-- dump date 20140619_235402 -- class Genbank::misc_feature -- table misc_feature_note -- id note 908937000001 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 908937000002 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 908937000003 Walker A motif; other site 908937000004 ATP binding site [chemical binding]; other site 908937000005 Walker B motif; other site 908937000006 arginine finger; other site 908937000007 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 908937000008 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 908937000009 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 908937000010 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 908937000011 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 908937000012 CoA-binding domain; Region: CoA_binding_3; pfam13727 908937000013 Bacterial sugar transferase; Region: Bac_transf; pfam02397 908937000014 Bacterial Ig-like domain (group 3); Region: Big_3; pfam07523 908937000015 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937000016 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937000017 SusD family; Region: SusD; pfam07980 908937000018 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937000019 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937000020 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937000021 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937000022 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 908937000023 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 908937000024 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937000025 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937000026 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 908937000027 Acyltransferase family; Region: Acyl_transf_3; pfam01757 908937000028 Helix-turn-helix domain; Region: HTH_18; pfam12833 908937000029 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937000030 CAAX protease self-immunity; Region: Abi; pfam02517 908937000031 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 908937000032 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 908937000033 active site 908937000034 Riboflavin kinase; Region: Flavokinase; pfam01687 908937000035 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 908937000036 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 908937000037 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 908937000038 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 908937000039 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 908937000040 motif II; other site 908937000041 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 908937000042 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 908937000043 classical (c) SDRs; Region: SDR_c; cd05233 908937000044 NAD(P) binding site [chemical binding]; other site 908937000045 active site 908937000046 YCII-related domain; Region: YCII; cl00999 908937000047 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 908937000048 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937000049 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 908937000050 DNA binding residues [nucleotide binding] 908937000051 AAK_NAGK-like: N-Acetyl-L-glutamate kinase (NAGK)-like . Included in this CD are the Escherichia coli and Pseudomonas aeruginosa type NAGKs which catalyze the phosphorylation of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine...; Region: AAK_NAGK-like; cd04238 908937000052 nucleotide binding site [chemical binding]; other site 908937000053 N-acetyl-L-glutamate binding site [chemical binding]; other site 908937000054 arginine decarboxylase; Provisional; Region: PRK05354 908937000055 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 908937000056 dimer interface [polypeptide binding]; other site 908937000057 active site 908937000058 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 908937000059 catalytic residues [active] 908937000060 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 908937000061 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 908937000062 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 908937000063 ADP binding site [chemical binding]; other site 908937000064 magnesium binding site [ion binding]; other site 908937000065 putative shikimate binding site; other site 908937000066 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 908937000067 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 908937000068 active site 908937000069 interdomain interaction site; other site 908937000070 putative metal-binding site [ion binding]; other site 908937000071 nucleotide binding site [chemical binding]; other site 908937000072 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 908937000073 domain I; other site 908937000074 DNA binding groove [nucleotide binding] 908937000075 phosphate binding site [ion binding]; other site 908937000076 domain II; other site 908937000077 domain III; other site 908937000078 nucleotide binding site [chemical binding]; other site 908937000079 catalytic site [active] 908937000080 domain IV; other site 908937000081 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 908937000082 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 908937000083 Predicted membrane protein [Function unknown]; Region: COG3059 908937000084 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 908937000085 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_22; cd04681 908937000086 nudix motif; other site 908937000087 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 908937000088 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 908937000089 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 908937000090 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 908937000091 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 908937000092 RNase E interface [polypeptide binding]; other site 908937000093 trimer interface [polypeptide binding]; other site 908937000094 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 908937000095 RNase E interface [polypeptide binding]; other site 908937000096 trimer interface [polypeptide binding]; other site 908937000097 active site 908937000098 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 908937000099 putative nucleic acid binding region [nucleotide binding]; other site 908937000100 G-X-X-G motif; other site 908937000101 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 908937000102 RNA binding site [nucleotide binding]; other site 908937000103 domain interface; other site 908937000104 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 908937000105 EamA-like transporter family; Region: EamA; pfam00892 908937000106 EamA-like transporter family; Region: EamA; pfam00892 908937000107 Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate...; Region: PRTase_typeII; cl17275 908937000108 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 908937000109 active site 908937000110 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 908937000111 Fibronectin type 3 domain; Region: FN3; smart00060 908937000112 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 908937000113 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 908937000114 binding surface 908937000115 TPR motif; other site 908937000116 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 908937000117 binding surface 908937000118 TPR motif; other site 908937000119 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 908937000120 binding surface 908937000121 TPR motif; other site 908937000122 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 908937000123 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 908937000124 dimer interface [polypeptide binding]; other site 908937000125 phosphorylation site [posttranslational modification] 908937000126 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 908937000127 ATP binding site [chemical binding]; other site 908937000128 Mg2+ binding site [ion binding]; other site 908937000129 G-X-G motif; other site 908937000130 Response regulator receiver domain; Region: Response_reg; pfam00072 908937000131 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 908937000132 active site 908937000133 phosphorylation site [posttranslational modification] 908937000134 intermolecular recognition site; other site 908937000135 dimerization interface [polypeptide binding]; other site 908937000136 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937000137 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937000138 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 908937000139 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 908937000140 putative substrate binding site [chemical binding]; other site 908937000141 putative ATP binding site [chemical binding]; other site 908937000142 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 908937000143 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 908937000144 putative substrate translocation pore; other site 908937000145 Glycosyl hydrolases family 32; Region: Glyco_32; smart00640 908937000146 Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996 908937000147 substrate binding [chemical binding]; other site 908937000148 active site 908937000149 Glycosyl hydrolases family 32 C terminal; Region: Glyco_hydro_32C; pfam08244 908937000150 Beta-fructosidases (levanase/invertase) [Carbohydrate transport and metabolism]; Region: SacC; COG1621 908937000151 Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996 908937000152 substrate binding [chemical binding]; other site 908937000153 active site 908937000154 Glycosyl hydrolases family 32 C terminal; Region: Glyco_hydro_32C; pfam08244 908937000155 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937000156 SusD family; Region: SusD; pfam07980 908937000157 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937000158 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937000159 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 908937000160 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 908937000161 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937000162 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 908937000163 D-xylose ABC transporter, substrate-binding protein; Region: xylF; TIGR02634 908937000164 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 908937000165 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 908937000166 dimer interface [polypeptide binding]; other site 908937000167 phosphorylation site [posttranslational modification] 908937000168 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 908937000169 ATP binding site [chemical binding]; other site 908937000170 Mg2+ binding site [ion binding]; other site 908937000171 G-X-G motif; other site 908937000172 Response regulator receiver domain; Region: Response_reg; pfam00072 908937000173 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 908937000174 active site 908937000175 phosphorylation site [posttranslational modification] 908937000176 intermolecular recognition site; other site 908937000177 dimerization interface [polypeptide binding]; other site 908937000178 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937000179 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937000180 Predicted transcriptional regulators [Transcription]; Region: COG1733 908937000181 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 908937000182 Cupin domain; Region: Cupin_2; pfam07883 908937000183 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 908937000184 Beta-galactosidase/beta-glucuronidase [Carbohydrate transport and metabolism]; Region: LacZ; COG3250 908937000185 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 908937000186 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 908937000187 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 908937000188 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 908937000189 protein binding site [polypeptide binding]; other site 908937000190 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 908937000191 Catalytic dyad [active] 908937000192 Protein of unknown function (DUF3791); Region: DUF3791; pfam12668 908937000193 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 908937000194 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 908937000195 hypothetical protein; Validated; Region: PRK02001 908937000196 Sm1 motif; other site 908937000197 RNA binding site [nucleotide binding]; other site 908937000198 transcription termination factor NusA; Region: NusA; TIGR01953 908937000199 NusA N-terminal domain; Region: NusA_N; pfam08529 908937000200 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 908937000201 RNA binding site [nucleotide binding]; other site 908937000202 homodimer interface [polypeptide binding]; other site 908937000203 NusA-like KH domain; Region: KH_5; pfam13184 908937000204 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 908937000205 G-X-X-G motif; other site 908937000206 translation initiation factor IF-2; Region: IF-2; TIGR00487 908937000207 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 908937000208 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 908937000209 G1 box; other site 908937000210 putative GEF interaction site [polypeptide binding]; other site 908937000211 GTP/Mg2+ binding site [chemical binding]; other site 908937000212 Switch I region; other site 908937000213 G2 box; other site 908937000214 G3 box; other site 908937000215 Switch II region; other site 908937000216 G4 box; other site 908937000217 G5 box; other site 908937000218 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 908937000219 Translation-initiation factor 2; Region: IF-2; pfam11987 908937000220 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 908937000221 putative ABC transporter; Region: ycf24; CHL00085 908937000222 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 908937000223 FeS assembly ATPase SufC; Region: sufC; TIGR01978 908937000224 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 908937000225 Walker A/P-loop; other site 908937000226 ATP binding site [chemical binding]; other site 908937000227 Q-loop/lid; other site 908937000228 ABC transporter signature motif; other site 908937000229 Walker B; other site 908937000230 D-loop; other site 908937000231 H-loop/switch region; other site 908937000232 Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]; Region: SufB; COG0719 908937000233 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 908937000234 FeS assembly protein SufD; Region: sufD; TIGR01981 908937000235 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 908937000236 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 908937000237 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 908937000238 catalytic residue [active] 908937000239 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 908937000240 RNA/DNA hybrid binding site [nucleotide binding]; other site 908937000241 active site 908937000242 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 908937000243 Predicted transcriptional regulator [Transcription]; Region: COG2378 908937000244 WYL domain; Region: WYL; pfam13280 908937000245 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937000246 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937000247 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937000248 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937000249 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 908937000250 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 908937000251 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 908937000252 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 908937000253 M6 family metalloprotease domain; Region: M6dom_TIGR03296 908937000254 SGNH_hydrolase subfamily, similar to the putative arylesterase/acylhydrolase from the rumen anaerobe Prevotella bryantii XynE. The P. bryantii XynE gene is located in a xylanase gene cluster. SGNH hydrolases are a diverse family of lipases and esterases; Region: XynE_like; cd01830 908937000255 active site 908937000256 catalytic triad [active] 908937000257 oxyanion hole [active] 908937000258 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 908937000259 phosphoglyceromutase; Provisional; Region: PRK05434 908937000260 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 908937000261 ligand binding site [chemical binding]; other site 908937000262 active site 908937000263 UGI interface [polypeptide binding]; other site 908937000264 catalytic site [active] 908937000265 Protein of unknown function (DUF3109); Region: DUF3109; pfam11307 908937000266 Helix-turn-helix domain; Region: HTH_18; pfam12833 908937000267 Alpha-L-rhamnosidase N-terminal domain; Region: Bac_rhamnosid_N; pfam08531 908937000268 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 908937000269 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 908937000270 ATP binding site [chemical binding]; other site 908937000271 Mg2+ binding site [ion binding]; other site 908937000272 G-X-G motif; other site 908937000273 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 908937000274 anchoring element; other site 908937000275 dimer interface [polypeptide binding]; other site 908937000276 ATP binding site [chemical binding]; other site 908937000277 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 908937000278 active site 908937000279 metal binding site [ion binding]; metal-binding site 908937000280 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 908937000281 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 908937000282 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 908937000283 Recombination protein O N terminal; Region: RecO_N; pfam11967 908937000284 Recombination protein O C terminal; Region: RecO_C; pfam02565 908937000285 Yqey-like protein; Region: YqeY; cl17540 908937000286 cell division protein FtsZ; Validated; Region: PRK09330 908937000287 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 908937000288 nucleotide binding site [chemical binding]; other site 908937000289 SulA interaction site; other site 908937000290 cell division protein FtsA; Region: ftsA; TIGR01174 908937000291 Cell division protein FtsA; Region: FtsA; smart00842 908937000292 Cell division protein FtsA; Region: FtsA; pfam14450 908937000293 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 908937000294 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 908937000295 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 908937000296 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 908937000297 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 908937000298 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 908937000299 homodimer interface [polypeptide binding]; other site 908937000300 active site 908937000301 Bacterial cell division membrane protein [Cell division and chromosome partitioning]; Region: FtsW; COG0772 908937000302 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 908937000303 UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]; Region: MurD; COG0771 908937000304 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 908937000305 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 908937000306 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 908937000307 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 908937000308 Mg++ binding site [ion binding]; other site 908937000309 putative catalytic motif [active] 908937000310 putative substrate binding site [chemical binding]; other site 908937000311 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 908937000312 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 908937000313 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 908937000314 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 908937000315 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 908937000316 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 908937000317 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 908937000318 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by...; Region: PASTA_Pbp2x-like_2; cd06575 908937000319 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 908937000320 MraW methylase family; Region: Methyltransf_5; cl17771 908937000321 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 908937000322 MraZ protein; Region: MraZ; pfam02381 908937000323 MraZ protein; Region: MraZ; pfam02381 908937000324 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 908937000325 putative acyl-acceptor binding pocket; other site 908937000326 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 908937000327 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 908937000328 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 908937000329 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 908937000330 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 908937000331 trimer interface [polypeptide binding]; other site 908937000332 active site 908937000333 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 908937000334 binding surface 908937000335 TPR motif; other site 908937000336 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 908937000337 binding surface 908937000338 TPR motif; other site 908937000339 TPR repeat; Region: TPR_11; pfam13414 908937000340 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 908937000341 TPR motif; other site 908937000342 Tetratricopeptide repeat; Region: TPR_12; pfam13424 908937000343 binding surface 908937000344 Domain of unknown function (DUF4292); Region: DUF4292; pfam14125 908937000345 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3883 908937000346 Peptidase family M23; Region: Peptidase_M23; pfam01551 908937000347 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 908937000348 M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases; Region: M20_ArgE_DapE_like5; cd05651 908937000349 metal binding site [ion binding]; metal-binding site 908937000350 dimer interface [polypeptide binding]; other site 908937000351 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 908937000352 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937000353 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 908937000354 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 908937000355 acyl-activating enzyme (AAE) consensus motif; other site 908937000356 putative AMP binding site [chemical binding]; other site 908937000357 putative active site [active] 908937000358 putative CoA binding site [chemical binding]; other site 908937000359 peptide chain release factor 2; Validated; Region: prfB; PRK00578 908937000360 This domain is found in peptide chain release factors; Region: PCRF; smart00937 908937000361 RF-1 domain; Region: RF-1; pfam00472 908937000362 CYTH-like Clostridium thermocellum TTM-like subgroup 1; Region: CYTH-like_CthTTM-like_1; cd07891 908937000363 putative active site [active] 908937000364 putative metal binding residues [ion binding]; other site 908937000365 signature motif; other site 908937000366 putative dimer interface [polypeptide binding]; other site 908937000367 putative phosphate binding site [ion binding]; other site 908937000368 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 908937000369 Na2 binding site [ion binding]; other site 908937000370 putative substrate binding site 1 [chemical binding]; other site 908937000371 Na binding site 1 [ion binding]; other site 908937000372 putative substrate binding site 2 [chemical binding]; other site 908937000373 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 908937000374 Na2 binding site [ion binding]; other site 908937000375 putative substrate binding site 1 [chemical binding]; other site 908937000376 Na binding site 1 [ion binding]; other site 908937000377 putative substrate binding site 2 [chemical binding]; other site 908937000378 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 908937000379 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 908937000380 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 908937000381 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 908937000382 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 908937000383 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 908937000384 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 908937000385 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 908937000386 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937000387 AAA ATPase domain; Region: AAA_16; pfam13191 908937000388 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 908937000389 dihydropteroate synthase; Region: DHPS; TIGR01496 908937000390 substrate binding pocket [chemical binding]; other site 908937000391 dimer interface [polypeptide binding]; other site 908937000392 inhibitor binding site; inhibition site 908937000393 Uncharacterized conserved protein [Function unknown]; Region: COG1624 908937000394 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 908937000395 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 908937000396 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 908937000397 propionate/acetate kinase; Provisional; Region: PRK12379 908937000398 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 908937000399 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 908937000400 substrate binding site [chemical binding]; other site 908937000401 ATP binding site [chemical binding]; other site 908937000402 anaerobic sulfatase-maturating enzyme; Region: sulfatase_rSAM; TIGR03942 908937000403 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 908937000404 FeS/SAM binding site; other site 908937000405 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 908937000406 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 908937000407 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 908937000408 putative active site [active] 908937000409 putative metal binding site [ion binding]; other site 908937000410 Domain of unknown function DUF59; Region: DUF59; cl00941 908937000411 hypothetical protein; Reviewed; Region: PRK00024 908937000412 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 908937000413 MPN+ (JAMM) motif; other site 908937000414 Zinc-binding site [ion binding]; other site 908937000415 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 908937000416 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 908937000417 active site 908937000418 elongation factor P; Validated; Region: PRK00529 908937000419 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 908937000420 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 908937000421 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 908937000422 RNA binding site [nucleotide binding]; other site 908937000423 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 908937000424 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 908937000425 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 908937000426 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 908937000427 RNA binding surface [nucleotide binding]; other site 908937000428 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 908937000429 active site 908937000430 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 908937000431 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 908937000432 ATP-grasp domain; Region: ATP-grasp_4; cl17255 908937000433 NigD-like protein; Region: NigD; pfam12667 908937000434 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 908937000435 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 908937000436 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 908937000437 catalytic residue [active] 908937000438 N-acetylornithine