233412004139 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-like...; Region: YgdL_like; cd00755 233412004140 putative ATP binding site [chemical binding]; other site 233412004141 putative substrate interface [chemical binding]; other site 233412004142 ABC transporter ATPase component; Reviewed; Region: PRK11147 233412004143 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 233412004144 Walker A/P-loop; other site 233412004145 ATP binding site [chemical binding]; other site 233412004146 ABC transporter signature motif; other site 233412004147 Walker B; other site 233412004148 D-loop; other site 233412004149 H-loop/switch region; other site 233412004150 ABC transporter; Region: ABC_tran_2; pfam12848 233412004151 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 233412004152 DNA gyrase subunit A; Validated; Region: PRK05560 233412004153 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 233412004154 CAP-like domain; other site 233412004155 active site 233412004156 primary dimer interface [polypeptide binding]; other site 233412004157 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 233412004158 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 233412004159 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 233412004160 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 233412004161 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 233412004162 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 233412004163 Pyrimidine dimer DNA glycosylase; Region: Pyr_excise; pfam03013 233412004164 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 233412004165 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 233412004166 S-adenosylmethionine binding site [chemical binding]; other site 233412004167 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 233412004168 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 233412004169 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 233412004170 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 233412004171 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 233412004172 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 233412004173 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 233412004174 Protein export membrane protein; Region: SecD_SecF; pfam02355 233412004175 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 233412004176 Ferritin-like domain; Region: Ferritin; pfam00210 233412004177 ferroxidase diiron center [ion binding]; other site 233412004178 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 233412004179 Ferritin-like domain; Region: Ferritin; pfam00210 233412004180 ferroxidase diiron center [ion binding]; other site 233412004181 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 233412004182 Sulfate transporter family; Region: Sulfate_transp; pfam00916 233412004183 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 233412004184 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 233412004185 Walker A motif; other site 233412004186 ATP binding site [chemical binding]; other site 233412004187 Walker B motif; other site 233412004188 arginine finger; other site 233412004189 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 233412004190 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 233412004191 RuvA N terminal domain; Region: RuvA_N; pfam01330 233412004192 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 233412004193 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 233412004194 active site 233412004195 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 233412004196 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 233412004197 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 233412004198 amidase catalytic site [active] 233412004199 Zn binding residues [ion binding]; other site 233412004200 substrate binding site [chemical binding]; other site 233412004201 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 233412004202 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 233412004203 active site 233412004204 ATP-dependent helicase HepA; Validated; Region: PRK04914 233412004205 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 233412004206 ATP binding site [chemical binding]; other site 233412004207 putative Mg++ binding site [ion binding]; other site 233412004208 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 233412004209 nucleotide binding region [chemical binding]; other site 233412004210 ATP-binding site [chemical binding]; other site 233412004211 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 233412004212 TRAM domain; Region: TRAM; pfam01938 233412004213 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 233412004214 S-adenosylmethionine binding site [chemical binding]; other site 233412004215 molybdopterin synthase sulfurylase MoeB; Region: moeB; TIGR02355 233412004216 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 233412004217 ATP binding site [chemical binding]; other site 233412004218 substrate interface [chemical binding]; other site 233412004219 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 233412004220 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 233412004221 dimer interface [polypeptide binding]; other site 233412004222 putative functional site; other site 233412004223 putative MPT binding site; other site 233412004224 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 233412004225 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 233412004226 Walker A/P-loop; other site 233412004227 ATP binding site [chemical binding]; other site 233412004228 Q-loop/lid; other site 233412004229 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 233412004230 ABC transporter; Region: ABC_tran_2; pfam12848 233412004231 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 233412004232 hypothetical protein; Provisional; Region: PRK05415 233412004233 Domain of unknown function (DUF697); Region: DUF697; cl12064 233412004234 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 233412004235 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 233412004236 FMN binding site [chemical binding]; other site 233412004237 active site 233412004238 catalytic residues [active] 233412004239 substrate binding site [chemical binding]; other site 233412004240 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 233412004241 DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]; Region: DjlA; COG1076 233412004242 putative metal binding site [ion binding]; other site 233412004243 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 233412004244 HSP70 interaction site [polypeptide binding]; other site 233412004245 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 233412004246 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 233412004247 ligand binding site [chemical binding]; other site 233412004248 translocation protein TolB; Provisional; Region: tolB; PRK01742 233412004249 TolB amino-terminal domain; Region: TolB_N; pfam04052 233412004250 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 233412004251 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 233412004252 outer membrane integrity protein, N-terminal fragment; HDp1774A 233412004253 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 233412004254 colicin uptake protein TolR; Provisional; Region: PRK11024 233412004255 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 233412004256 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 233412004257 active site 233412004258 cyd operon protein YbgE; Region: cyd_oper_ybgE; TIGR02112 233412004259 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 233412004260 cytochrome d oxidase, subunit II (cydB); Region: cydB; TIGR00203 233412004261 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 233412004262 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 233412004263 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 233412004264 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 233412004265 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 233412004266 ring oligomerisation interface [polypeptide binding]; other site 233412004267 ATP/Mg binding site [chemical binding]; other site 233412004268 stacking interactions; other site 233412004269 hinge regions; other site 233412004270 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 233412004271 oligomerisation interface [polypeptide binding]; other site 233412004272 mobile loop; other site 233412004273 roof hairpin; other site 233412004274 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 233412004275 active site 233412004276 8-oxo-dGMP binding site [chemical binding]; other site 233412004277 nudix motif; other site 233412004278 metal binding site [ion binding]; metal-binding site 233412004279 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 233412004280 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; cl17251 233412004281 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 233412004282 SEC-C motif; Region: SEC-C; pfam02810 233412004283 Protein of unknown function (DUF2547); Region: DUF2547; pfam10818 233412004284 Protein of unknown function (DUF721); Region: DUF721; cl02324 233412004285 BolA-like protein; Region: BolA; cl00386 233412004286 Uncharacterized lipoprotein; Region: Lipoprotein_16; pfam03923 233412004287 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 233412004288 RNA methyltransferase, RsmE family; Region: TIGR00046 233412004289 hypothetical protein; Validated; Region: PRK00228 233412004290 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 233412004291 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 233412004292 Domain of unknown function DUF21; Region: DUF21; pfam01595 233412004293 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 233412004294 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-called...; Region: CBS_pair; cd02205 233412004295 Transporter associated domain; Region: CorC_HlyC; smart01091 233412004296 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 233412004297 23S rRNA binding site [nucleotide binding]; other site 233412004298 L21 binding site [polypeptide binding]; other site 233412004299 L13 binding site [polypeptide binding]; other site 233412004300 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 233412004301 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 233412004302 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 233412004303 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 233412004304 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 233412004305 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 233412004306 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 233412004307 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 233412004308 active site 233412004309 dimer interface [polypeptide binding]; other site 233412004310 motif 1; other site 233412004311 motif 2; other site 233412004312 motif 3; other site 233412004313 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 233412004314 anticodon binding site; other site 233412004315 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 233412004316 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 233412004317 Maf-like protein; Region: Maf; pfam02545 233412004318 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 233412004319 active site 233412004320 dimer interface [polypeptide binding]; other site 233412004321 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 233412004322 THUMP domain of thiamine biosynthesis protein ThiI; Region: THUMP_ThiI; cd11716 233412004323 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 233412004324 Ligand Binding Site [chemical binding]; other site 233412004325 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 233412004326 active site residue [active] 233412004327 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 233412004328 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 233412004329 GDP-binding site [chemical binding]; other site 233412004330 ACT binding site; other site 233412004331 IMP binding site; other site 233412004332 FtsH protease regulator HflC; Provisional; Region: PRK11029 233412004333 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 233412004334 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 