carbamoyltransferase; Reviewed; Region: PRK04523 908937000439 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 908937000440 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 908937000441 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 908937000442 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 908937000443 putative catalytic cysteine [active] 908937000444 gamma-glutamyl kinase; Provisional; Region: PRK05429 908937000445 AAK_G5K_ProB: Glutamate-5-kinase (G5K) catalyzes glutamate-dependent ATP cleavage; G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, in the first and controlling step of proline (and, in mammals, ornithine)...; Region: AAK_G5K_ProB; cd04242 908937000446 nucleotide binding site [chemical binding]; other site 908937000447 homotetrameric interface [polypeptide binding]; other site 908937000448 putative phosphate binding site [ion binding]; other site 908937000449 putative allosteric binding site; other site 908937000450 PUA domain; Region: PUA; pfam01472 908937000451 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 908937000452 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 908937000453 acyl-activating enzyme (AAE) consensus motif; other site 908937000454 AMP binding site [chemical binding]; other site 908937000455 active site 908937000456 CoA binding site [chemical binding]; other site 908937000457 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 908937000458 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 908937000459 non-specific DNA binding site [nucleotide binding]; other site 908937000460 salt bridge; other site 908937000461 sequence-specific DNA binding site [nucleotide binding]; other site 908937000462 Cupin domain; Region: Cupin_2; pfam07883 908937000463 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 908937000464 pyrroline-5-carboxylate reductase; Region: proC; TIGR00112 908937000465 acetylornithine aminotransferase; Provisional; Region: PRK02627 908937000466 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 908937000467 inhibitor-cofactor binding pocket; inhibition site 908937000468 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937000469 catalytic residue [active] 908937000470 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 908937000471 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 908937000472 PspC domain; Region: PspC; pfam04024 908937000473 argininosuccinate synthase; Provisional; Region: PRK13820 908937000474 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 908937000475 Ligand Binding Site [chemical binding]; other site 908937000476 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 908937000477 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 908937000478 Coenzyme A binding pocket [chemical binding]; other site 908937000479 Arginine repressor [Transcription]; Region: ArgR; COG1438 908937000480 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 908937000481 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 908937000482 Pectate lyase superfamily protein; Region: Pectate_lyase_3; pfam12708 908937000483 Probable polygalacturonase At3g15720; Region: PLN03003; cl14103 908937000484 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937000485 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937000486 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 908937000487 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937000488 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937000489 SusD family; Region: SusD; pfam07980 908937000490 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 908937000491 Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins; Region: GDPD_AtGDE_like; cd08566 908937000492 putative active site [active] 908937000493 catalytic site [active] 908937000494 putative metal binding site [ion binding]; other site 908937000495 oligomer interface [polypeptide binding]; other site 908937000496 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 908937000497 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 908937000498 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 908937000499 catalytic core [active] 908937000500 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 908937000501 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 908937000502 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 908937000503 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 908937000504 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 908937000505 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 908937000506 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 908937000507 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 908937000508 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 908937000509 Protein of unknown function (DUF2795); Region: DUF2795; pfam11387 908937000510 Bacteroidetes-specific putative membrane protein; Region: Bac_Flav_fam_1; TIGR03519 908937000511 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 908937000512 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 908937000513 gliding motility-associated protein GldL; Region: GldL_gliding; TIGR03513 908937000514 gliding motility-associated protein GldM; Region: GldM_gliding; TIGR03517 908937000515 GldM N-terminal domain; Region: GldM_N; pfam12081 908937000516 Coronavirus endopeptidase C30; Region: Peptidase_C30; pfam05409 908937000517 GldM C-terminal domain; Region: GldM_C; pfam12080 908937000518 gliding motility associated protien GldN; Region: GldN; TIGR03523 908937000519 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 908937000520 Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]; Region: PriA; COG1198 908937000521 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 908937000522 ATP binding site [chemical binding]; other site 908937000523 putative Mg++ binding site [ion binding]; other site 908937000524 helicase superfamily c-terminal domain; Region: HELICc; smart00490 908937000525 ATP-binding site [chemical binding]; other site 908937000526 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 908937000527 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 908937000528 Walker A motif; other site 908937000529 ATP binding site [chemical binding]; other site 908937000530 Walker B motif; other site 908937000531 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 908937000532 7TM-HD extracellular; Region: 7TMR-HDED; pfam07697 908937000533 7TM receptor with intracellular HD hydrolase; Region: 7TM-7TMR_HD; pfam07698 908937000534 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 908937000535 Zn2+ binding site [ion binding]; other site 908937000536 Mg2+ binding site [ion binding]; other site 908937000537 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 908937000538 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 908937000539 HIGH motif; other site 908937000540 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 908937000541 active site 908937000542 KMSKS motif; other site 908937000543 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 908937000544 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 908937000545 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 908937000546 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 908937000547 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937000548 homodimer interface [polypeptide binding]; other site 908937000549 catalytic residue [active] 908937000550 Protein of unknown function (DUF3737); Region: DUF3737; pfam12541 908937000551 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 908937000552 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937000553 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 908937000554 DNA binding residues [nucleotide binding] 908937000555 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 908937000556 FecR protein; Region: FecR; pfam04773 908937000557 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937000558 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 908937000559 Malate/lactate dehydrogenases [Energy production and conversion]; Region: Mdh; COG0039 908937000560 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl17195 908937000561 NAD(P) binding site [chemical binding]; other site 908937000562 LDH/MDH dimer interface [polypeptide binding]; other site 908937000563 substrate binding site [chemical binding]; other site 908937000564 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 908937000565 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 908937000566 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 908937000567 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 908937000568 active site 908937000569 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 908937000570 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 908937000571 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 908937000572 active site 908937000573 DNA binding site [nucleotide binding] 908937000574 Int/Topo IB signature motif; other site 908937000575 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 908937000576 30S subunit binding site; other site 908937000577 elongation factor Tu; Reviewed; Region: PRK12735 908937000578 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 908937000579 G1 box; other site 908937000580 GEF interaction site [polypeptide binding]; other site 908937000581 GTP/Mg2+ binding site [chemical binding]; other site 908937000582 Switch I region; other site 908937000583 G2 box; other site 908937000584 G3 box; other site 908937000585 Switch II region; other site 908937000586 G4 box; other site 908937000587 G5 box; other site 908937000588 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 908937000589 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 908937000590 Antibiotic Binding Site [chemical binding]; other site 908937000591 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 908937000592 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 908937000593 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 908937000594 putative homodimer interface [polypeptide binding]; other site 908937000595 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 908937000596 heterodimer interface [polypeptide binding]; other site 908937000597 homodimer interface [polypeptide binding]; other site 908937000598 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 908937000599 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 908937000600 23S rRNA interface [nucleotide binding]; other site 908937000601 L7/L12 interface [polypeptide binding]; other site 908937000602 putative thiostrepton binding site; other site 908937000603 L25 interface [polypeptide binding]; other site 908937000604 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 908937000605 mRNA/rRNA interface [nucleotide binding]; other site 908937000606 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 908937000607 23S rRNA interface [nucleotide binding]; other site 908937000608 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 908937000609 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 908937000610 core dimer interface [polypeptide binding]; other site 908937000611 peripheral dimer interface [polypeptide binding]; other site 908937000612 L10 interface [polypeptide binding]; other site 908937000613 L11 interface [polypeptide binding]; other site 908937000614 putative EF-Tu interaction site [polypeptide binding]; other site 908937000615 putative EF-G interaction site [polypeptide binding]; other site 908937000616 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 908937000617 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 908937000618 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 908937000619 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 908937000620 RPB12 interaction site [polypeptide binding]; other site 908937000621 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 908937000622 RPB11 interaction site [polypeptide binding]; other site 908937000623 RPB12 interaction site [polypeptide binding]; other site 908937000624 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 908937000625 RPB3 interaction site [polypeptide binding]; other site 908937000626 RPB1 interaction site [polypeptide binding]; other site 908937000627 RPB11 interaction site [polypeptide binding]; other site 908937000628 RPB10 interaction site [polypeptide binding]; other site 908937000629 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 908937000630 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 908937000631 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 908937000632 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 908937000633 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 908937000634 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 908937000635 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 908937000636 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 908937000637 DNA binding site [nucleotide binding] 908937000638 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 908937000639 cytochrome c nitrate reductase, small subunit; Region: cytochr_NrfH; TIGR03153 908937000640 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 908937000641 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; PRK11125 908937000642 ResB-like family; Region: ResB; pfam05140 908937000643 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 908937000644 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937000645 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937000646 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937000647 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937000648 Glycosyl hydrolases family 35; Region: Glyco_hydro_35; pfam01301 908937000649 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 908937000650 PQQ-like domain; Region: PQQ_2; pfam13360 908937000651 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 908937000652 Protein of unknown function (DUF3467); Region: DUF3467; pfam11950 908937000653 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 908937000654 putative active site [active] 908937000655 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 908937000656 S17 interaction site [polypeptide binding]; other site 908937000657 S8 interaction site; other site 908937000658 16S rRNA interaction site [nucleotide binding]; other site 908937000659 streptomycin interaction site [chemical binding]; other site 908937000660 23S rRNA interaction site [nucleotide binding]; other site 908937000661 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 908937000662 30S ribosomal protein S7; Validated; Region: PRK05302 908937000663 elongation factor G; Reviewed; Region: PRK12739 908937000664 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 908937000665 G1 box; other site 908937000666 putative GEF interaction site [polypeptide binding]; other site 908937000667 GTP/Mg2+ binding site [chemical binding]; other site 908937000668 Switch I region; other site 908937000669 G2 box; other site 908937000670 G3 box; other site 908937000671 Switch II region; other site 908937000672 G4 box; other site 908937000673 G5 box; other site 908937000674 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 908937000675 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 908937000676 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 908937000677 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 908937000678 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 908937000679 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 908937000680 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 908937000681 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 908937000682 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 908937000683 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 908937000684 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 908937000685 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 908937000686 putative translocon binding site; other site 908937000687 protein-rRNA interface [nucleotide binding]; other site 908937000688 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 908937000689 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 908937000690 G-X-X-G motif; other site 908937000691 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 908937000692 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 908937000693 23S rRNA interface [nucleotide binding]; other site 908937000694 5S rRNA interface [nucleotide binding]; other site 908937000695 putative antibiotic binding site [chemical binding]; other site 908937000696 L25 interface [polypeptide binding]; other site 908937000697 L27 interface [polypeptide binding]; other site 908937000698 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 908937000699 23S rRNA interface [nucleotide binding]; other site 908937000700 putative translocon interaction site; other site 908937000701 signal recognition particle (SRP54) interaction site; other site 908937000702 L23 interface [polypeptide binding]; other site 908937000703 trigger factor interaction site; other site 908937000704 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 908937000705 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 908937000706 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 908937000707 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 908937000708 RNA binding site [nucleotide binding]; other site 908937000709 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 908937000710 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 908937000711 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 908937000712 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 908937000713 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 908937000714 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 908937000715 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 908937000716 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 908937000717 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 908937000718 5S rRNA interface [nucleotide binding]; other site 908937000719 23S rRNA interface [nucleotide binding]; other site 908937000720 L5 interface [polypeptide binding]; other site 908937000721 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 908937000722 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 908937000723 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 908937000724 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 908937000725 23S rRNA binding site [nucleotide binding]; other site 908937000726 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 908937000727 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 908937000728 SecY translocase; Region: SecY; pfam00344 908937000729 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 908937000730 active site 908937000731 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 908937000732 rRNA binding site [nucleotide binding]; other site 908937000733 predicted 30S ribosome binding site; other site 908937000734 Ribosomal protein L36; Region: Ribosomal_L36; pfam00444 908937000735 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 908937000736 30S ribosomal protein S13; Region: bact_S13; TIGR03631 908937000737 30S ribosomal protein S11; Validated; Region: PRK05309 908937000738 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 908937000739 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 908937000740 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 908937000741 RNA binding surface [nucleotide binding]; other site 908937000742 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 908937000743 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 908937000744 alphaNTD - beta interaction site [polypeptide binding]; other site 908937000745 alphaNTD homodimer interface [polypeptide binding]; other site 908937000746 alphaNTD - beta' interaction site [polypeptide binding]; other site 908937000747 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 908937000748 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 908937000749 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 908937000750 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 908937000751 glutamate dehydrogenase; Provisional; Region: PRK14030 908937000752 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 908937000753 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 908937000754 NAD(P) binding site [chemical binding]; other site 908937000755 Helix-turn-helix domain; Region: HTH_18; pfam12833 908937000756 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937000757 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 908937000758 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937000759 Walker A/P-loop; other site 908937000760 ATP binding site [chemical binding]; other site 908937000761 Q-loop/lid; other site 908937000762 ABC transporter signature motif; other site 908937000763 Walker B; other site 908937000764 D-loop; other site 908937000765 H-loop/switch region; other site 908937000766 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 908937000767 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 908937000768 putative substrate translocation pore; other site 908937000769 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937000770 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 908937000771 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 908937000772 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 908937000773 intersubunit interface [polypeptide binding]; other site 908937000774 active site 908937000775 zinc binding site [ion binding]; other site 908937000776 Na+ binding site [ion binding]; other site 908937000777 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 908937000778 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 908937000779 putative substrate binding site [chemical binding]; other site 908937000780 putative ATP binding site [chemical binding]; other site 908937000781 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 908937000782 active site 908937000783 adenylate kinase; Reviewed; Region: adk; PRK00279 908937000784 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 908937000785 AMP-binding site [chemical binding]; other site 908937000786 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 908937000787 GTPase CgtA; Reviewed; Region: obgE; PRK12298 908937000788 GTP1/OBG; Region: GTP1_OBG; pfam01018 908937000789 Obg GTPase; Region: Obg; cd01898 908937000790 G1 box; other site 908937000791 GTP/Mg2+ binding site [chemical binding]; other site 908937000792 Switch I region; other site 908937000793 G2 box; other site 908937000794 G3 box; other site 908937000795 Switch II region; other site 908937000796 G4 box; other site 908937000797 G5 box; other site 908937000798 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 908937000799 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 908937000800 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 908937000801 Peptidase family M23; Region: Peptidase_M23; pfam01551 908937000802 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 908937000803 Peptidase family M23; Region: Peptidase_M23; pfam01551 908937000804 5-aminoimidazole-4-carboxamide ribonucleotide transformylase; Provisional; Region: PRK07106 908937000805 AICAR transformylase/IMP cyclohydrolase PurH (only IMP cyclohydrolase domain in Aful) [Nucleotide transport and metabolism]; Region: PurH; COG0138 908937000806 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 908937000807 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 908937000808 Escherichia coli UshA-like family, N-terminal metallophosphatase domain; Region: MPP_UshA_N_like; cd00845 908937000809 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 908937000810 active site 908937000811 metal binding site [ion binding]; metal-binding site 908937000812 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 908937000813 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 908937000814 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 908937000815 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 908937000816 binding surface 908937000817 TPR motif; other site 908937000818 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 908937000819 TPR motif; other site 908937000820 binding surface 908937000821 PBP superfamily domain; Region: PBP_like_2; pfam12849 908937000822 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 908937000823 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 908937000824 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 908937000825 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 908937000826 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 908937000827 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 908937000828 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 908937000829 aspartate aminotransferase; Provisional; Region: PRK05764 908937000830 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 908937000831 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937000832 homodimer interface [polypeptide binding]; other site 908937000833 catalytic residue [active] 908937000834 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 908937000835 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 908937000836 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 908937000837 dimerization interface [polypeptide binding]; other site 908937000838 active site 908937000839 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 908937000840 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 908937000841 rod shape-determining protein MreB; Provisional; Region: PRK13927 908937000842 MreB and similar proteins; Region: MreB_like; cd10225 908937000843 nucleotide binding site [chemical binding]; other site 908937000844 Mg binding site [ion binding]; other site 908937000845 putative protofilament interaction site [polypeptide binding]; other site 908937000846 RodZ interaction site [polypeptide binding]; other site 908937000847 rod shape-determining protein MreC; Provisional; Region: PRK13922 908937000848 rod shape-determining protein MreC; Region: MreC; pfam04085 908937000849 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 908937000850 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 908937000851 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 908937000852 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 908937000853 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 908937000854 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 908937000855 GldH lipoprotein; Region: GldH_lipo; pfam14109 908937000856 PSP1 C-terminal conserved region; Region: PSP1; cl00770 908937000857 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 908937000858 DNA polymerase III, delta subunit; Region: DNA_pol3_delta2; pfam13177 908937000859 DNA polymerase III subunit delta'; Validated; Region: PRK08485 908937000860 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 908937000861 FAD binding site [chemical binding]; other site 908937000862 Protein of unknown function, DUF488; Region: DUF488; cl01246 908937000863 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 908937000864 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 908937000865 non-specific DNA interactions [nucleotide binding]; other site 908937000866 DNA binding site [nucleotide binding] 908937000867 sequence specific DNA binding site [nucleotide binding]; other site 908937000868 putative cAMP binding site [chemical binding]; other