233412004335 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 233412004336 HflK protein; Region: hflK; TIGR01933 233412004337 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 233412004338 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 233412004339 catalytic residues [active] 233412004340 xanthine permease; Region: pbuX; TIGR03173 233412004341 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 233412004342 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 233412004343 GIY-YIG motif/motif A; other site 233412004344 active site 233412004345 catalytic site [active] 233412004346 putative DNA binding site [nucleotide binding]; other site 233412004347 metal binding site [ion binding]; metal-binding site 233412004348 UvrB/uvrC motif; Region: UVR; pfam02151 233412004349 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 233412004350 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 233412004351 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 233412004352 YccA-like proteins; Region: YccA_like; cd10433 233412004353 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]; Region: DsrC; COG2920 233412004354 sulfur relay protein, TusE/DsrC/DsvC family; Region: dsrC_tusE_dsvC; TIGR03342 233412004355 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 233412004356 Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that...; Region: PsaA; cd01137 233412004357 metal binding site [ion binding]; metal-binding site 233412004358 manganese/iron transporter ATP-binding protein; Provisional; Region: PRK15056 233412004359 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 233412004360 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 233412004361 active site 233412004362 DNA polymerase III subunits gamma and tau; Validated; Region: PRK07994 233412004363 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 233412004364 Walker A motif; other site 233412004365 ATP binding site [chemical binding]; other site 233412004366 Walker B motif; other site 233412004367 arginine finger; other site 233412004368 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 233412004369 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 233412004370 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 233412004371 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 233412004372 Walker A/P-loop; other site 233412004373 ATP binding site [chemical binding]; other site 233412004374 Q-loop/lid; other site 233412004375 ABC transporter signature motif; other site 233412004376 Walker B; other site 233412004377 D-loop; other site 233412004378 H-loop/switch region; other site 233412004379 inner membrane transport permease; Provisional; Region: PRK15066 233412004380 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 233412004381 molybdate transporter periplasmic protein; Provisional; Region: modA; PRK10677 233412004382 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 233412004383 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 233412004384 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412004385 dimer interface [polypeptide binding]; other site 233412004386 conserved gate region; other site 233412004387 putative PBP binding loops; other site 233412004388 ABC-ATPase subunit interface; other site 233412004389 molybdate transporter ATP-binding protein; Provisional; Region: modC; PRK11144 233412004390 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 233412004391 Walker A/P-loop; other site 233412004392 ATP binding site [chemical binding]; other site 233412004393 Q-loop/lid; other site 233412004394 ABC transporter signature motif; other site 233412004395 Walker B; other site 233412004396 D-loop; other site 233412004397 H-loop/switch region; other site 233412004398 TOBE domain; Region: TOBE; pfam03459 233412004399 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 233412004400 putative coenzyme Q binding site [chemical binding]; other site 233412004401 hypothetical protein; Validated; Region: PRK01777 233412004402 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 233412004403 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 233412004404 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 233412004405 catalytic site [active] 233412004406 G-X2-G-X-G-K; other site 233412004407 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 233412004408 active site 233412004409 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 233412004410 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 233412004411 metal binding site [ion binding]; metal-binding site 233412004412 dimer interface [polypeptide binding]; other site 233412004413 rRNA operon variant 2 difference region; HDprRNA5d 233412004414 Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]; Region: WecG; COG1922 233412004415 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; cd06533 233412004416 putative common antigen polymerase; Provisional; Region: PRK02975 233412004417 4-alpha-L-fucosyltransferase glycosyl transferase group 56; Region: Glyco_transf_56; pfam07429 233412004418 polysaccharide biosynthesis protein, N-terminal fragment; HDp1837A 233412004419 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 233412004420 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 233412004421 inhibitor-cofactor binding pocket; inhibition site 233412004422 pyridoxal 5'-phosphate binding site [chemical binding]; other site 233412004423 catalytic residue [active] 233412004424 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 233412004425 Coenzyme A binding pocket [chemical binding]; other site 233412004426 UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional; Region: wecC; PRK11064 233412004427 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 233412004428 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 233412004429 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 233412004430 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 233412004431 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 233412004432 homodimer interface [polypeptide binding]; other site 233412004433 active site 233412004434 undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphatetransferase; Region: ECA_wecA; TIGR02380 233412004435 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 233412004436 Mg++ binding site [ion binding]; other site 233412004437 putative catalytic motif [active] 233412004438 substrate binding site [chemical binding]; other site 233412004439 N-acetylglucosamine-6-phosphate deacetylase; Region: nagA; TIGR00221 233412004440 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 233412004441 active site 233412004442 dimer interface [polypeptide binding]; other site 233412004443 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 233412004444 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or...; Region: GlcN6P_deaminase; cd01399 233412004445 active site 233412004446 trimer interface [polypeptide binding]; other site 233412004447 allosteric site; other site 233412004448 active site lid [active] 233412004449 hexamer (dimer of trimers) interface [polypeptide binding]; other site 233412004450 N-acetylneuraminate lyase, C-terminal fragment; HDp1850A 233412004451 N-acetylneuraminate lyase; Provisional; Region: PRK04147 233412004452 N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL); Region: NAL; cd00954 233412004453 inhibitor site; inhibition site 233412004454 active site 233412004455 dimer interface [polypeptide binding]; other site 233412004456 catalytic residue [active] 233412004457 Putative N-acetylmannosamine-6-phosphate epimerase [Carbohydrate transport and metabolism]; Region: NanE; COG3010 233412004458 N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family of...; Region: NanE; cd04729 233412004459 putative active site cavity [active] 233412004460 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 233412004461 Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1- carboxylate synthase (MenD) and related proteins; Region: TPP_PYR_MenD; cd07037 233412004462 dimer interface [polypeptide binding]; other site 233412004463 tetramer interface [polypeptide binding]; other site 233412004464 PYR/PP interface [polypeptide binding]; other site 233412004465 TPP binding site [chemical binding]; other site 233412004466 Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key...; Region: TPP_SHCHC_synthase; cd02009 233412004467 TPP-binding site; other site 233412004468 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Provisional; Region: PRK11126 233412004469 Putative serine esterase (DUF676); Region: DUF676; pfam05057 233412004470 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for...; Region: KGPDC_HPS; cd04726 233412004471 active site 233412004472 dimer interface [polypeptide binding]; other site 233412004473 magnesium binding site [ion binding]; other site 233412004474 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 233412004475 active site 233412004476 phosphorylation site [posttranslational modification] 233412004477 PTS system ascorbate-specific transporter subunits IICB; Provisional; Region: PRK09548 233412004478 Uncharacterized protein conserved in bacteria [Function unknown]; Region: SgaT; COG3037 233412004479 PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a...; Region: PTS_IIB_ascorbate; cd05563 233412004480 active site 233412004481 P-loop; other site 233412004482 phosphorylation site [posttranslational modification] 233412004483 putative L-ascorbate 6-phosphate lactonase; Provisional; Region: PRK11709 233412004484 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 233412004485 transcriptional repressor UlaR; Provisional; Region: PRK13509 233412004486 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; pfam08220 233412004487 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 233412004488 putative L-xylulose 5-phosphate 3-epimerase; Reviewed; Region: PRK13210 233412004489 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 233412004490 AP (apurinic/apyrimidinic) site pocket; other site 233412004491 DNA interaction; other site 233412004492 Metal-binding active site; metal-binding site 233412004493 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 233412004494 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; cd00398 233412004495 intersubunit interface [polypeptide binding]; other site 233412004496 active site 233412004497 Zn2+ binding site [ion binding]; other site 233412004498 peptidylprolyl isomerase; PPIase, fragment; HDp1867A 233412004499 competence protein homolog, N-terminal fragment; HDp1870A 233412004500 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Reviewed; Region: ubiF; PRK08020 233412004501 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 233412004502 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; pfam03222 233412004503 aromatic amino acid transport protein; Region: araaP; TIGR00837 233412004504 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 233412004505 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 233412004506 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 233412004507 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 233412004508 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 233412004509 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 233412004510 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 233412004511 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 233412004512 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 233412004513 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 233412004514 DNA binding site [nucleotide binding] 233412004515 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 233412004516 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 233412004517 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 233412004518 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 233412004519 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 233412004520 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 233412004521 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 233412004522 RPB3 interaction site [polypeptide binding]; other site 233412004523 RPB1 interaction site [polypeptide binding]; other site 233412004524 RPB11 interaction