site 908937000869 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 908937000870 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; cl17915 908937000871 motif II; other site 908937000872 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 908937000873 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 908937000874 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 908937000875 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 908937000876 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 908937000877 uncharacterized bacterial subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB family; Region: EcCorA_ZntB-like_u2; cd12827 908937000878 Cl binding site [ion binding]; other site 908937000879 oligomer interface [polypeptide binding]; other site 908937000880 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 908937000881 Protein export membrane protein; Region: SecD_SecF; cl14618 908937000882 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 908937000883 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 908937000884 HlyD family secretion protein; Region: HlyD_3; pfam13437 908937000885 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 908937000886 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937000887 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937000888 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937000889 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937000890 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937000891 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 908937000892 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937000893 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 908937000894 active site 908937000895 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 908937000896 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 908937000897 metal binding site [ion binding]; metal-binding site 908937000898 dimer interface [polypeptide binding]; other site 908937000899 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 908937000900 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 908937000901 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 908937000902 S-adenosylmethionine binding site [chemical binding]; other site 908937000903 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 908937000904 GAF domain; Region: GAF_2; pfam13185 908937000905 ribosome recycling factor; Reviewed; Region: frr; PRK00083 908937000906 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 908937000907 hinge region; other site 908937000908 GTPase RsgA; Reviewed; Region: PRK00098 908937000909 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 908937000910 RNA binding site [nucleotide binding]; other site 908937000911 homodimer interface [polypeptide binding]; other site 908937000912 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 908937000913 GTPase/Zn-binding domain interface [polypeptide binding]; other site 908937000914 GTP/Mg2+ binding site [chemical binding]; other site 908937000915 G4 box; other site 908937000916 G5 box; other site 908937000917 G1 box; other site 908937000918 Switch I region; other site 908937000919 G2 box; other site 908937000920 G3 box; other site 908937000921 Switch II region; other site 908937000922 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cl00089 908937000923 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 908937000924 active site 908937000925 substrate binding site [chemical binding]; other site 908937000926 Mg2+ binding site [ion binding]; other site 908937000927 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 908937000928 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 908937000929 putative catalytic site [active] 908937000930 putative metal binding site [ion binding]; other site 908937000931 putative phosphate binding site [ion binding]; other site 908937000932 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 908937000933 putative active site [active] 908937000934 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 908937000935 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 908937000936 Sugar specificity; other site 908937000937 Pyrimidine base specificity; other site 908937000938 ATP-binding site [chemical binding]; other site 908937000939 Restriction endonuclease EcoRV; Region: Endonuc-EcoRV; pfam09233 908937000940 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 908937000941 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 908937000942 catalytic core [active] 908937000943 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937000944 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937000945 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937000946 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937000947 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 908937000948 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 908937000949 DNA binding site [nucleotide binding] 908937000950 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 908937000951 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 908937000952 ligand binding site [chemical binding]; other site 908937000953 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 908937000954 Bacterial sugar transferase; Region: Bac_transf; pfam02397 908937000955 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 908937000956 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 908937000957 Mg++ binding site [ion binding]; other site 908937000958 putative catalytic motif [active] 908937000959 substrate binding site [chemical binding]; other site 908937000960 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 908937000961 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 908937000962 metal-binding site 908937000963 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 908937000964 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 908937000965 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 908937000966 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 908937000967 inhibitor-cofactor binding pocket; inhibition site 908937000968 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937000969 catalytic residue [active] 908937000970 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 908937000971 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 908937000972 Glycoside hydrolase family 15, N-terminal domain; Region: GH15_N; cl07672 908937000973 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 908937000974 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 908937000975 Aminoglycoside 3-N-acetyltransferase; Region: Antibiotic_NAT; cl01051 908937000976 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsE; COG3524 908937000977 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 908937000978 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 908937000979 SLBB domain; Region: SLBB; pfam10531 908937000980 SLBB domain; Region: SLBB; pfam10531 908937000981 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 908937000982 SLBB domain; Region: SLBB; pfam10531 908937000983 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 908937000984 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 908937000985 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 908937000986 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937000987 Walker A/P-loop; other site 908937000988 ATP binding site [chemical binding]; other site 908937000989 Q-loop/lid; other site 908937000990 ABC transporter signature motif; other site 908937000991 Walker B; other site 908937000992 D-loop; other site 908937000993 H-loop/switch region; other site 908937000994 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 908937000995 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 908937000996 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937000997 Walker A/P-loop; other site 908937000998 ATP binding site [chemical binding]; other site 908937000999 Q-loop/lid; other site 908937001000 ABC transporter signature motif; other site 908937001001 Walker B; other site 908937001002 D-loop; other site 908937001003 H-loop/switch region; other site 908937001004 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 908937001005 S-adenosylmethionine binding site [chemical binding]; other site 908937001006 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 908937001007 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937001008 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 908937001009 DNA binding residues [nucleotide binding] 908937001010 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 908937001011 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 908937001012 Radical SAM superfamily; Region: Radical_SAM; pfam04055 908937001013 FeS/SAM binding site; other site 908937001014 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 908937001015 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 908937001016 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 908937001017 Lipocalin-like domain; Region: Lipocalin_6; pfam13944 908937001018 Bacterial proteins similar to Porphyromonas gingivalis HmuY; Region: HmuY; cd12105 908937001019 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 908937001020 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 908937001021 N-terminal plug; other site 908937001022 ligand-binding site [chemical binding]; other site 908937001023 Methyltransferase domain; Region: Methyltransf_31; pfam13847 908937001024 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 908937001025 S-adenosylmethionine binding site [chemical binding]; other site 908937001026 zinc-dependent metalloproteinase lipoprotein, BF0631 family; Region: metzin_BF0631; TIGR03952 908937001027 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 908937001028 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 908937001029 hinge; other site 908937001030 active site 908937001031 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 908937001032 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 908937001033 TPR motif; other site 908937001034 binding surface 908937001035 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 908937001036 binding surface 908937001037 TPR motif; other site 908937001038 Tetratricopeptide repeat; Region: TPR_12; pfam13424 908937001039 Response regulator receiver domain; Region: Response_reg; pfam00072 908937001040 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 908937001041 active site 908937001042 phosphorylation site [posttranslational modification] 908937001043 intermolecular recognition site; other site 908937001044 dimerization interface [polypeptide binding]; other site 908937001045 PglZ domain; Region: PglZ; pfam08665 908937001046 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 908937001047 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 908937001048 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 908937001049 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 908937001050 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 908937001051 active site 908937001052 PHP Thumb interface [polypeptide binding]; other site 908937001053 metal binding site [ion binding]; metal-binding site 908937001054 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 908937001055 generic binding surface II; other site 908937001056 generic binding surface I; other site 908937001057 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 908937001058 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 908937001059 catalytic residues [active] 908937001060 Gram-negative bacterial tonB protein; Region: TonB; cl10048 908937001061 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 908937001062 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 908937001063 Glycogen synthase; Region: Glycogen_syn; pfam05693 908937001064 This family is most closely related to the oligosaccharide phosphorylase domain family and other unidentified sequences. Oligosaccharide phosphorylase catalyzes the breakdown of oligosaccharides into glucose-1-phosphate units. They are important...; Region: GT1_Glycogen_Phosphorylase_like; cd04299 908937001065 putative homodimer interface [polypeptide binding]; other site 908937001066 putative active site pocket [active] 908937001067 alpha-glucan phosphorylases; Region: more_P_ylases; TIGR02094 908937001068 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 908937001069 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 908937001070 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937001071 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 908937001072 Alginate Lyase A1-III; enzymatically depolymerizes alginate, a complex copolymer of beta-D-mannuronate and alpha-L-guluronate, by cleaving the beta-(1,4) glycosidic bond; Region: AlgLyase; cl00179 908937001073 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 908937001074 Alpha-L-rhamnosidase N-terminal domain; Region: Bac_rhamnosid_N; pfam08531 908937001075 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; pfam05592 908937001076 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 908937001077 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 908937001078 catalytic residues [active] 908937001079 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 908937001080 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 908937001081 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 908937001082 catalytic residues [active] 908937001083 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 908937001084 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 908937001085 catalytic residues [active] 908937001086 Phosphoglycerate kinase; Region: PGK; pfam00162 908937001087 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 908937001088 substrate binding site [chemical binding]; other site 908937001089 hinge regions; other site 908937001090 ADP binding site [chemical binding]; other site 908937001091 catalytic site [active] 908937001092 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 908937001093 Ligand Binding Site [chemical binding]; other site 908937001094 DNA repair protein RadA; Provisional; Region: PRK11823 908937001095 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 908937001096 Walker A motif/ATP binding site; other site 908937001097 ATP binding site [chemical binding]; other site 908937001098 Walker B motif; other site 908937001099 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 908937001100 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 908937001101 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 908937001102 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 908937001103 transcription termination factor Rho; Provisional; Region: PRK12608 908937001104 RNA binding site [nucleotide binding]; other site 908937001105 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 908937001106 multimer interface [polypeptide binding]; other site 908937001107 Walker A motif; other site 908937001108 ATP binding site [chemical binding]; other site 908937001109 Walker B motif; other site 908937001110 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 908937001111 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 908937001112 RNA binding site [nucleotide binding]; other site 908937001113 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 908937001114 RNA binding site [nucleotide binding]; other site 908937001115 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 908937001116 RNA binding site [nucleotide binding]; other site 908937001117 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 908937001118 RNA binding site [nucleotide binding]; other site 908937001119 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 908937001120 RNA binding site [nucleotide binding]; other site 908937001121 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 908937001122 RNA binding site [nucleotide binding]; other site 908937001123 Family of unknown function (DUF490); Region: DUF490; pfam04357 908937001124 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 908937001125 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 908937001126 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 908937001127 FMN-binding domain; Region: FMN_bind; cl01081 908937001128 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 908937001129 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 908937001130 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 908937001131 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 908937001132 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 908937001133 catalytic loop [active] 908937001134 iron binding site [ion binding]; other site 908937001135 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 908937001136 FAD binding pocket [chemical binding]; other site 908937001137 FAD binding motif [chemical binding]; other site 908937001138 phosphate binding motif [ion binding]; other site 908937001139 beta-alpha-beta structure motif; other site 908937001140 NAD binding pocket [chemical binding]; other site 908937001141 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 908937001142 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 908937001143 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 908937001144 active site 908937001145 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 908937001146 active site 908937001147 thiamine phosphate binding site [chemical binding]; other site 908937001148 pyrophosphate binding site [ion binding]; other site 908937001149 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 908937001150 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 908937001151 active site 908937001152 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 908937001153 dimer interface [polypeptide binding]; other site 908937001154 catalytic residues [active] 908937001155 substrate binding site [chemical binding]; other site 908937001156 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 908937001157 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 908937001158 dimer interface [polypeptide binding]; other site 908937001159 ssDNA binding site [nucleotide binding]; other site 908937001160 tetramer (dimer of dimers) interface [polypeptide binding]; other site 908937001161 gliding motility-associated protein GldE; Region: GldE; TIGR03520 908937001162 Domain of unknown function DUF21; Region: DUF21; pfam01595 908937001163 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 908937001164 Transporter associated domain; Region: CorC_HlyC; smart01091 908937001165 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 908937001166 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 908937001167 gliding motility-associated lipoprotein GldB; Region: GldB_lipo; TIGR03514 908937001168 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 908937001169 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 908937001170 Transglutaminase-like superfamily; Region: Transglut_core; cl17362 908937001171 Domain of Unknown Function with PDB structure (DUF3857); Region: DUF3857; pfam12969 908937001172 tryptophan synthase subunit beta; Reviewed; Region: PRK12391 908937001173 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 908937001174 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 908937001175 catalytic residue [active] 908937001176 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937001177 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937001178 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937001179 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 908937001180 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 908937001181 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 908937001182 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 908937001183 catalytic residues [active] 908937001184 dimer interface [polypeptide binding]; other site 908937001185 Lipocalin-like domain; Region: Lipocalin_4; pfam13648 908937001186 Domain of unknown function (DUF718); Region: DUF718; pfam05336 908937001187 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 908937001188 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 908937001189 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 908937001190 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 908937001191 Inorganic H+ pyrophosphatase; Region: H_PPase; pfam03030 908937001192 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 908937001193 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 908937001194 homodimer interface [polypeptide binding]; other site 908937001195 substrate-cofactor binding pocket; other site 908937001196 catalytic residue [active] 908937001197 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 908937001198 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 908937001199 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 908937001200 generic binding surface II; other site 908937001201 generic binding surface I; other site 908937001202 Peptidase S8 family domain, uncharacterized subfamily 9; Region: Peptidases_S8_9; cd07493 908937001203 active site 908937001204 catalytic triad [active] 908937001205 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 908937001206 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 908937001207 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 908937001208 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 908937001209 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 908937001210 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 908937001211 ATP-grasp domain; Region: ATP-grasp; pfam02222 908937001212 WxcM-like, C-terminal; Region: FdtA; pfam05523 908937001213 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 908937001214 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 908937001215 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 908937001216 inhibitor-cofactor binding pocket; inhibition site 908937001217 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937001218 catalytic residue [active] 908937001219 DNA topoisomerase III; Provisional; Region: PRK07726 908937001220 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 908937001221 active site 908937001222 putative interdomain interaction site [polypeptide binding]; other site 908937001223 putative metal-binding site [ion binding]; other site 908937001224 putative nucleotide binding site [chemical binding]; other site 908937001225 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 908937001226 domain I; other site 908937001227 DNA binding groove [nucleotide binding] 908937001228 phosphate binding site [ion binding]; other site 908937001229 domain II; other site 908937001230 domain III; other site 908937001231 nucleotide binding site [chemical binding]; other site 908937001232 catalytic site [active] 908937001233 domain IV; other site 908937001234 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 908937001235 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 908937001236 ABC-2 type transporter; Region: ABC2_membrane; cl17235 908937001237 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 908937001238 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 908937001239 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 908937001240 HlyD family secretion protein; Region: HlyD_3; pfam13437 908937001241 Outer membrane efflux protein; Region: OEP; pfam02321 908937001242 Outer membrane efflux protein; Region: OEP; pfam02321 908937001243 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 908937001244 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 908937001245 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 908937001246 active site 908937001247 Repair protein; Region: Repair_PSII; pfam04536 908937001248 LemA family; Region: LemA; cl00742 908937001249 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 908937001250 N-acetyl-D-glucosamine binding site [chemical binding]; other site 908937001251 catalytic residue [active] 908937001252 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 908937001253 active site 908937001254 catalytic triad [active] 908937001255 oxyanion hole [active] 908937001256 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 908937001257 active site 908937001258 DHH family; Region: DHH; pfam01368 908937001259 phosphoglucosamine mutase; Region: Arch_GlmM; TIGR03990 908937001260 The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine...; Region: phosphohexomutase; cl03757 908937001261 active site 908937001262 substrate binding site [chemical binding]; other site 908937001263 metal binding site [ion binding]; metal-binding site 908937001264 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 908937001265 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937001266 Walker A/P-loop; other site 908937001267 ATP binding site [chemical binding]; other site 908937001268 Q-loop/lid; other site 908937001269 ABC transporter signature motif; other site 908937001270 Walker B; other site 908937001271 D-loop; other site 908937001272 H-loop/switch region; other site 908937001273 ABC transporter; Region: ABC_tran_2; pfam12848 908937001274 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 908937001275 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 908937001276 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 908937001277 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 908937001278 dimer interface [polypeptide binding]; other site 908937001279 motif 1; other site 908937001280 active site 908937001281 motif 2; other site 908937001282 motif 3; other site 908937001283 Domain of unknown function (DUF4348); Region: DUF4348; pfam14254 908937001284 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 908937001285 FAD binding domain; Region: FAD_binding_4; pfam01565 908937001286 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 908937001287 putative hydrolase; Provisional; Region: PRK02113 908937001288 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 908937001289 Predicted acetyltransferase [General function prediction only]; Region: COG2388 908937001290 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_ox_2; pfam12900 908937001291 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 908937001292 dimer interface [polypeptide binding]; other site 908937001293 ADP-ribose binding site [chemical binding]; other site 908937001294 active site 908937001295 nudix motif; other site 908937001296 metal binding site [ion binding]; metal-binding site 908937001297 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 908937001298 RNA polymerase sigma factor, cyanobacterial RpoD-like family; Region: Sig70-cyanoRpoD; TIGR02997 908937001299 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937001300 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 908937001301 Sigma-70, region 4; Region: Sigma70_r4; pfam04545 908937001302 DNA binding residues [nucleotide binding] 908937001303 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 908937001304 TRAM domain; Region: TRAM; cl01282 908937001305 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 908937001306 S-adenosylmethionine binding site [chemical binding]; other site 908937001307 pyruvate phosphate dikinase; Provisional; Region: PRK09279 908937001308 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 908937001309 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 908937001310 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 908937001311 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 908937001312 dimer interface [polypeptide