site [polypeptide binding]; other site 233412004525 RPB10 interaction site [polypeptide binding]; other site 233412004526 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 233412004527 core dimer interface [polypeptide binding]; other site 233412004528 peripheral dimer interface [polypeptide binding]; other site 233412004529 L10 interface [polypeptide binding]; other site 233412004530 L11 interface [polypeptide binding]; other site 233412004531 putative EF-Tu interaction site [polypeptide binding]; other site 233412004532 putative EF-G interaction site [polypeptide binding]; other site 233412004533 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 233412004534 23S rRNA interface [nucleotide binding]; other site 233412004535 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 233412004536 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds...; Region: Ribosomal_L1; cd00403 233412004537 mRNA/rRNA interface [nucleotide binding]; other site 233412004538 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 233412004539 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 233412004540 23S rRNA interface [nucleotide binding]; other site 233412004541 L7/L12 interface [polypeptide binding]; other site 233412004542 putative thiostrepton binding site; other site 233412004543 L25 interface [polypeptide binding]; other site 233412004544 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 233412004545 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 233412004546 putative homodimer interface [polypeptide binding]; other site 233412004547 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 233412004548 heterodimer interface [polypeptide binding]; other site 233412004549 homodimer interface [polypeptide binding]; other site 233412004550 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 233412004551 Predicted membrane protein [Function unknown]; Region: COG1297 233412004552 putative oligopeptide transporter, OPT family; Region: TIGR00733 233412004553 DNA protecting protein DprA; Region: dprA; TIGR00732 233412004554 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 233412004555 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 233412004556 active site 233412004557 catalytic residues [active] 233412004558 metal binding site [ion binding]; metal-binding site 233412004559 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 233412004560 ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional; Region: rfaD; PRK11150 233412004561 NADP binding site [chemical binding]; other site 233412004562 homopentamer interface [polypeptide binding]; other site 233412004563 substrate binding site [chemical binding]; other site 233412004564 active site 233412004565 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 233412004566 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3691 233412004567 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 233412004568 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 233412004569 glutaminase active site [active] 233412004570 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 233412004571 dimer interface [polypeptide binding]; other site 233412004572 active site 233412004573 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 233412004574 dimer interface [polypeptide binding]; other site 233412004575 active site 233412004576 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 233412004577 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 233412004578 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 233412004579 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 233412004580 FeS/SAM binding site; other site 233412004581 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 233412004582 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 233412004583 hypothetical protein; Provisional; Region: PRK02119 233412004584 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 233412004585 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 233412004586 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 233412004587 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 233412004588 YheO-like PAS domain; Region: PAS_6; pfam08348 233412004589 HTH domain; Region: HTH_22; pfam13309 233412004590 sulfur transfer complex subunit TusD; Validated; Region: PRK00207 233412004591 sulfur relay protein TusC/DsrF; Region: sulf_tusC_dsrF; TIGR03010 233412004592 DsrH like protein; Region: DsrH; cl17347 233412004593 rRNA operon variant 2 difference region; HDprRNA6d 233412004594 glutamate racemase; Provisional; Region: PRK00865 233412004595 uridine phosphorylase, central fragment; HDp1907B 233412004596 uridine phosphorylase, N-terminal fragment; HDp1907A 233412004597 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 233412004598 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 233412004599 putative DNA binding site [nucleotide binding]; other site 233412004600 putative Zn2+ binding site [ion binding]; other site 233412004601 AsnC family; Region: AsnC_trans_reg; pfam01037 233412004602 Asparagine synthetase (aspartate-ammonia ligase) (AsnA) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II...; Region: AsnA; cd00645 233412004603 dimer interface [polypeptide binding]; other site 233412004604 active site 233412004605 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 233412004606 TMAO/DMSO reductase; Reviewed; Region: PRK05363 233412004607 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 233412004608 Moco binding site; other site 233412004609 metal coordination site [ion binding]; other site 233412004610 RNA polymerase sigma factor; Provisional; Region: PRK12530 233412004611 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 233412004612 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 233412004613 DNA binding residues [nucleotide binding] 233412004614 prolyl-tRNA synthetase; Provisional; Region: PRK09194 233412004615 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 233412004616 dimer interface [polypeptide binding]; other site 233412004617 motif 1; other site 233412004618 active site 233412004619 motif 2; other site 233412004620 