binding]; other site 908937001313 active site 908937001314 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14971 908937001315 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 908937001316 Walker A motif; other site 908937001317 ATP binding site [chemical binding]; other site 908937001318 Walker B motif; other site 908937001319 arginine finger; other site 908937001320 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 908937001321 Septum formation initiator; Region: DivIC; pfam04977 908937001322 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 908937001323 dihydroorotase; Reviewed; Region: PRK09236 908937001324 Amidohydrolase; Region: Amidohydro_5; pfam13594 908937001325 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 908937001326 active site 908937001327 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 908937001328 phosphodiesterase YaeI; Provisional; Region: PRK11340 908937001329 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 908937001330 putative active site [active] 908937001331 putative metal binding site [ion binding]; other site 908937001332 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 908937001333 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 908937001334 putative acyl-acceptor binding pocket; other site 908937001335 DPM1_like represents putative enzymes similar to eukaryotic DPM1; Region: DPM1_like; cd06442 908937001336 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 908937001337 Ligand binding site; other site 908937001338 Putative Catalytic site; other site 908937001339 DXD motif; other site 908937001340 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 908937001341 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 908937001342 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 908937001343 ATP binding site [chemical binding]; other site 908937001344 putative Mg++ binding site [ion binding]; other site 908937001345 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 908937001346 nucleotide binding region [chemical binding]; other site 908937001347 ATP-binding site [chemical binding]; other site 908937001348 TRCF domain; Region: TRCF; pfam03461 908937001349 Major Facilitator Superfamily; Region: MFS_1; pfam07690 908937001350 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 908937001351 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 908937001352 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 908937001353 membrane protein insertase; Provisional; Region: PRK01318 908937001354 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 908937001355 CTP synthetase; Validated; Region: pyrG; PRK05380 908937001356 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 908937001357 Catalytic site [active] 908937001358 active site 908937001359 UTP binding site [chemical binding]; other site 908937001360 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 908937001361 active site 908937001362 putative oxyanion hole; other site 908937001363 catalytic triad [active] 908937001364 Protein of unknown function (DUF3078); Region: DUF3078; pfam11276 908937001365 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937001366 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 908937001367 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 908937001368 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 908937001369 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 908937001370 FMN binding site [chemical binding]; other site 908937001371 dimer interface [polypeptide binding]; other site 908937001372 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 908937001373 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 908937001374 Maf-like protein; Region: Maf; pfam02545 908937001375 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 908937001376 active site 908937001377 dimer interface [polypeptide binding]; other site 908937001378 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 908937001379 Sulfatase; Region: Sulfatase; pfam00884 908937001380 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 908937001381 L-fucose transporter; Provisional; Region: PRK10133; cl17665 908937001382 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 908937001383 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 908937001384 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 908937001385 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 908937001386 NodB motif; other site 908937001387 active site 908937001388 catalytic site [active] 908937001389 metal binding site [ion binding]; metal-binding site 908937001390 Protein of unknown function (DUF2723); Region: DUF2723; pfam11028 908937001391 HD domain; Region: HD_4; pfam13328 908937001392 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 908937001393 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 908937001394 synthetase active site [active] 908937001395 NTP binding site [chemical binding]; other site 908937001396 metal binding site [ion binding]; metal-binding site 908937001397 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 908937001398 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 908937001399 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 908937001400 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 908937001401 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 908937001402 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_1; cd04870 908937001403 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_2; cd04871 908937001404 phosphoserine phosphatase SerB; Region: serB; TIGR00338 908937001405 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 908937001406 motif II; other site 908937001407 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 908937001408 Protein of unknown function (DUF1044); Region: DUF1044; cl01955 908937001409 Protein of unknown function (DUF1460); Region: DUF1460; pfam07313 908937001410 Domain of unknown function (DUF4421); Region: DUF4421; pfam14391 908937001411 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 908937001412 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 908937001413 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 908937001414 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 908937001415 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 908937001416 Malic enzyme, N-terminal domain; Region: malic; pfam00390 908937001417 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 908937001418 putative NAD(P) binding site [chemical binding]; other site 908937001419 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 908937001420 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 908937001421 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 908937001422 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 908937001423 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 908937001424 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 908937001425 acyl-activating enzyme (AAE) consensus motif; other site 908937001426 putative AMP binding site [chemical binding]; other site 908937001427 putative active site [active] 908937001428 putative CoA binding site [chemical binding]; other site 908937001429 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 908937001430 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 908937001431 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 908937001432 acyl-activating enzyme (AAE) consensus motif; other site 908937001433 AMP binding site [chemical binding]; other site 908937001434 active site 908937001435 CoA binding site [chemical binding]; other site 908937001436 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 908937001437 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 908937001438 FtsX-like permease family; Region: FtsX; pfam02687 908937001439 aspartate aminotransferase; Provisional; Region: PRK07568 908937001440 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 908937001441 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937001442 homodimer interface [polypeptide binding]; other site 908937001443 catalytic residue [active] 908937001444 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 908937001445 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 908937001446 ligand binding site [chemical binding]; other site 908937001447 flexible hinge region; other site 908937001448 GTP-binding protein LepA; Provisional; Region: PRK05433 908937001449 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 908937001450 G1 box; other site 908937001451 putative GEF interaction site [polypeptide binding]; other site 908937001452 GTP/Mg2+ binding site [chemical binding]; other site 908937001453 Switch I region; other site 908937001454 G2 box; other site 908937001455 G3 box; other site 908937001456 Switch II region; other site 908937001457 G4 box; other site 908937001458 G5 box; other site 908937001459 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 908937001460 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 908937001461 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 908937001462 hypothetical protein; Provisional; Region: PRK12378 908937001463 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 908937001464 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 908937001465 putative tRNA-binding site [nucleotide binding]; other site 908937001466 B3/4 domain; Region: B3_4; pfam03483 908937001467 tRNA synthetase B5 domain; Region: B5; pfam03484 908937001468 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 908937001469 dimer interface [polypeptide binding]; other site 908937001470 motif 1; other site 908937001471 motif 3; other site 908937001472 motif 2; other site 908937001473 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 908937001474 Predicted membrane protein [Function unknown]; Region: COG2860 908937001475 UPF0126 domain; Region: UPF0126; pfam03458 908937001476 UPF0126 domain; Region: UPF0126; pfam03458 908937001477 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 908937001478 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 908937001479 putative ligand binding site [chemical binding]; other site 908937001480 putative NAD binding site [chemical binding]; other site 908937001481 catalytic site [active] 908937001482 recombination factor protein RarA; Reviewed; Region: PRK13342 908937001483 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 908937001484 Walker A motif; other site 908937001485 ATP binding site [chemical binding]; other site 908937001486 Walker B motif; other site 908937001487 arginine finger; other site 908937001488 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 908937001489 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 908937001490 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 908937001491 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 908937001492 putative CoA binding site [chemical binding]; other site 908937001493 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 908937001494 trimer interface [polypeptide binding]; other site 908937001495 active site 908937001496 UDP-GlcNAc binding site [chemical binding]; other site 908937001497 lipid binding site [chemical binding]; lipid-binding site 908937001498 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed; Region: PRK13188 908937001499 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 908937001500 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 908937001501 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 908937001502 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 908937001503 active site 908937001504 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 908937001505 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 908937001506 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 908937001507 Transglycosylase; Region: Transgly; pfam00912 908937001508 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 908937001509 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 908937001510 metal binding site 2 [ion binding]; metal-binding site 908937001511 putative DNA binding helix; other site 908937001512 metal binding site 1 [ion binding]; metal-binding site 908937001513 dimer interface [polypeptide binding]; other site 908937001514 structural Zn2+ binding site [ion binding]; other site 908937001515 Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are...; Region: Rhamnogalacturan_acetylesterase_like; cd01821 908937001516 active site 908937001517 catalytic triad [active] 908937001518 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 908937001519 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 908937001520 dimer interface [polypeptide binding]; other site 908937001521 motif 1; other site 908937001522 active site 908937001523 motif 2; other site 908937001524 motif 3; other site 908937001525 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 908937001526 anticodon binding site; other site 908937001527 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 908937001528 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 908937001529 GDP-binding site [chemical binding]; other site 908937001530 ACT binding site; other site 908937001531 IMP binding site; other site 908937001532 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 908937001533 metal binding site 2 [ion binding]; metal-binding site 908937001534 putative DNA binding helix; other site 908937001535 metal binding site 1 [ion binding]; metal-binding site 908937001536 dimer interface [polypeptide binding]; other site 908937001537 structural Zn2+ binding site [ion binding]; other site 908937001538 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 908937001539 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 908937001540 catalytic residue [active] 908937001541 Initiator Replication protein; Region: Rep_3; pfam01051 908937001542 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 908937001543 Uncharacterized conserved protein [Function unknown]; Region: COG4198 908937001544 Protein of unknown function (DUF1015); Region: DUF1015; pfam06245 908937001545 Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_like_3; cd12174 908937001546 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 908937001547 putative ligand binding site [chemical binding]; other site 908937001548 putative NAD binding site [chemical binding]; other site 908937001549 putative catalytic site [active] 908937001550 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 908937001551 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 908937001552 catalytic residue [active] 908937001553 DEAD-like helicases superfamily; Region: DEXDc; smart00487 908937001554 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 908937001555 ATP binding site [chemical binding]; other site 908937001556 putative Mg++ binding site [ion binding]; other site 908937001557 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 908937001558 nucleotide binding region [chemical binding]; other site 908937001559 ATP-binding site [chemical binding]; other site 908937001560 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 908937001561 RNA binding site [nucleotide binding]; other site 908937001562 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 908937001563 binding surface 908937001564 TPR motif; other site 908937001565 TPR repeat; Region: TPR_11; pfam13414 908937001566 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937001567 SusD family; Region: SusD; pfam07980 908937001568 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937001569 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937001570 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937001571 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937001572 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 908937001573 Quinolinate phosphoribosyl transferase, N-terminal domain; Region: QRPTase_N; pfam02749 908937001574 2',3'-cyclic-nucleotide 2'-phosphodiesterase; Region: CycNucDiestase; TIGR01390 908937001575 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 908937001576 active site 908937001577 metal binding site [ion binding]; metal-binding site 908937001578 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 908937001579 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 908937001580 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 908937001581 putative NADH binding site [chemical binding]; other site 908937001582 putative active site [active] 908937001583 nudix motif; other site 908937001584 putative metal binding site [ion binding]; other site 908937001585 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 908937001586 putative transporter; Validated; Region: PRK03818 908937001587 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 908937001588 TrkA-C domain; Region: TrkA_C; pfam02080 908937001589 TrkA-C domain; Region: TrkA_C; pfam02080 908937001590 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 908937001591 Sporulation related domain; Region: SPOR; pfam05036 908937001592 phosphopeptide binding site; other site 908937001593 FHA domain; Region: FHA; pfam00498 908937001594 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 908937001595 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 908937001596 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 908937001597 putative active site [active] 908937001598 putative substrate binding site [chemical binding]; other site 908937001599 putative cosubstrate binding site; other site 908937001600 catalytic site [active] 908937001601 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13181 908937001602 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 908937001603 putative active site [active] 908937001604 oxyanion strand; other site 908937001605 catalytic triad [active] 908937001606 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1...; Region: HisA; cd04732 908937001607 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 908937001608 catalytic residues [active] 908937001609 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 908937001610 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 908937001611 substrate binding site [chemical binding]; other site 908937001612 glutamase interaction surface [polypeptide binding]; other site 908937001613 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 908937001614 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]; Region: HisI; COG0139 908937001615 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 908937001616 metal binding site [ion binding]; metal-binding site 908937001617 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937001618 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 908937001619 Walker A/P-loop; other site 908937001620 ATP binding site [chemical binding]; other site 908937001621 Q-loop/lid; other site 908937001622 ABC transporter signature motif; other site 908937001623 Walker B; other site 908937001624 D-loop; other site 908937001625 H-loop/switch region; other site 908937001626 aspartate kinase III; Validated; Region: PRK09084 908937001627 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 908937001628 nucleotide binding site [chemical binding]; other site 908937001629 substrate binding site [chemical binding]; other site 908937001630 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC-like_1; cd04912 908937001631 dimer interface [polypeptide binding]; other site 908937001632 allosteric regulatory binding pocket; other site 908937001633 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 908937001634 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 908937001635 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 908937001636 active site 908937001637 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 908937001638 substrate binding site [chemical binding]; other site 908937001639 catalytic residues [active] 908937001640 dimer interface [polypeptide binding]; other site 908937001641 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 908937001642 active site 908937001643 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 908937001644 Firmicute fructose-1,6-bisphosphatase; Region: FBPase_2; pfam06874 908937001645 Domain of unknown function (DUF3127); Region: DUF3127; pfam11325 908937001646 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 908937001647 DNA polymerase III subunit beta; Validated; Region: PRK05643 908937001648 putative DNA binding surface [nucleotide binding]; other site 908937001649 dimer interface [polypeptide binding]; other site 908937001650 beta-clamp/clamp loader binding surface; other site 908937001651 beta-clamp/translesion DNA polymerase binding surface; other site 908937001652 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 908937001653 active site 908937001654 catalytic site [active] 908937001655 substrate binding site [chemical binding]; other site 908937001656 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 908937001657 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 908937001658 Walker A/P-loop; other site 908937001659 ATP binding site [chemical binding]; other site 908937001660 Q-loop/lid; other site 908937001661 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 908937001662 ABC transporter signature motif; other site 908937001663 Walker B; other site 908937001664 D-loop; other site 908937001665 H-loop/switch region; other site 908937001666 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 908937001667 Anaphase-promoting complex, cyclosome, subunit 3; Region: Apc3; pfam12895 908937001668 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 908937001669 binding surface 908937001670 TPR motif; other site 908937001671 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 908937001672 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 908937001673 S-adenosylmethionine binding site [chemical binding]; other site 908937001674 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 908937001675 IHF - DNA interface [nucleotide binding]; other site 908937001676 IHF dimer interface [polypeptide binding]; other site 908937001677 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 908937001678 IHF - DNA interface [nucleotide binding]; other site 908937001679 IHF dimer interface [polypeptide binding]; other site 908937001680 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 908937001681 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 908937001682 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 908937001683 FeS/SAM binding site; other site 908937001684 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 908937001685 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 908937001686 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 908937001687 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 908937001688 Part of AAA domain; Region: AAA_19; pfam13245 908937001689 Family description; Region: UvrD_C_2; pfam13538 908937001690 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 908937001691 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 908937001692 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 908937001693 Clp amino terminal domain; Region: Clp_N; pfam02861 908937001694 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 908937001695 Walker A motif; other site 908937001696 ATP binding site [chemical binding]; other site 908937001697 Walker B motif; other site 908937001698 arginine finger; other site 908937001699 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 908937001700 Walker A motif; other site 908937001701 ATP binding site [chemical binding]; other site 908937001702 Walker B motif; other site 908937001703 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 908937001704 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 908937001705 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 908937001706 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 908937001707 TM1410 hypothetical-related protein; Region: DUF297; cl00997 908937001708 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 908937001709 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 908937001710 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 908937001711 G1 box; other site 908937001712 GTP/Mg2+ binding site [chemical binding]; other site 908937001713 Switch I region; other site 908937001714 G2 box; other site 908937001715 G3 box; other site 908937001716 Switch II region; other site 908937001717 G4 box; other site 908937001718 G5 box; other site 908937001719 Nucleoside recognition; Region: Gate; pfam07670 908937001720 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 908937001721 Nucleoside recognition; Region: Gate; pfam07670 908937001722 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 908937001723 Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes; Region: Motor_domain; cl00286 908937001724 ATP-binding site [chemical binding]; other site 908937001725 PhoH-like protein; Region: PhoH; pfam02562 908937001726 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 908937001727 ATP binding site [chemical binding]; other site 908937001728 active site 908937001729 substrate binding site [chemical binding]; other site 908937001730 Shikimate 5-dehydrogenase [Amino acid transport and metabolism]; Region: AroE; COG0169 908937001731 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 908937001732 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 908937001733 shikimate binding site; other site 908937001734 NAD(P) binding site [chemical binding]; other site 908937001735 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 908937001736 dimerization interface [polypeptide binding]; other site 908937001737 ATP binding site [chemical binding]; other site 908937001738 peptide chain release factor 1; Validated; Region: prfA; PRK00591 908937001739 This domain is found in peptide chain release factors; Region: PCRF; smart00937 908937001740 RF-1 domain; Region: RF-1; pfam00472 908937001741 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 908937001742 active site 908937001743 dimer interface [polypeptide binding]; other site 908937001744 Protein of unknown function (DUF2582); Region: DUF2582; pfam10771 908937001745 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 908937001746 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 908937001747 Coenzyme A binding pocket [chemical binding]; other site 908937001748 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 908937001749 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 908937001750 Probable Catalytic site; other site 908937001751 metal-binding site 908937001752 recombination protein RecR; Reviewed; Region: recR; PRK00076 908937001753 RecR protein; Region: RecR; pfam02132 908937001754 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 908937001755 putative active site [active] 908937001756 putative metal-binding site [ion binding]; other site 908937001757 tetramer interface [polypeptide binding]; other site 908937001758 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 908937001759 Carbon starvation protein CstA; Region: CstA; pfam02554 908937001760 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 908937001761 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 908937001762 Carbon starvation protein CstA; Region: CstA; pfam02554 908937001763 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 908937001764 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 908937001765 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 908937001766 active site 908937001767 catalytic motif [active] 908937001768 Zn binding site [ion binding]; other site 908937001769 Right handed beta helix region; Region: Beta_helix; pfam13229 908937001770 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 908937001771 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 908937001772 motif II; other site 908937001773 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 908937001774 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 908937001775 S-adenosylmethionine binding site [chemical binding]; other site 908937001776 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 908937001777 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 908937001778 active site 908937001779 putative DNA-binding cleft [nucleotide binding]; other site 908937001780 dimer interface [polypeptide binding]; other site 908937001781 putative molybdenum transport ATP-binding protein ModF; Provisional; Region: PRK10938 908937001782 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937001783 Walker A/P-loop; other site 908937001784 ATP binding site [chemical binding]; other site 908937001785 Q-loop/lid; other site 908937001786 ABC transporter signature motif; other site 908937001787 Walker B; other site 908937001788 D-loop; other site 908937001789 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937001790 Walker A/P-loop; other site 908937001791 ATP binding site [chemical binding]; other site 908937001792 Q-loop/lid; other site 908937001793 ABC transporter signature motif; other site 908937001794 Walker B; other site 908937001795 D-loop; other site 908937001796 H-loop/switch region; other site 908937001797 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 908937001798 catalytic site [active] 908937001799 putative active site [active] 908937001800 putative substrate binding site [chemical binding]; other site 908937001801 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 908937001802 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 908937001803 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 908937001804 putative RNA binding site [nucleotide binding]; other site 908937001805 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 908937001806 S-adenosylmethionine binding site [chemical binding]; other site 908937001807 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 908937001808 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 908937001809 Ligand Binding Site [chemical binding]; other site 908937001810 TilS substrate C-terminal domain; Region: TilS_C; smart00977 908937001811 Domain of unknown function (DUF4301); Region: DUF4301; pfam14134 908937001812 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 908937001813 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 908937001814 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 908937001815 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 908937001816 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 908937001817 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 908937001818 RNA binding surface [nucleotide binding]; other site 908937001819 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 908937001820 active site 908937001821 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937001822 Walker A/P-loop; other site 908937001823 ATP binding site [chemical binding]; other site 908937001824 ABC transporter; Region: ABC_tran; pfam00005 908937001825 Q-loop/lid; other site 908937001826 ABC transporter signature motif; other site 908937001827 Walker B; other site 908937001828 D-loop; other site 908937001829 H-loop/switch region; other site 908937001830 RNA methyltransferase, RsmE family; Region: TIGR00046 908937001831 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 908937001832 UvrB/uvrC motif; Region: UVR; pfam02151 908937001833 nucleoside transporter; Region: 2A0110; TIGR00889 908937001834 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937001835 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937001836 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937001837 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937001838 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937001839 Protein of unknown function (DUF3256); Region: DUF3256; pfam11644 908937001840 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 908937001841 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 908937001842 N-acetyl-D-glucosamine binding site [chemical binding]; other site 908937001843 catalytic residue [active] 908937001844 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 908937001845 ATP phosphoribosyltransferase; Region: hisG; TIGR00070 908937001846 ATP phosphoribosyltransferase, C-terminal domain; Region: HisG_C-term; TIGR03455 908937001847 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 908937001848 histidinol dehydrogenase; Region: hisD; TIGR00069 908937001849 NAD binding site [chemical binding]; other site 908937001850 dimerization interface [polypeptide binding]; other site 908937001851 product binding site; other site 908937001852 substrate binding site [chemical binding]; other site 908937001853 zinc binding site [ion binding]; other site 908937001854 catalytic residues [active] 908937001855 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 908937001856 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 908937001857 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937001858 homodimer interface [polypeptide binding]; other site 908937001859 catalytic residue [active] 908937001860 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]; Region: GlgB; COG0296 908937001861 N-terminal Early set domain associated with the catalytic domain of eukaryotic glycogen branching enzyme (also called 1,4 alpha glucan branching enzyme); Region: E_set_GBE_euk_N; cd02854 908937001862 Alpha amylase catalytic domain found in bacterial and eukaryotic branching enzymes; Region: AmyAc_bac_euk_BE; cd11321 908937001863 active site 908937001864 catalytic site [active] 908937001865 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 908937001866 Domain of unknown function (DUF386); Region: DUF386; cl01047 908937001867 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4642 908937001868 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4642 908937001869 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 908937001870 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 908937001871 Ligand binding site; other site 908937001872 oligomer interface; other site 908937001873 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 908937001874 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 908937001875 HSP70 interaction site [polypeptide binding]; other site 908937001876 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 908937001877 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 908937001878 dimer interface [polypeptide binding]; other site 908937001879 30S ribosomal protein S16; Provisional; Region: rpsP; PRK14521 908937001880 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 908937001881 UDP-glucose 4-epimerase; Region: PLN02240 908937001882 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 908937001883 NAD binding site [chemical binding]; other site 908937001884 homodimer interface [polypeptide binding]; other site 908937001885 active site 908937001886 substrate binding site [chemical binding]; other site 908937001887 electron transport complex, RnfABCDGE type, A subunit; Region: rnfA; TIGR01943 908937001888 electron transport complex RsxE subunit; Provisional; Region: PRK12405 908937001889 FMN-binding domain; Region: FMN_bind; cl01081 908937001890 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 908937001891 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 908937001892 SLBB domain; Region: SLBB; pfam10531 908937001893 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 908937001894 ferredoxin; Validated; Region: PRK07118 908937001895 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 908937001896 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 908937001897 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 908937001898 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 908937001899 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 908937001900 ligand binding site [chemical binding]; other site 908937001901 Reovirus sigma C capsid protein; Region: Reo_sigmaC; pfam04582 908937001902 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 908937001903 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 908937001904 RNA polymerase sigma factor, cyanobacterial RpoD-like family; Region: Sig70-cyanoRpoD; TIGR02997 908937001905 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937001906 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 908937001907 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 908937001908 DNA binding residues [nucleotide binding] 908937001909 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 908937001910 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 908937001911 NTPase; Region: NTPase_1; cl17478 908937001912 AAA domain; Region: AAA_28; pfam13521 908937001913 CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases; Region: CYTH-like_Pase; cl11964 908937001914 putative active site; other site 908937001915 putative metal binding residues [ion binding]; other site 908937001916 putative triphosphate binding site [ion binding]; other site 908937001917 signature motif; other site 908937001918 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 908937001919 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 908937001920 Substrate-binding site [chemical binding]; other site 908937001921 Substrate specificity [chemical binding]; other site 908937001922 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 908937001923 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 908937001924 Substrate-binding site [chemical binding]; other site 908937001925 Substrate specificity [chemical binding]; other site 908937001926 Catalytic domain of Protein Kinases; Region: PKc; cd00180 908937001927 active site 908937001928 ATP binding site [chemical binding]; other site 908937001929 substrate binding site [chemical binding]; other site 908937001930 activation loop (A-loop); other site 908937001931 Domain of unknown function (DUF3943); Region: DUF3943; pfam13084 908937001932 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 908937001933 TPR motif; other site 908937001934 binding surface 908937001935 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 908937001936 enolase; Provisional; Region: eno; PRK00077 908937001937 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 908937001938 dimer interface [polypeptide binding]; other site 908937001939 metal binding site [ion binding]; metal-binding site 908937001940 substrate binding pocket [chemical binding]; other site 908937001941 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 908937001942 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 908937001943 motif II; other site 908937001944 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 908937001945 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 908937001946 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 908937001947 Rubredoxin [Energy production and conversion]; Region: COG1773 908937001948 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 908937001949 iron binding site [ion binding]; other site 908937001950 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 908937001951 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 908937001952 Walker A/P-loop; other site 908937001953 ATP binding site [chemical binding]; other site 908937001954 Q-loop/lid; other site 908937001955 ABC transporter signature motif; other site 908937001956 Walker B; other site 908937001957 D-loop; other site 908937001958 H-loop/switch region; other site 908937001959 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 908937001960 FtsX-like permease family; Region: FtsX; pfam02687 908937001961 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 908937001962 FtsX-like permease family; Region: FtsX; pfam02687 908937001963 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 908937001964 Acidobacterial duplicated orphan permease; Region: ADOP; TIGR03434 908937001965 FtsX-like permease family; Region: FtsX; pfam02687 908937001966 FtsX-like permease family; Region: FtsX; pfam02687 908937001967 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 908937001968 Fusion glycoprotein F0; Region: Fusion_gly; pfam00523 908937001969 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 908937001970 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 908937001971 HlyD family secretion protein; Region: HlyD_3; pfam13437 908937001972 Outer membrane efflux protein; Region: OEP; pfam02321 908937001973 Outer membrane efflux protein; Region: OEP; pfam02321 908937001974 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 908937001975 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 908937001976 active site 908937001977 phosphorylation site [posttranslational modification] 908937001978 intermolecular recognition site; other site 908937001979 dimerization interface [polypeptide binding]; other site 908937001980 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 908937001981 Walker A motif; other site 908937001982 ATP binding site [chemical binding]; other site 908937001983 Walker B motif; other site 908937001984 arginine finger; other site 908937001985 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 908937001986 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 908937001987 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 908937001988 ATP binding site [chemical binding]; other site 908937001989 Mg2+ binding site [ion binding]; other site 908937001990 G-X-G motif; other site 908937001991 N-terminal domain of glycoside hydrolase family 94 and related domains; Region: GH94N_like; cl17067 908937001992 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; pfam05592 908937001993 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 908937001994 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 908937001995 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 908937001996 acyl-activating enzyme (AAE) consensus motif; other site 908937001997 AMP binding site [chemical binding]; other site 908937001998 active site 908937001999 CoA binding site [chemical binding]; other site 908937002000 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937002001 TIGR02646 family protein; Region: TIGR02646 908937002002 Predicted ATP-binding protein involved in virulence [General function prediction only]; Region: COG3950 908937002003 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937002004 Walker A/P-loop; other site 908937002005 ATP binding site [chemical binding]; other site 908937002006 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 908937002007 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 908937002008 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 908937002009 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 908937002010 cation binding site [ion binding]; other site 908937002011 Probable polygalacturonase At3g15720; Region: PLN03003; cl14103 908937002012 Pectate lyase superfamily protein; Region: Pectate_lyase_3; pfam12708 908937002013 CrcB-like protein; Region: CRCB; cl09114 908937002014 Rubrerythrin [Energy production and conversion]; Region: COG1592 908937002015 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 908937002016 iron binding site [ion binding]; other site 908937002017 Rubrerythrin [Energy production and conversion]; Region: COG1592 908937002018 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 908937002019 binuclear metal center [ion binding]; other site 908937002020 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 908937002021 iron binding site [ion binding]; other site 908937002022 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 908937002023 active site 908937002024 muropeptide transporter; Reviewed; Region: ampG; PRK11902 908937002025 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 908937002026 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 908937002027 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 908937002028 nucleotide binding site [chemical binding]; other site 908937002029 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: murQ; PRK05441 908937002030 N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid...; Region: SIS_Etherase; cd05007 908937002031 putative active site [active] 908937002032 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 908937002033 putative active site [active] 908937002034 putative catalytic site [active] 908937002035 Helix-turn-helix domain; Region: HTH_18; pfam12833 908937002036 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937002037 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 908937002038 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937002039 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 908937002040 DNA binding residues [nucleotide binding] 908937002041 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK12315 908937002042 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 908937002043 TPP-binding site; other site 908937002044 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 908937002045 PYR/PP interface [polypeptide binding]; other site 908937002046 dimer interface [polypeptide binding]; other site 908937002047 TPP binding site [chemical binding]; other site 908937002048 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 908937002049 FMN-binding domain; Region: FMN_bind; pfam04205 908937002050 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 908937002051 4Fe-4S binding domain; Region: Fer4_5; pfam12801 908937002052 NAD(P)H:flavin oxidoreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes; Region: NADPH_oxidoreductase_1; cd02150 908937002053 putative FMN binding site [chemical binding]; other site 908937002054 CAAX protease self-immunity; Region: Abi; pfam02517 908937002055 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 908937002056 Transglycosylase; Region: Transgly; pfam00912 908937002057 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 908937002058 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 908937002059 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 908937002060 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 908937002061 aspartate carbamoyltransferase regulatory subunit; Reviewed; Region: PRK00893 908937002062 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 908937002063 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 908937002064 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 908937002065 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 908937002066 dimer interface [polypeptide binding]; other site 908937002067 active site 908937002068 glycine-pyridoxal phosphate binding site [chemical binding]; other site 908937002069 folate binding site [chemical binding]; other site 908937002070 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 908937002071 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 908937002072 SmpB-tmRNA interface; other site 908937002073 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 908937002074 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 908937002075 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Region: MetH; COG1410 908937002076 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 908937002077 substrate binding pocket [chemical binding]; other site 908937002078 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 908937002079 B12 binding site [chemical binding]; other site 908937002080 cobalt ligand [ion binding]; other site 908937002081 methionine aminopeptidase; Provisional; Region: PRK12318 908937002082 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 908937002083 active site 908937002084 UGMP family protein; Validated; Region: PRK09604 908937002085 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 908937002086 Competence-damaged protein; Region: CinA; pfam02464 908937002087 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 908937002088 catalytic residues [active] 908937002089 dimer interface [polypeptide binding]; other site 908937002090 Transcriptional regulators [Transcription]; Region: MarR; COG1846 908937002091 MarR family; Region: MarR; pfam01047 908937002092 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 908937002093 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 908937002094 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 908937002095 FeS/SAM binding site; other site 908937002096 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 908937002097 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 908937002098 Probable Catalytic site; other site 908937002099 metal-binding site 908937002100 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; smart00471 908937002101 Zn2+ binding site [ion binding]; other site 908937002102 Mg2+ binding site [ion binding]; other site 908937002103 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 908937002104 UbiA prenyltransferase family; Region: UbiA; pfam01040 908937002105 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 908937002106 tartrate dehydrogenase; Region: TTC; TIGR02089 908937002107 (R)-citramalate synthase; Provisional; Region: PRK09389 908937002108 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 908937002109 active site 908937002110 catalytic residues [active] 908937002111 metal binding site [ion binding]; metal-binding site 908937002112 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; pfam08502 908937002113 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 908937002114 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 908937002115 substrate binding site [chemical binding]; other site 908937002116 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 908937002117 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 908937002118 substrate binding site [chemical binding]; other site 908937002119 ligand binding site [chemical binding]; other site 908937002120 2-isopropylmalate synthase; Validated; Region: PRK00915 908937002121 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 908937002122 active site 908937002123 catalytic residues [active] 908937002124 metal binding site [ion binding]; metal-binding site 908937002125 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; pfam08502 908937002126 replicative DNA helicase; Region: DnaB; TIGR00665 908937002127 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 908937002128 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 908937002129 Walker A motif; other site 908937002130 ATP binding site [chemical binding]; other site 908937002131 Walker B motif; other site 908937002132 DNA binding loops [nucleotide binding] 908937002133 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14609 908937002134 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 908937002135 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 908937002136 Subunit A of Class III extradiol dioxygenases; Region: Extradiol_Dioxygenase_3A_like; cl06673 908937002137 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 908937002138 ligand binding site [chemical binding]; other site 908937002139 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 908937002140 FecCD transport family; Region: FecCD; pfam01032 908937002141 ABC-ATPase subunit interface; other site 908937002142 dimer interface [polypeptide binding]; other site 908937002143 putative PBP binding regions; other site 908937002144 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 908937002145 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 908937002146 intersubunit interface [polypeptide binding]; other site 908937002147 Uncharacterized conserved protein [Function unknown]; Region: COG3391 908937002148 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 908937002149 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937002150 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 908937002151 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 908937002152 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 908937002153 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 908937002154 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 908937002155 phosphonoacetate hydrolase; Region: hydr_PhnA; TIGR02335 908937002156 mannonate dehydratase; Provisional; Region: PRK03906 908937002157 mannonate dehydratase; Region: uxuA; TIGR00695 908937002158 D-mannonate oxidoreductase; Provisional; Region: PRK08277 908937002159 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 908937002160 NAD(P) binding site [chemical binding]; other site 908937002161 active site 908937002162 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 908937002163 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 908937002164 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 908937002165 glutamate dehydrogenase; Provisional; Region: PRK14031 908937002166 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 908937002167 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 908937002168 NAD(P) binding site [chemical binding]; other site 908937002169 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 908937002170 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 908937002171 substrate-cofactor binding pocket; other site 908937002172 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937002173 catalytic residue [active] 908937002174 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 908937002175 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 908937002176 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 908937002177 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 908937002178 S-adenosylmethionine binding site [chemical binding]; other site 908937002179 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 908937002180 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 908937002181 Walker A motif; other site 908937002182 ATP binding site [chemical binding]; other site 908937002183 Walker B motif; other site 908937002184 arginine finger; other site 908937002185 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 908937002186 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 908937002187 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 908937002188 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 908937002189 Predicted permeases [General function prediction only]; Region: COG0795 908937002190 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 908937002191 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 908937002192 ATP binding site [chemical binding]; other site 908937002193 Mg++ binding site [ion binding]; other site 908937002194 motif III; other site 908937002195 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 908937002196 nucleotide binding region [chemical binding]; other site 908937002197 ATP-binding site [chemical binding]; other site 908937002198 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 908937002199 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 908937002200 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 908937002201 AAA domain; Region: AAA_14; pfam13173 908937002202 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 908937002203 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 908937002204 dimer interface [polypeptide binding]; other site 908937002205 PYR/PP interface [polypeptide binding]; other site 908937002206 TPP