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 233412004621 putative deacylase active site [active] 233412004622 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 233412004623 active site 233412004624 motif 3; other site 233412004625 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 233412004626 anticodon binding site; other site 233412004627 YadA-like C-terminal region; Region: YadA; pfam03895 233412004628 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 233412004629 Pathogenicity locus; Region: Cdd1; pfam11731 233412004630 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 233412004631 generic binding surface II; other site 233412004632 ssDNA binding site; other site 233412004633 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 233412004634 ATP binding site [chemical binding]; other site 233412004635 putative Mg++ binding site [ion binding]; other site 233412004636 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 233412004637 nucleotide binding region [chemical binding]; other site 233412004638 ATP-binding site [chemical binding]; other site 233412004639 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 233412004640 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 233412004641 Zn2+ binding site [ion binding]; other site 233412004642 Mg2+ binding site [ion binding]; other site 233412004643 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 233412004644 synthetase active site [active] 233412004645 NTP binding site [chemical binding]; other site 233412004646 metal binding site [ion binding]; metal-binding site 233412004647 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 233412004648 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 233412004649 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 233412004650 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 233412004651 substrate binding site [chemical binding]; other site 233412004652 oxyanion hole (OAH) forming residues; other site 233412004653 trimer interface [polypeptide binding]; other site 233412004654 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 233412004655 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 233412004656 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 233412004657 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 233412004658 substrate binding site [chemical binding]; other site 233412004659 hexamer interface [polypeptide binding]; other site 233412004660 metal binding site [ion binding]; metal-binding site 233412004661 acyl carrier protein; Provisional; Region: acpP; PRK00982 233412004662 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 233412004663 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 233412004664 dimerization interface [polypeptide binding]; other site 233412004665 thymidylate kinase; Validated; Region: tmk; PRK00698 233412004666 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 233412004667 TMP-binding site; other site 233412004668 ATP-binding site [chemical binding]; other site 233412004669 DNA polymerase III subunit delta'; Validated; Region: PRK06871 233412004670 DNA polymerase III subunit delta'; Validated; Region: PRK08485 233412004671 DNA polymerase III, delta subunit, C terminal; Region: DNApol3-delta_C; pfam09115 233412004672 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 233412004673 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 233412004674 active site 233412004675 Protein of unknown function (DUF1523); Region: DUF1523; pfam07509 233412004676 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 233412004677 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 233412004678 putative active site [active] 233412004679 putative metal binding site [ion binding]; other site 233412004680 Protein of unknown function (DUF454); Region: DUF454; cl01063 233412004681 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 233412004682 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 233412004683 active site 233412004684 Int/Topo IB signature motif; other site 233412004685 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 233412004686 tRNA binding surface [nucleotide binding]; other site 233412004687 anticodon binding site; other site 233412004688 DALR anticodon binding domain; Region: DALR_1; pfam05746 233412004689 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 233412004690 dimer interface [polypeptide binding]; other site 233412004691 motif 1; other site 233412004692 active site 233412004693 motif 2; other site 233412004694 motif 3; other site 233412004695 Cupin superfamily protein; Region: Cupin_4; pfam08007 233412004696 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 233412004697 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 233412004698 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 233412004699 RimM N-terminal domain; Region: RimM; pfam01782 233412004700 PRC-barrel domain; Region: PRC; pfam05239 233412004701 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 233412004702 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 233412004703 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 233412004704 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 233412004705 alphaNTD homodimer interface [polypeptide binding]; other site 233412004706 alphaNTD - beta interaction site [polypeptide binding]; other site 233412004707 alphaNTD - beta' interaction site [polypeptide binding]; other site 233412004708 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 233412004709 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 233412004710 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 233412004711 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 233412004712 RNA binding surface [nucleotide binding]; other site 233412004713 30S ribosomal protein S11; Validated; Region: PRK05309 233412004714 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 233412004715 30S ribosomal protein S13; Region: bact_S13; TIGR03631 233412004716 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 233412004717 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 233412004718 