binding site [chemical binding]; other site 908937002207 substrate binding site [chemical binding]; other site 908937002208 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 908937002209 Domain of unknown function; Region: EKR; pfam10371 908937002210 4Fe-4S binding domain; Region: Fer4_6; pfam12837 908937002211 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 908937002212 TPP-binding site [chemical binding]; other site 908937002213 dimer interface [polypeptide binding]; other site 908937002214 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 908937002215 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 908937002216 active site 908937002217 nucleophile elbow; other site 908937002218 Aminopeptidase P, N-terminal domain; Region: AMP_N; smart01011 908937002219 proline aminopeptidase P II; Provisional; Region: PRK10879 908937002220 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 908937002221 active site 908937002222 Peptidase C1-like family; Region: Peptidase_C1_2; cl17447 908937002223 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 908937002224 DHH family; Region: DHH; pfam01368 908937002225 DHHA1 domain; Region: DHHA1; pfam02272 908937002226 Superfamily II DNA helicase [DNA replication, recombination, and repair]; Region: RecQ; COG0514 908937002227 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 908937002228 ATP binding site [chemical binding]; other site 908937002229 putative Mg++ binding site [ion binding]; other site 908937002230 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 908937002231 nucleotide binding region [chemical binding]; other site 908937002232 ATP-binding site [chemical binding]; other site 908937002233 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 908937002234 ketol-acid reductoisomerase; Region: ilvC; TIGR00465 908937002235 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 908937002236 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 908937002237 active site 908937002238 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 908937002239 active site 2 [active] 908937002240 Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]; Region: IlvH; COG0440 908937002241 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 908937002242 putative valine binding site [chemical binding]; other site 908937002243 dimer interface [polypeptide binding]; other site 908937002244 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 908937002245 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 908937002246 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 908937002247 PYR/PP interface [polypeptide binding]; other site 908937002248 dimer interface [polypeptide binding]; other site 908937002249 TPP binding site [chemical binding]; other site 908937002250 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 908937002251 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 908937002252 TPP-binding site [chemical binding]; other site 908937002253 dimer interface [polypeptide binding]; other site 908937002254 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 908937002255 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 908937002256 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 908937002257 ligand binding site [chemical binding]; other site 908937002258 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; pfam06964 908937002259 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14185 908937002260 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 908937002261 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 908937002262 homodimer interface [polypeptide binding]; other site 908937002263 NADP binding site [chemical binding]; other site 908937002264 substrate binding site [chemical binding]; other site 908937002265 signal recognition particle protein; Provisional; Region: PRK10867 908937002266 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 908937002267 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 908937002268 P loop; other site 908937002269 GTP binding site [chemical binding]; other site 908937002270 Signal peptide binding domain; Region: SRP_SPB; pfam02978 908937002271 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 908937002272 prephenate dehydrogenase; Validated; Region: PRK08507 908937002273 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 908937002274 Chorismate mutase type II; Region: CM_2; smart00830 908937002275 LL-diaminopimelate aminotransferase; Provisional; Region: PRK09276 908937002276 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 908937002277 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937002278 homodimer interface [polypeptide binding]; other site 908937002279 catalytic residue [active] 908937002280 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 908937002281 Prephenate dehydratase; Region: PDT; pfam00800 908937002282 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 908937002283 putative L-Phe binding site [chemical binding]; other site 908937002284 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 908937002285 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 908937002286 metal-binding site [ion binding] 908937002287 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 908937002288 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 908937002289 active site 908937002290 motif I; other site 908937002291 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 908937002292 motif II; other site 908937002293 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 908937002294 metal-binding site [ion binding] 908937002295 Uncharacterized protein conserved in Bacteroidetes; Region: Bacuni_01323_like; cd12871 908937002296 Copper chaperone [Inorganic ion transport and metabolism]; Region: CopZ; COG2608 908937002297 metal-binding site [ion binding] 908937002298 Helix-turn-helix domain; Region: HTH_18; pfam12833 908937002299 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937002300 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 908937002301 putative efflux protein, MATE family; Region: matE; TIGR00797 908937002302 methionine sulfoxide reductase B; Provisional; Region: PRK00222 908937002303 bifunctional methionine sulfoxide reductase B/A protein; Provisional; Region: PRK05550 908937002304 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 908937002305 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 908937002306 active site 908937002307 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 908937002308 homodimer interface [polypeptide binding]; other site 908937002309 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 908937002310 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 908937002311 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 908937002312 Peptidase family M48; Region: Peptidase_M48; pfam01435 908937002313 C-N hydrolase family amidase; Provisional; Region: PRK10438 908937002314 Xanthomonas campestris XC1258 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases); Region: Xc-1258_like; cd07575 908937002315 putative active site [active] 908937002316 catalytic triad [active] 908937002317 dimer interface [polypeptide binding]; other site 908937002318 multimer interface [polypeptide binding]; other site 908937002319 indolepyruvate ferredoxin oxidoreductase, alpha subunit; Region: IOR_alpha; TIGR03336 908937002320 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 908937002321 dimer interface [polypeptide binding]; other site 908937002322 PYR/PP interface [polypeptide binding]; other site 908937002323 TPP binding site [chemical binding]; other site 908937002324 substrate binding site [chemical binding]; other site 908937002325 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 908937002326 TPP-binding site; other site 908937002327 indolepyruvate oxidoreductase subunit beta; Reviewed; Region: PRK06853 908937002328 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 908937002329 hypothetical protein; Provisional; Region: PRK07550 908937002330 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 908937002331 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937002332 homodimer interface [polypeptide binding]; other site 908937002333 catalytic residue [active] 908937002334 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 908937002335 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 908937002336 acyl-activating enzyme (AAE) consensus motif; other site 908937002337 AMP binding site [chemical binding]; other site 908937002338 active site 908937002339 CoA binding site [chemical binding]; other site 908937002340 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains; Region: ACT_Bt0572_1; cd04908 908937002341 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 908937002342 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 908937002343 CoenzymeA binding site [chemical binding]; other site 908937002344 subunit interaction site [polypeptide binding]; other site 908937002345 PHB binding site; other site 908937002346 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 908937002347 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 908937002348 Uncharacterized conserved protein [Function unknown]; Region: COG0327 908937002349 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 908937002350 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 908937002351 Putative zinc ribbon domain; Region: DUF164; pfam02591 908937002352 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 908937002353 putative metal binding site [ion binding]; other site 908937002354 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 908937002355 HSP70 interaction site [polypeptide binding]; other site 908937002356 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N_2; pfam13588 908937002357 DNA polymerase III, delta subunit [DNA replication, recombination, and repair]; Region: HolA; COG1466 908937002358 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 908937002359 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 908937002360 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 908937002361 non-specific DNA binding site [nucleotide binding]; other site 908937002362 salt bridge; other site 908937002363 sequence-specific DNA binding site [nucleotide binding]; other site 908937002364 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiB; COG0543 908937002365 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to...; Region: DHOD_e_trans; cd06218 908937002366 FAD binding pocket [chemical binding]; other site 908937002367 FAD binding motif [chemical binding]; other site 908937002368 phosphate binding motif [ion binding]; other site 908937002369 beta-alpha-beta structure motif; other site 908937002370 NAD binding pocket [chemical binding]; other site 908937002371 Iron coordination center [ion binding]; other site 908937002372 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 908937002373 Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. 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...; Region: DHOD_1B_like; cd04740 908937002374 heterodimer interface [polypeptide binding]; other site 908937002375 active site 908937002376 FMN binding site [chemical binding]; other site 908937002377 homodimer interface [polypeptide binding]; other site 908937002378 substrate binding site [chemical binding]; other site 908937002379 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 908937002380 active site 908937002381 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 908937002382 active site 908937002383 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 908937002384 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 908937002385 Tetramer interface [polypeptide binding]; other site 908937002386 active site 908937002387 FMN-binding site [chemical binding]; other site 908937002388 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 908937002389 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 908937002390 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 908937002391 Protein of unknown function (DUF2023); Region: DUF2023; pfam09633 908937002392 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i)...; Region: GH20_chitobiase-like; cd06563 908937002393 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 908937002394 active site 908937002395 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 908937002396 muropeptide transporter; Validated; Region: ampG; cl17669 908937002397 Stage II sporulation protein; Region: SpoIID; pfam08486 908937002398 SpoIID/LytB domain; Region: SpoIID_LytB; TIGR02669 908937002399 Transposase; Region: DEDD_Tnp_IS110; pfam01548 908937002400 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 908937002401 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 908937002402 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14466 908937002403 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 908937002404 FeS/SAM binding site; other site 908937002405 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 908937002406 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 908937002407 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 908937002408 phage shock protein operon transcriptional activator; Provisional; Region: pspF; PRK11608 908937002409 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 908937002410 Walker A motif; other site 908937002411 ATP binding site [chemical binding]; other site 908937002412 Walker B motif; other site 908937002413 arginine finger; other site 908937002414 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 908937002415 Lipopolysaccharide-assembly; Region: LptE; pfam04390 908937002416 preprotein translocase subunit SecG; Reviewed; Region: secG; PRK06870 908937002417 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 908937002418 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 908937002419 N-terminal plug; other site 908937002420 ligand-binding site [chemical binding]; other site 908937002421 The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2 and several proteins of...; Region: ML; cl00274 908937002422 NlpE N-terminal domain; Region: NlpE; pfam04170 908937002423 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_M15_4; pfam13539 908937002424 protoporphyrinogen oxidase; Region: PLN02576 908937002425 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 908937002426 Oligomerisation domain; Region: Oligomerisation; pfam02410 908937002427 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 908937002428 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 908937002429 Walker A motif; other site 908937002430 ATP binding site [chemical binding]; other site 908937002431 Walker B motif; other site 908937002432 arginine finger; other site 908937002433 Peptidase family M41; Region: Peptidase_M41; pfam01434 908937002434 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 908937002435 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 908937002436 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 908937002437 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 908937002438 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 908937002439 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 908937002440 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 908937002441 P-loop; other site 908937002442 Magnesium ion binding site [ion binding]; other site 908937002443 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 908937002444 Magnesium ion binding site [ion binding]; other site 908937002445 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 908937002446 ParB-like nuclease domain; Region: ParBc; pfam02195 908937002447 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 908937002448 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 908937002449 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 908937002450 N-acetyl-D-glucosamine binding site [chemical binding]; other site 908937002451 catalytic residue [active] 908937002452 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 908937002453 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 908937002454 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 908937002455 Zn2+ binding site [ion binding]; other site 908937002456 Mg2+ binding site [ion binding]; other site 908937002457 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 908937002458 synthetase active site [active] 908937002459 NTP binding site [chemical binding]; other site 908937002460 metal binding site [ion binding]; metal-binding site 908937002461 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 908937002462 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 908937002463 putative pectinesterase; Region: PLN02432; cl01911 908937002464 Pectinesterase; Region: Pectinesterase; pfam01095 908937002465 Pectate lyase; Region: Pec_lyase_C; cl01593 908937002466 putative pectinesterase; Region: PLN02432; cl01911 908937002467 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 908937002468 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 908937002469 DNA binding residues [nucleotide binding] 908937002470 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 908937002471 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 908937002472 motif 1; other site 908937002473 active site 908937002474 motif 2; other site 908937002475 motif 3; other site 908937002476 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 908937002477 DHHA1 domain; Region: DHHA1; pfam02272 908937002478 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 908937002479 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 908937002480 putative active site [active] 908937002481 putative metal binding site [ion binding]; other site 908937002482 SprT homologues; Region: SprT; cl01182 908937002483 AAA domain; Region: AAA_30; pfam13604 908937002484 Family description; Region: UvrD_C_2; pfam13538 908937002485 Protein of unknown function (DUF3822); Region: DUF3822; pfam12864 908937002486 Conserved hypothetical protein 95; Region: Cons_hypoth95; pfam03602 908937002487 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 908937002488 S-adenosylmethionine binding site [chemical binding]; other site 908937002489 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 908937002490 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 908937002491 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 908937002492 putative active site [active] 908937002493 catalytic site [active] 908937002494 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 908937002495 putative active site [active] 908937002496 catalytic site [active] 908937002497 DNA primase, catalytic core; Region: dnaG; TIGR01391 908937002498 CHC2 zinc finger; Region: zf-CHC2; pfam01807 908937002499 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 908937002500 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 908937002501 active site 908937002502 metal binding site [ion binding]; metal-binding site 908937002503 interdomain interaction site; other site 908937002504 Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are...; Region: Rhamnogalacturan_acetylesterase_like; cd01821 908937002505 active site 908937002506 catalytic triad [active] 908937002507 Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are...; Region: Rhamnogalacturan_acetylesterase_like; cd01821 908937002508 active site 908937002509 catalytic triad [active] 908937002510 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 908937002511 Ligand binding site [chemical binding]; other site 908937002512 Electron transfer flavoprotein domain; Region: ETF; pfam01012 908937002513 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 908937002514 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 908937002515 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 908937002516 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 908937002517 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 908937002518 active site 908937002519 Acyl-CoA dehydrogenase C terminal; Region: AcylCoA_dehyd_C; pfam12186 908937002520 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 908937002521 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 908937002522 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 908937002523 PIF1-like helicase; Region: PIF1; pfam05970 908937002524 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 908937002525 Walker A motif; other site 908937002526 ATP binding site [chemical binding]; other site 908937002527 Walker B motif; other site 908937002528 Family description; Region: UvrD_C_2; pfam13538 908937002529 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 908937002530 Competence protein; Region: Competence; pfam03772 908937002531 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 908937002532 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 908937002533 non-specific DNA binding site [nucleotide binding]; other site 908937002534 salt bridge; other site 908937002535 sequence-specific DNA binding site [nucleotide binding]; other site 908937002536 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 908937002537 Putative effector of murein hydrolase LrgA [General function prediction only]; Region: COG1380 908937002538 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 908937002539 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 908937002540 Mechanosensitive ion channel; Region: MS_channel; pfam00924 908937002541 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 908937002542 D-alanyl-D-alanine carboxypeptidase, serine-type, PBP4 family; Region: PBP4; TIGR00666 908937002543 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 908937002544 Domain of unknown function (DUF1200); Region: DUF1200; pfam06713 908937002545 KilA-N domain; Region: KilA-N; pfam04383 908937002546 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 908937002547 Plasmid recombination enzyme; Region: Mob_Pre; pfam01076 908937002548 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 908937002549 active site 908937002550 metal binding site [ion binding]; metal-binding site 908937002551 interdomain interaction site; other site 908937002552 Virulence-associated protein E; Region: VirE; pfam05272 908937002553 Helix-turn-helix domain; Region: HTH_17; pfam12728 908937002554 Helix-turn-helix domain; Region: HTH_17; pfam12728 908937002555 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 908937002556 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 908937002557 GLPGLI family protein; Region: GLPGLI; TIGR01200 908937002558 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the...; Region: INT_Tn4399; cd01185 908937002559 Int/Topo IB signature motif; other site 908937002560 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 908937002561 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 908937002562 active site 908937002563 DNA binding site [nucleotide binding] 908937002564 Int/Topo IB signature motif; other site 908937002565 PIN domain; Region: PIN_3; cl17397 908937002566 cell surface protein SprA; Region: surface_SprA; TIGR04189 908937002567 Motility related/secretion protein; Region: SprA_N; pfam14349 908937002568 Motility related/secretion protein; Region: SprA_N; pfam14349 908937002569 Motility related/secretion protein; Region: SprA_N; pfam14349 908937002570 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 908937002571 RuvA N terminal domain; Region: RuvA_N; pfam01330 908937002572 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 908937002573 diaminopimelate dehydrogenase; Region: DAP-DH; TIGR01921 908937002574 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 908937002575 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 908937002576 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 908937002577 putative active site [active] 908937002578 putative metal binding site [ion binding]; other site 908937002579 FMN-binding domain; Region: FMN_bind; pfam04205 908937002580 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 908937002581 putative catalytic site [active] 908937002582 putative metal binding site [ion binding]; other site 908937002583 putative phosphate binding site [ion binding]; other site 908937002584 Peptidase C1B subfamily (MEROPS database nomenclature); composed of eukaryotic bleomycin hydrolases (BH) and bacterial aminopeptidases C (pepC). The proteins of this subfamily contain a large insert relative to the C1A peptidase (papain) subfamily. BH is...; Region: Peptidase_C1B; cd00585 908937002585 trimer interface [polypeptide binding]; other site 908937002586 active site 908937002587 G bulge; other site 908937002588 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 908937002589 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 908937002590 TPP-binding site; other site 908937002591 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 908937002592 PYR/PP interface [polypeptide binding]; other site 908937002593 dimer interface [polypeptide binding]; other site 908937002594 TPP binding site [chemical binding]; other site 908937002595 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 908937002596 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 908937002597 TrkA-N domain; Region: TrkA_N; pfam02254 908937002598 TrkA-C domain; Region: TrkA_C; pfam02080 908937002599 TrkA-N domain; Region: TrkA_N; pfam02254 908937002600 TrkA-C domain; Region: TrkA_C; pfam02080 908937002601 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 908937002602 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 908937002603 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 908937002604 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 908937002605 Potassium binding sites [ion binding]; other site 908937002606 Cesium cation binding sites [ion binding]; other site 908937002607 recombinase A; Provisional; Region: recA; PRK09354 908937002608 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 908937002609 hexamer interface [polypeptide binding]; other site 908937002610 Walker A motif; other site 908937002611 ATP binding site [chemical binding]; other site 908937002612 Walker B motif; other site 908937002613 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 908937002614 rhamnulose-1-phosphate aldolase; Provisional; Region: PRK03634 908937002615 intersubunit interface [polypeptide binding]; other site 908937002616 active site 908937002617 Zn2+ binding site [ion binding]; other site 908937002618 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 908937002619 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 908937002620 putative active site [active] 908937002621 putative metal binding site [ion binding]; other site 908937002622 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937002623 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937002624 SusD family; Region: SusD; pfam07980 908937002625 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937002626 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937002627 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937002628 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 908937002629 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937002630 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937002631 SusD family; Region: SusD; pfam07980 908937002632 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937002633 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937002634 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937002635 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 908937002636 L-rhamnose-proton symport protein (RhaT); Region: RhaT; cl05728 