SecY translocase; Region: SecY; pfam00344 233412004719 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 233412004720 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 233412004721 23S rRNA binding site [nucleotide binding]; other site 233412004722 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 233412004723 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 233412004724 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 233412004725 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 233412004726 23S rRNA interface [nucleotide binding]; other site 233412004727 L21e interface [polypeptide binding]; other site 233412004728 5S rRNA interface [nucleotide binding]; other site 233412004729 L27 interface [polypeptide binding]; other site 233412004730 L5 interface [polypeptide binding]; other site 233412004731 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 233412004732 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 233412004733 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 233412004734 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 233412004735 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 233412004736 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 233412004737 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 233412004738 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 233412004739 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 233412004740 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 233412004741 RNA binding site [nucleotide binding]; other site 233412004742 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 233412004743 IS1 transposase; Region: DDE_Tnp_IS1; pfam03400 233412004744 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 233412004745 InsA N-terminal domain; Region: Zn_Tnp_IS1; pfam03811 233412004746 InsA C-terminal domain; Region: HTH_Tnp_IS1; pfam12759 233412004747 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 233412004748 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 233412004749 23S rRNA interface [nucleotide binding]; other site 233412004750 putative translocon interaction site; other site 233412004751 signal recognition particle (SRP54) interaction site; other site 233412004752 L23 interface [polypeptide binding]; other site 233412004753 trigger factor interaction site; other site 233412004754 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 233412004755 23S rRNA interface [nucleotide binding]; other site 233412004756 5S rRNA interface [nucleotide binding]; other site 233412004757 putative antibiotic binding site [chemical binding]; other site 233412004758 L25 interface [polypeptide binding]; other site 233412004759 L27 interface [polypeptide binding]; other site 233412004760 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 233412004761 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 233412004762 G-X-X-G motif; other site 233412004763 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 233412004764 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 233412004765 protein-rRNA interface [nucleotide binding]; other site 233412004766 putative translocon binding site; other site 233412004767 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 233412004768 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 233412004769 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 233412004770 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 233412004771 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 233412004772 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 233412004773 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 233412004774 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 233412004775 TfoX N-terminal domain; Region: TfoX_N; cl17592 233412004776 TfoX C-terminal domain; Region: TfoX_C; pfam04994 233412004777 fumarate hydratase; Reviewed; Region: fumC; PRK00485 233412004778 Class II fumarases; Region: Fumarase_classII; cd01362 233412004779 active site 233412004780 tetramer interface [polypeptide binding]; other site 233412004781 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 233412004782 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 233412004783 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 233412004784 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 233412004785 TrkA-N domain; Region: TrkA_N; pfam02254 233412004786 TrkA-C domain; Region: TrkA_C; pfam02080 233412004787 TrkA-N domain; Region: TrkA_N; pfam02254 233412004788 TrkA-C domain; Region: TrkA_C; pfam02080 233412004789 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...; Region: NusB_Sun; cl00223 233412004790 putative RNA binding site [nucleotide binding]; other site 233412004791 16S rRNA methyltransferase B; Provisional; Region: PRK10901 233412004792 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 233412004793 S-adenosylmethionine binding site [chemical binding]; other site 233412004794 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 233412004795 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 233412004796 G1 box; other site 233412004797 putative GEF interaction site [polypeptide binding]; other site 233412004798 GTP/Mg2+ binding site [chemical binding]; other site 233412004799 Switch I region; other site 233412004800 G2 box; other site 233412004801 G3 box; other site 233412004802 Switch II region; other site 233412004803 G4 box; other site 233412004804 G5 box; other site 233412004805 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 233412004806 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 233412004807 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 233412004808 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 233412004809 seryl-tRNA(sec) selenium transferase; Region: selA; TIGR00474 233412004810 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 233412004811 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 233412004812 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 233412004813 catalytic residue [active] 233412004814 FMN-binding protein MioC; Provisional; Region: PRK09004 233412004815 signal