908937002637 L-rhamnose isomerase; Provisional; Region: PRK01076 908937002638 Predicted sugar isomerase [Cell envelope biogenesis, outer membrane]; Region: COG4952; cl17900 908937002639 L-rhamnulose kinases; a subfamily of the FGGY family of carbohydrate kinases; Region: FGGY_RhuK; cd07771 908937002640 N- and C-terminal domain interface [polypeptide binding]; other site 908937002641 rhamnulokinase; Region: rhamnulo_kin; TIGR02627 908937002642 active site 908937002643 putative catalytic site [active] 908937002644 metal binding site [ion binding]; metal-binding site 908937002645 ATP binding site [chemical binding]; other site 908937002646 carbohydrate binding site [chemical binding]; other site 908937002647 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 908937002648 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 908937002649 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 908937002650 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937002651 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937002652 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937002653 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 908937002654 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 908937002655 dimer interface [polypeptide binding]; other site 908937002656 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937002657 catalytic residue [active] 908937002658 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 908937002659 EamA-like transporter family; Region: EamA; pfam00892 908937002660 EamA-like transporter family; Region: EamA; pfam00892 908937002661 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937002662 AAA domain; Region: AAA_21; pfam13304 908937002663 Walker A/P-loop; other site 908937002664 ATP binding site [chemical binding]; other site 908937002665 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 908937002666 Q-loop/lid; other site 908937002667 ABC transporter signature motif; other site 908937002668 Walker B; other site 908937002669 D-loop; other site 908937002670 H-loop/switch region; other site 908937002671 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 908937002672 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 908937002673 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 908937002674 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 908937002675 nucleotide binding site [chemical binding]; other site 908937002676 NEF interaction site [polypeptide binding]; other site 908937002677 SBD interface [polypeptide binding]; other site 908937002678 Bacteriophage abortive infection AbiH; Region: AbiH; pfam14253 908937002679 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937002680 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 908937002681 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 908937002682 non-specific DNA binding site [nucleotide binding]; other site 908937002683 salt bridge; other site 908937002684 sequence-specific DNA binding site [nucleotide binding]; other site 908937002685 BRO family, N-terminal domain; Region: Bro-N; cl10591 908937002686 Protein involved in cell division [Cell division and chromosome partitioning]; Region: Fic; COG2184 908937002687 Fic/DOC family; Region: Fic; pfam02661 908937002688 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937002689 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937002690 SusD family; Region: SusD; pfam07980 908937002691 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937002692 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937002693 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937002694 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 908937002695 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937002696 CAAX protease self-immunity; Region: Abi; pfam02517 908937002697 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 908937002698 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 908937002699 active site 908937002700 Zn binding site [ion binding]; other site 908937002701 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 908937002702 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 908937002703 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 908937002704 glycyl-tRNA synthetase; Provisional; Region: PRK04173 908937002705 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 908937002706 motif 1; other site 908937002707 Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3...; Region: GlyRS-like_core; cd00774 908937002708 active site 908937002709 motif 2; other site 908937002710 motif 3; other site 908937002711 GlyRS Glycyl-anticodon binding domain. GlyRS 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: GlyRS_anticodon; cd00858 908937002712 anticodon binding site; other site 908937002713 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 908937002714 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 908937002715 acyl-activating enzyme (AAE) consensus motif; other site 908937002716 AMP binding site [chemical binding]; other site 908937002717 active site 908937002718 CoA binding site [chemical binding]; other site 908937002719 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 908937002720 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 908937002721 DNA topoisomerase IV subunit A; Provisional; Region: PRK12758 908937002722 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; cl00148 908937002723 CAP-like domain; other site 908937002724 active site 908937002725 primary dimer interface [polypeptide binding]; other site 908937002726 Interphotoreceptor retinoid-binding protein; serine protease family S41; Region: Peptidase_S41_IRBP; cd07563 908937002727 active site triad [active] 908937002728 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 908937002729 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 908937002730 RNA binding site [nucleotide binding]; other site 908937002731 Glycosyl hydrolase family 10; Region: Glyco_hydro_10; cl01495 908937002732 Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are...; Region: Rhamnogalacturan_acetylesterase_like; cd01821 908937002733 active site 908937002734 catalytic triad [active] 908937002735 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937002736 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937002737 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937002738 Fasciclin domain; Region: Fasciclin; cl02663 908937002739 Fasciclin domain; Region: Fasciclin; cl02663 908937002740 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937002741 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937002742 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937002743 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937002744 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 908937002745 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937002746 Glycosyl hydrolase family 43; Region: GH43_6; cd08985 908937002747 active site 908937002748 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 908937002749 sugar binding site [chemical binding]; other site 908937002750 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 908937002751 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 908937002752 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 908937002753 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 908937002754 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 908937002755 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 908937002756 dimer interface [polypeptide binding]; other site 908937002757 phosphorylation site [posttranslational modification] 908937002758 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 908937002759 ATP binding site [chemical binding]; other site 908937002760 Mg2+ binding site [ion binding]; other site 908937002761 G-X-G motif; other site 908937002762 Response regulator receiver domain; Region: Response_reg; pfam00072 908937002763 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 908937002764 active site 908937002765 phosphorylation site [posttranslational modification] 908937002766 intermolecular recognition site; other site 908937002767 dimerization interface [polypeptide binding]; other site 908937002768 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937002769 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937002770 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 908937002771 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 908937002772 Domain of unknown function (DUF303); Region: DUF303; pfam03629 908937002773 hypothetical protein; Provisional; Region: PRK07758 908937002774 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 908937002775 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i)...; Region: GH20_chitobiase-like; cd06563 908937002776 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 908937002777 active site 908937002778 Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold...; Region: Sialidase; cd00260 908937002779 catalytic site [active] 908937002780 BNR repeat-like domain; Region: BNR_2; pfam13088 908937002781 Asp-box motif; other site 908937002782 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cl00183 908937002783 dimerization interface [polypeptide binding]; other site 908937002784 putative active cleft [active] 908937002785 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 908937002786 Class I aldolases; Region: Aldolase_Class_I; cl17187 908937002787 catalytic residue [active] 908937002788 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 908937002789 Major Facilitator Superfamily; Region: MFS_1; pfam07690 908937002790 putative substrate translocation pore; other site 908937002791 cyclically-permuted mutarotase family protein; Region: mutarot_permut; TIGR03548 908937002792 Galactose oxidase, central domain; Region: Kelch_3; cl02701 908937002793 Creatinine amidohydrolase; Region: Creatininase; pfam02633 908937002794 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 908937002795 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 908937002796 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 908937002797 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 908937002798 Beta galactosidase small chain; Region: Bgal_small_N; cl03787 908937002799 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 908937002800 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937002801 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937002802 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 908937002803 Endo-beta-N-acetylglucosaminidase D [Carbohydrate transport and metabolism]; Region: COG4724 908937002804 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 908937002805 active site 908937002806 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 908937002807 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937002808 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937002809 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 908937002810 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 908937002811 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 908937002812 active site 908937002813 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 908937002814 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 908937002815 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 908937002816 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937002817 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 908937002818 DNA binding residues [nucleotide binding] 908937002819 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 908937002820 FecR protein; Region: FecR; pfam04773 908937002821 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 908937002822 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 908937002823 active site 908937002824 trimer interface [polypeptide binding]; other site 908937002825 allosteric site; other site 908937002826 active site lid [active] 908937002827 hexamer (dimer of trimers) interface [polypeptide binding]; other site 908937002828 glucosamine-6-phosphate deaminase-like protein; Validated; Region: PRK02122 908937002829 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 908937002830 active site 908937002831 trimer interface [polypeptide binding]; other site 908937002832 allosteric site; other site 908937002833 active site lid [active] 908937002834 hexamer (dimer of trimers) interface [polypeptide binding]; other site 908937002835 GlcNAc-PI de-N-acetylase; Region: PIG-L; pfam02585 908937002836 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 908937002837 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 908937002838 muropeptide transporter; Reviewed; Region: ampG; PRK11902 908937002839 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 908937002840 putative substrate translocation pore; other site 908937002841 Domain of unknown function (DUF377); Region: DUF377; pfam04041 908937002842 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 908937002843 active site 908937002844 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 908937002845 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 908937002846 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 908937002847 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 908937002848 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 908937002849 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 908937002850 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 908937002851 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 908937002852 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 908937002853 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 908937002854 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 908937002855 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 908937002856 Ligand Binding Site [chemical binding]; other site 908937002857 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 908937002858 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 908937002859 Walker A/P-loop; other site 908937002860 ATP binding site [chemical binding]; other site 908937002861 Q-loop/lid; other site 908937002862 ABC transporter signature motif; other site 908937002863 Walker B; other site 908937002864 D-loop; other site 908937002865 H-loop/switch region; other site 908937002866 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 908937002867 S1 domain; Region: S1_2; pfam13509 908937002868 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 908937002869 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 908937002870 putative dimer interface [polypeptide binding]; other site 908937002871 putative anticodon binding site; other site 908937002872 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 908937002873 homodimer interface [polypeptide binding]; other site 908937002874 motif 1; other site 908937002875 motif 2; other site 908937002876 active site 908937002877 motif 3; other site 908937002878 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 908937002879 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 908937002880 RNA binding surface [nucleotide binding]; other site 908937002881 Pseudouridine synthases, RsuA subfamily; Region: PseudoU_synth_RsuA_like; cd02870 908937002882 active site 908937002883 adenylosuccinate lyase; Provisional; Region: PRK09285 908937002884 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 908937002885 tetramer interface [polypeptide binding]; other site 908937002886 active site 908937002887 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 908937002888 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002889 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002890 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002891 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002892 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002893 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002894 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 908937002895 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002896 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002897 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002898 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 908937002899 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002900 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002901 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002902 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 908937002903 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002904 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002905 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002906 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002907 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002908 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 908937002909 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002910 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002911 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 908937002912 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 908937002913 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 908937002914 ligand binding site [chemical binding]; other site 908937002915 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 908937002916 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 908937002917 ATP binding site [chemical binding]; other site 908937002918 Mg2+ binding site [ion binding]; other site 908937002919 G-X-G motif; other site 908937002920 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 908937002921 ATP binding site [chemical binding]; other site 908937002922 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 908937002923 OstA-like protein; Region: OstA_2; pfam13100 908937002924 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 908937002925 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 908937002926 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 908937002927 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK02998 908937002928 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 908937002929 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 908937002930 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 908937002931 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 908937002932 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 908937002933 active site 908937002934 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 908937002935 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 908937002936 ATP binding site [chemical binding]; other site 908937002937 putative Mg++ binding site [ion binding]; other site 908937002938 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 908937002939 nucleotide binding region [chemical binding]; other site 908937002940 ATP-binding site [chemical binding]; other site 908937002941 RQC domain; Region: RQC; pfam09382 908937002942 HRDC domain; Region: HRDC; pfam00570 908937002943 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 908937002944 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 908937002945 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 908937002946 Walker A motif; other site 908937002947 ATP binding site [chemical binding]; other site 908937002948 Walker B motif; other site 908937002949 arginine finger; other site 908937002950 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 908937002951 Clp protease; Region: CLP_protease; pfam00574 908937002952 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 908937002953 oligomer interface [polypeptide binding]; other site 908937002954 active site residues [active] 908937002955 trigger factor; Region: tig; TIGR00115 908937002956 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 908937002957 Divergent AAA domain; Region: AAA_4; pfam04326 908937002958 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 908937002959 FaeA-like protein; Region: FaeA; pfam04703 908937002960 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 908937002961 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 908937002962 Walker A/P-loop; other site 908937002963 ATP binding site [chemical binding]; other site 908937002964 Q-loop/lid; other site 908937002965 ABC transporter signature motif; other site 908937002966 Walker B; other site 908937002967 D-loop; other site 908937002968 H-loop/switch region; other site 908937002969 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 908937002970 Permease; Region: Permease; pfam02405 908937002971 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 908937002972 putative active site [active] 908937002973 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 908937002974 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 908937002975 Walker A/P-loop; other site 908937002976 ATP binding site [chemical binding]; other site 908937002977 Q-loop/lid; other site 908937002978 ABC transporter signature motif; other site 908937002979 Walker B; other site 908937002980 D-loop; other site 908937002981 H-loop/switch region; other site 908937002982 Lumazine-binding domain; Region: Lumazine_bd; pfam12870 908937002983 GTP-binding protein Der; Reviewed; Region: PRK00093 908937002984 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 908937002985 G1 box; other site 908937002986 GTP/Mg2+ binding site [chemical binding]; other site 908937002987 Switch I region; other site 908937002988 G2 box; other site 908937002989 Switch II region; other site 908937002990 G3 box; other site 908937002991 G4 box; other site 908937002992 G5 box; other site 908937002993 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 908937002994 G1 box; other site 908937002995 GTP/Mg2+ binding site [chemical binding]; other site 908937002996 Switch I region; other site 908937002997 G2 box; other site 908937002998 G3 box; other site 908937002999 Switch II region; other site 908937003000 G4 box; other site 908937003001 G5 box; other site 908937003002 GTPase Era; Reviewed; Region: era; PRK00089 908937003003 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 908937003004 G1 box; other site 908937003005 GTP/Mg2+ binding site [chemical binding]; other site 908937003006 Switch I region; other site 908937003007 G2 box; other site 908937003008 Switch II region; other site 908937003009 G3 box; other site 908937003010 G4 box; other site 908937003011 G5 box; other site 908937003012 KH domain; Region: KH_2; pfam07650 908937003013 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 908937003014 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 908937003015 dimer interface [polypeptide binding]; other site 908937003016 active site 908937003017 CoA binding pocket [chemical binding]; other site 908937003018 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 908937003019 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 908937003020 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 908937003021 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 908937003022 ATP binding site [chemical binding]; other site 908937003023 Mg2+ binding site [ion binding]; other site 908937003024 G-X-G motif; other site 908937003025 serine O-acetyltransferase; Region: cysE; TIGR01172 908937003026 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 908937003027 trimer interface [polypeptide binding]; other site 908937003028 active site 908937003029 substrate binding site [chemical binding]; other site 908937003030 CoA binding site [chemical binding]; other site 908937003031 Uncharacterized conserved protein [Function unknown]; Region: COG1284 908937003032 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 908937003033 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 908937003034 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 908937003035 isocitrate dehydrogenase; Validated; Region: PRK08299 908937003036 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 908937003037 ligand binding site [chemical binding]; other site 908937003038 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 908937003039 substrate binding site [chemical binding]; other site 908937003040 active site 908937003041 Chromate transporter; Region: Chromate_transp; pfam02417 908937003042 Chromate transporter; Region: Chromate_transp; pfam02417 908937003043 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 908937003044 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat1; cd02203 908937003045 dimerization interface [polypeptide binding]; other site 908937003046 ATP binding site [chemical binding]; other site 908937003047 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat2; cd02204 908937003048 dimerization interface [polypeptide binding]; other site 908937003049 ATP binding site [chemical binding]; other site 908937003050 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 908937003051 putative active site [active] 908937003052 catalytic triad [active] 908937003053 Cyclomaltodextrinase, N-terminal; Region: Cyc-maltodext_N; pfam09087 908937003054 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins; Region: AmyAc_bac_CMD_like_3; cd11340 908937003055 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 908937003056 Ca binding site [ion binding]; other site 908937003057 active site 908937003058 homodimer interface [polypeptide binding]; other site 908937003059 catalytic site [active] 908937003060 Cyclo-malto-dextrinase C-terminal domain; Region: Cyc-maltodext_C; pfam10438 908937003061 pullulanase, type I; Region: pulA_typeI; TIGR02104 908937003062 Early set domain associated with the catalytic domain of pullulanase (also called dextrinase and alpha-dextrin endo-1,6-alpha glucosidase); Region: E_set_Pullulanase; cd02860 908937003063 Alpha amylase catalytic domain found in Pullulanase (also called dextrinase; alpha-dextrin endo-1,6-alpha glucosidase), limit dextrinase, and related proteins; Region: AmyAc_Pullulanase_LD-like; cd11341 908937003064 Ca binding site [ion binding]; other site 908937003065 active site 908937003066 catalytic site [active] 908937003067 Domain of unknown function (DUF3372); Region: DUF3372; pfam11852 908937003068 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 908937003069 4-alpha-glucanotransferase; Region: PLN02950 908937003070 The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is...; Region: CBM20; cl15347 908937003071 starch-binding site 2 [chemical binding]; other site 908937003072 starch-binding site 1 [chemical binding]; other site 908937003073 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 908937003074 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 908937003075 active site 908937003076 MgtC family; Region: MgtC; pfam02308 908937003077 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 908937003078 Major Facilitator Superfamily; Region: MFS_1; pfam07690 908937003079 putative substrate translocation pore; other site 908937003080 S23 ribosomal protein; Region: Ribosomal_S23p; cl05287 908937003081 four helix bundle protein; Region: TIGR02436 908937003082 Transcriptional regulators [Transcription]; Region: PurR; COG1609 908937003083 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 908937003084 DNA binding site [nucleotide binding] 908937003085 domain linker motif; other site 908937003086 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 908937003087 dimerization interface [polypeptide binding]; other site 908937003088 ligand binding site [chemical binding]; other site 908937003089 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937003090 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937003091 