recognition particle protein; Provisional; Region: PRK10867 233412004816 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 233412004817 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 233412004818 P loop; other site 233412004819 GTP binding site [chemical binding]; other site 233412004820 Signal peptide binding domain; Region: SRP_SPB; pfam02978 233412004821 conserved hypothetical transport protein, N-terminal fragment; HDp2000A 233412004822 murein transglycosylase C; Provisional; Region: mltC; PRK11671 233412004823 Domain of unknown function (DUF3393); Region: DUF3393; pfam11873 233412004824 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 233412004825 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 233412004826 N-acetyl-D-glucosamine binding site [chemical binding]; other site 233412004827 catalytic residue [active] 233412004828 oxidative damage protection protein; Provisional; Region: PRK05408 233412004829 adenine DNA glycosylase; Provisional; Region: PRK10880 233412004830 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 233412004831 minor groove reading motif; other site 233412004832 helix-hairpin-helix signature motif; other site 233412004833 substrate binding pocket [chemical binding]; other site 233412004834 active site 233412004835 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 233412004836 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 233412004837 DNA binding and oxoG recognition site [nucleotide binding] 233412004838 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 233412004839 active site 233412004840 HslU subunit interaction site [polypeptide binding]; other site 233412004841 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 233412004842 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 233412004843 Walker A motif; other site 233412004844 ATP binding site [chemical binding]; other site 233412004845 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 233412004846 Walker B motif; other site 233412004847 arginine finger; other site 233412004848 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 233412004849 phosphoribosylformylglycinamidine synthase, N-terminal fragment; HDp2010A 233412004850 phosphoribosylformylglycinamidine synthase, central fragment; HDp2010B 233412004851 Protein of unknown function, DUF417; Region: DUF417; cl01162 233412004852 lipoyl synthase; Provisional; Region: PRK05481 233412004853 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 233412004854 FeS/SAM binding site; other site 233412004855 lipoate-protein ligase B; Provisional; Region: PRK14342 233412004856 hypothetical protein; Provisional; Region: PRK04998 233412004857 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 233412004858 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional; Region: PRK10793 233412004859 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 233412004860 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 233412004861 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 233412004862 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 233412004863 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 233412004864 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 233412004865 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 233412004866 rRNA large subunit m3Psi methyltransferase RlmH; Region: tRNA_RlmH_YbeA; TIGR00246 233412004867 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 233412004868 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 233412004869 MutS domain I; Region: MutS_I; pfam01624 233412004870 MutS domain II; Region: MutS_II; pfam05188 233412004871 MutS domain III; Region: MutS_III; pfam05192 233412004872 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 233412004873 Walker A/P-loop; other site 233412004874 ATP binding site [chemical binding]; other site 233412004875 Q-loop/lid; other site 233412004876 ABC transporter signature motif; other site 233412004877 Walker B; other site 233412004878 D-loop; other site 233412004879 H-loop/switch region; other site 233412004880 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 (16,20)...; Region: OM_channels; cl17244 233412004881 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 233412004882 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 233412004883 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 233412004884 Cation transport protein; Region: TrkH; cl17365 233412004885 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 233412004886 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 233412004887 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 233412004888 putative active site [active] 233412004889 substrate binding site [chemical binding]; other site 233412004890 putative cosubstrate binding site; other site 233412004891 catalytic site [active] 233412004892 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 233412004893 substrate binding site [chemical binding]; other site 233412004894 Sigma-70, region 4; Region: Sigma70_r4; pfam04545 233412004895 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 233412004896 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 233412004897 Walker A/P-loop; other site 233412004898 ATP binding site [chemical binding]; other site 233412004899 Q-loop/lid; other site 233412004900 ABC transporter signature motif; other site 233412004901 Walker B; other site 233412004902 D-loop; other site 233412004903 H-loop/switch region; other site 233412004904 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 233412004905 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 233412004906 dimer interface [polypeptide binding]; other site 233412004907 conserved gate region; other site 233412004908 putative PBP binding loops; other site 233412004909 ABC-ATPase subunit interface; other site 233412004910 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 233412004911 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 233412004912 substrate binding pocket [chemical binding]; other site 233412004913 membrane-bound complex binding site; other site 233412004914 hinge residues; other site