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 908937003092 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937003093 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937003094 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937003095 SusE outer membrane protein; Region: SusE; pfam14292 908937003096 carbohydrate-binding modules Eb and Fb from SusE and SusF, respectively, and similar CBMs; Region: CBM-Eb_CBM-Fb; cd12965 908937003097 starch binding site [chemical binding]; other site 908937003098 carbohydrate-binding modules Ec and Fc from SusE and SusF, respectively, and similar CBMs; Region: CBM-Ec_CBM-Fc; cd12966 908937003099 starch binding site [chemical binding]; other site 908937003100 starch-binding loop; other site 908937003101 carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins; Region: CBM_SusE-F_like; cl17376 908937003102 starch binding site [chemical binding]; other site 908937003103 Uncharacterized subgroup of the CBM-SusE-F_like superfamily; Region: CBM_SusE-F_like_u1; cd12967 908937003104 starch binding site [chemical binding]; other site 908937003105 carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins; Region: CBM_SusE-F_like; cl17376 908937003106 starch binding site [chemical binding]; other site 908937003107 alpha-amylase; Region: PLN02361 908937003108 Alpha amylase catalytic domain found in archaeal, bacterial, and plant Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_arch_bac_plant_AmyA; cd11314 908937003109 active site 908937003110 Ca binding site [ion binding]; other site 908937003111 catalytic site [active] 908937003112 Glycosyl hydrolase family 53; Region: Glyco_hydro_53; cl06672 908937003113 four helix bundle suffix domain; Region: 4helix_suffix; TIGR04258 908937003114 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 908937003115 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 908937003116 HlyD family secretion protein; Region: HlyD_3; pfam13437 908937003117 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 908937003118 FtsX-like permease family; Region: FtsX; pfam02687 908937003119 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 908937003120 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 908937003121 FtsX-like permease family; Region: FtsX; pfam02687 908937003122 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 908937003123 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 908937003124 Walker A/P-loop; other site 908937003125 ATP binding site [chemical binding]; other site 908937003126 Q-loop/lid; other site 908937003127 ABC transporter signature motif; other site 908937003128 Walker B; other site 908937003129 D-loop; other site 908937003130 H-loop/switch region; other site 908937003131 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 908937003132 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 908937003133 catalytic residues [active] 908937003134 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 908937003135 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 908937003136 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 908937003137 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937003138 Walker A/P-loop; other site 908937003139 ATP binding site [chemical binding]; other site 908937003140 Q-loop/lid; other site 908937003141 ABC transporter signature motif; other site 908937003142 Walker B; other site 908937003143 D-loop; other site 908937003144 H-loop/switch region; other site 908937003145 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 908937003146 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03708 908937003147 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 908937003148 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 908937003149 DJ-1 family protein; Region: not_thiJ; TIGR01383 908937003150 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 908937003151 conserved cys residue [active] 908937003152 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 908937003153 substrate binding site; other site 908937003154 dimer interface; other site 908937003155 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 908937003156 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 908937003157 generic binding surface II; other site 908937003158 ssDNA binding site; other site 908937003159 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 908937003160 ATP binding site [chemical binding]; other site 908937003161 putative Mg++ binding site [ion binding]; other site 908937003162 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 908937003163 nucleotide binding region [chemical binding]; other site 908937003164 ATP-binding site [chemical binding]; other site 908937003165 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 908937003166 Peptidase family M23; Region: Peptidase_M23; pfam01551 908937003167 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 908937003168 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 908937003169 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 908937003170 metal-binding site 908937003171 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 908937003172 This family is most closely related to the GT1 family of glycosyltransferases. wcfI in Bacteroides fragilis has been shown to be involved in the capsular polysaccharide biosynthesis; Region: GT1_wcfI_like; cd03825 908937003173 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 908937003174 homotrimer interaction site [polypeptide binding]; other site 908937003175 zinc binding site [ion binding]; other site 908937003176 CDP-binding sites; other site 908937003177 Peptidase C25 family N-terminal domain, found in Arg-gingipain (Rgp), Lys-gingipain (Kgp) and related proteins; Region: Peptidase_C25_N; cd02258 908937003178 active site 908937003179 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 908937003180 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 908937003181 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 908937003182 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 908937003183 active site 908937003184 catalytic residues [active] 908937003185 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 908937003186 catalytic residues [active] 908937003187 elongation factor Ts; Provisional; Region: tsf; PRK09377 908937003188 UBA/TS-N domain; Region: UBA; pfam00627 908937003189 Elongation factor TS; Region: EF_TS; pfam00889 908937003190 Elongation factor TS; Region: EF_TS; pfam00889 908937003191 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 908937003192 rRNA interaction site [nucleotide binding]; other site 908937003193 S8 interaction site; other site 908937003194 putative laminin-1 binding site; other site 908937003195 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 908937003196 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 908937003197 23S rRNA interface [nucleotide binding]; other site 908937003198 L3 interface [polypeptide binding]; other site 908937003199 Alpha 1,6-fucosyltransferase similar to Bradyrhizobium NodZ; Region: NodZ_like; cd11548 908937003200 GDP-Fucose binding site [chemical binding]; other site 908937003201 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 908937003202 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 908937003203 Core-2/I-Branching enzyme; Region: Branch; pfam02485 908937003204 Glycosyl Hydrolase Family 88; Region: Glyco_hydro_88; pfam07470 908937003205 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 908937003206 active site 908937003207 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937003208 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937003209 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937003210 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937003211 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937003212 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937003213 SusD family; Region: SusD; pfam07980 908937003214 beta-D-galactosidase; Reviewed; Region: lacZ; PRK09525 908937003215 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 908937003216 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 908937003217 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 908937003218 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 908937003219 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 908937003220 Carbohydrate binding domain; Region: CBM_4_9; pfam02018 908937003221 Alpha-L-arabinofuranosidase [Carbohydrate transport and metabolism]; Region: AbfA; COG3534 908937003222 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; pfam06964 908937003223 Rhamnogalacturonan lyase of the polysaccharide lyase family 11; Region: RGL11; cd10318 908937003224 metal binding site [ion binding]; metal-binding site 908937003225 active site 908937003226 Uncharacterized protein related to glutamine synthetase [General function prediction only]; Region: COG3968 908937003227 Glutamine synthetase type III N terminal; Region: GSIII_N; pfam12437 908937003228 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 908937003229 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 908937003230 Enoyl-(Acyl carrier protein) reductase; Region: adh_short_C2; pfam13561 908937003231 NAD binding site [chemical binding]; other site 908937003232 homotetramer interface [polypeptide binding]; other site 908937003233 homodimer interface [polypeptide binding]; other site 908937003234 substrate binding site [chemical binding]; other site 908937003235 active site 908937003236 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 908937003237 active site 908937003238 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 908937003239 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 908937003240 RIP metalloprotease RseP; Region: TIGR00054 908937003241 active site 908937003242 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 908937003243 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 908937003244 putative substrate binding region [chemical binding]; other site 908937003245 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 908937003246 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 908937003247 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 908937003248 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 908937003249 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 908937003250 RimM N-terminal domain; Region: RimM; pfam01782 908937003251 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 908937003252 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 908937003253 hinge; other site 908937003254 active site 908937003255 Domain of unknown function (DUF4290); Region: DUF4290; pfam14123 908937003256 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 908937003257 Glycoprotease family; Region: Peptidase_M22; pfam00814 908937003258 hypothetical protein; Provisional; Region: PRK11820 908937003259 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 908937003260 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 908937003261 Guanylate kinase; Region: Guanylate_kin; pfam00625 908937003262 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 908937003263 catalytic site [active] 908937003264 G-X2-G-X-G-K; other site 908937003265 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 908937003266 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 908937003267 active site 908937003268 (T/H)XGH motif; other site 908937003269 Sulfatase; Region: Sulfatase; cl17466 908937003270 Acyltransferase family; Region: Acyl_transf_3; pfam01757 908937003271 Acyltransferase family; Region: Acyl_transf_3; pfam01757 908937003272 phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase; Provisional; Region: PRK12324 908937003273 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 908937003274 Predicted membrane protein [Function unknown]; Region: COG2246 908937003275 GtrA-like protein; Region: GtrA; pfam04138 908937003276 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 908937003277 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 908937003278 active site 908937003279 Thymidylate synthase complementing protein; Region: Thy1; cl03630 908937003280 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 908937003281 putative DNA binding helix; other site 908937003282 metal binding site 2 [ion binding]; metal-binding site 908937003283 metal binding site 1 [ion binding]; metal-binding site 908937003284 dimer interface [polypeptide binding]; other site 908937003285 structural Zn2+ binding site [ion binding]; other site 908937003286 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 908937003287 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 908937003288 minor groove reading motif; other site 908937003289 helix-hairpin-helix signature motif; other site 908937003290 substrate binding pocket [chemical binding]; other site 908937003291 active site 908937003292 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 908937003293 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 908937003294 DNA binding and oxoG recognition site [nucleotide binding] 908937003295 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 908937003296 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 908937003297 active site 908937003298 HIGH motif; other site 908937003299 KMSKS motif; other site 908937003300 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 908937003301 tRNA binding surface [nucleotide binding]; other site 908937003302 anticodon binding site; other site 908937003303 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 908937003304 dimer interface [polypeptide binding]; other site 908937003305 putative tRNA-binding site [nucleotide binding]; other site 908937003306 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 908937003307 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 908937003308 AAA domain; Region: AAA_11; pfam13086 908937003309 Part of AAA domain; Region: AAA_19; pfam13245 908937003310 AAA domain; Region: AAA_12; pfam13087 908937003311 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 908937003312 nucleoside/Zn binding site; other site 908937003313 dimer interface [polypeptide binding]; other site 908937003314 catalytic motif [active] 908937003315 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 908937003316 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); Region: NT5C; cl17836 908937003317 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 908937003318 substrate binding site; other site 908937003319 dimer interface; other site 908937003320 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 908937003321 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 908937003322 NAD(P) binding site [chemical binding]; other site 908937003323 active site 908937003324 LicD family; Region: LicD; pfam04991 908937003325 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 908937003326 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 908937003327 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 908937003328 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 908937003329 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 908937003330 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 908937003331 catalytic motif [active] 908937003332 Zn binding site [ion binding]; other site 908937003333 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 908937003334 RibD C-terminal domain; Region: RibD_C; pfam01872 908937003335 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 908937003336 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 908937003337 S-adenosylmethionine binding site [chemical binding]; other site 908937003338 RecX family; Region: RecX; pfam02631 908937003339 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 908937003340 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 908937003341 active site 908937003342 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 908937003343 active site 908937003344 argininosuccinate lyase; Provisional; Region: PRK00855 908937003345 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 908937003346 active sites [active] 908937003347 tetramer interface [polypeptide binding]; other site 908937003348 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 908937003349 iron-sulfur cluster [ion binding]; other site 908937003350 [2Fe-2S] cluster binding site [ion binding]; other site 908937003351 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 908937003352 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 908937003353 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 908937003354 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 908937003355 nucleotide binding site/active site [active] 908937003356 HIT family signature motif; other site 908937003357 catalytic residue [active] 908937003358 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 908937003359 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 908937003360 Substrate binding site; other site 908937003361 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 908937003362 substrate binding site [chemical binding]; other site 908937003363 ATP binding site [chemical binding]; other site 908937003364 putative transporter; Validated; Region: PRK03818 908937003365 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 908937003366 TrkA-C domain; Region: TrkA_C; pfam02080 908937003367 TrkA-C domain; Region: TrkA_C; pfam02080 908937003368 AspT/YidE/YbjL antiporter duplication domain; Region: YidE_YbjL_dupl; TIGR01625 908937003369 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 908937003370 sequence-specific DNA binding site [nucleotide binding]; other site 908937003371 salt bridge; other site 908937003372 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 908937003373 DNA methylase; Region: N6_N4_Mtase; cl17433 908937003374 DNA methylase; Region: N6_N4_Mtase; pfam01555 908937003375 Methyltransferase domain; Region: Methyltransf_26; pfam13659 908937003376 AAA ATPase domain; Region: AAA_15; pfam13175 908937003377 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937003378 Walker A/P-loop; other site 908937003379 ATP binding site [chemical binding]; other site 908937003380 Transposase; Region: DEDD_Tnp_IS110; pfam01548 908937003381 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 908937003382 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 908937003383 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 908937003384 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 908937003385 substrate binding site [chemical binding]; other site 908937003386 ATP binding site [chemical binding]; other site 908937003387 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 908937003388 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 908937003389 Walker A/P-loop; other site 908937003390 ATP binding site [chemical binding]; other site 908937003391 Q-loop/lid; other site 908937003392 ABC transporter signature motif; other site 908937003393 Walker B; other site 908937003394 D-loop; other site 908937003395 H-loop/switch region; other site 908937003396 Uncharacterized protein conserved in bacteria (DUF2264); Region: DUF2264; pfam10022 908937003397 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 908937003398 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 908937003399 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 908937003400 Walker A motif; other site 908937003401 ATP binding site [chemical binding]; other site 908937003402 Walker B motif; other site 908937003403 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 908937003404 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 908937003405 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 908937003406 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 908937003407 binding surface 908937003408 TPR motif; other site 908937003409 Tetratricopeptide repeat; Region: TPR_16; pfam13432 908937003410 AAA domain; Region: AAA_11; pfam13086 908937003411 Part of AAA domain; Region: AAA_19; pfam13245 908937003412 AAA domain; Region: AAA_30; pfam13604 908937003413 AAA domain; Region: AAA_12; pfam13087 908937003414 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 908937003415 Sulfatase; Region: Sulfatase; cl17466 908937003416 Glycosyl Hydrolase Family 88; Region: Glyco_hydro_88; pfam07470 908937003417 Lyase, N terminal; Region: Lyase_N; pfam09092 908937003418 Glycosaminoglycan (GAG) polysaccharide lyase family. This family consists of a group of secreted bacterial lyase enzymes capable of acting on glycosaminoglycans, such as hyaluronan and chondroitin, in the extracellular matrix of host tissues; Region: GAG_Lyase; cl17706 908937003419 substrate binding site [chemical binding]; other site 908937003420 catalytic residues [active] 908937003421 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937003422 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937003423 SusD family; Region: SusD; pfam07980 908937003424 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937003425 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937003426 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937003427 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 908937003428 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 908937003429 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 908937003430 Two component regulator propeller; Region: Reg_prop; pfam07494 908937003431 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 908937003432 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 908937003433 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 908937003434 dimer interface [polypeptide binding]; other site 908937003435 phosphorylation site [posttranslational modification] 908937003436 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 908937003437 ATP binding site [chemical binding]; other site 908937003438 Mg2+ binding site [ion binding]; other site 908937003439 G-X-G motif; other site 908937003440 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 908937003441 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 908937003442 active site 908937003443 phosphorylation site [posttranslational modification] 908937003444 intermolecular recognition site; other site 908937003445 dimerization interface [polypeptide binding]; other site 908937003446 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937003447 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937003448 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 908937003449 flavoprotein, HI0933 family; Region: TIGR00275 908937003450 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 908937003451 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 908937003452 Uncharacterized conserved protein [Function unknown]; Region: COG1284 908937003453 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 908937003454 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 908937003455 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 908937003456 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937003457 active site 908937003458 HIGH motif; other site 908937003459 nucleotide binding site [chemical binding]; other site 908937003460 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 908937003461 KMSK motif region; other site 908937003462 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 908937003463 tRNA binding surface [nucleotide binding]; other site 908937003464 anticodon binding site; other site 908937003465 RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Region: RNase_H; cd06222 908937003466 active site 908937003467 RNA/DNA hybrid binding site [nucleotide binding]; other site 908937003468 Transcriptional regulators [Transcription]; Region: MarR; COG1846 908937003469 Winged helix DNA-binding domain; Region: HTH_34; pfam13601 908937003470 Domain of unknown function (DUF1893); Region: TM1506; pfam08973 908937003471 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937003472 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937003473 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937003474 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 908937003475 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 908937003476 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937003477 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937003478 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 908937003479 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 908937003480 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 908937003481 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 908937003482 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 908937003483 catalytic residues [active] 908937003484 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 908937003485 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 908937003486 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 908937003487 catalytic residues [active] 908937003488 Domain of unknown function (DUF389); Region: DUF389; pfam04087 908937003489 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 908937003490 ACT domain-containing protein [General function prediction only]; Region: COG4747 908937003491 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains; Region: ACT_Bt0572_1; cd04908 908937003492 C-terminal ACT domain of a novel protein composed of just two ACT domains; Region: ACT_Bt0572_2; cd04882 908937003493 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 908937003494 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 908937003495 acyl-activating enzyme (AAE) consensus motif; other site 908937003496 AMP binding site [chemical binding]; other site 908937003497 active site 908937003498 CoA binding site [chemical binding]; other site 908937003499 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 908937003500 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 908937003501 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 908937003502 PhoU domain; Region: PhoU; pfam01895 908937003503 PhoU domain; Region: PhoU; pfam01895 908937003504 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 908937003505 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 908937003506 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 908937003507 PhoU domain; Region: PhoU; pfam01895 908937003508 PhoU domain; Region: PhoU; pfam01895 908937003509 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 908937003510 Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK); Region: UMPK_like; cd02028 908937003511 active site 908937003512 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 908937003513 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 908937003514 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 908937003515 dimer interface [polypeptide binding]; other site 908937003516 PYR/PP interface [polypeptide binding]; other site 908937003517 TPP binding site [chemical binding]; other site 908937003518 substrate binding site [chemical binding]; other site 908937003519 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 908937003520 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 908937003521 TPP-binding site [chemical binding]; other site 908937003522 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 908937003523 active site 908937003524 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 908937003525 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 908937003526 active site 908937003527 substrate-binding site [chemical binding]; other site 908937003528 metal-binding site [ion binding] 908937003529 ATP binding site [chemical binding]; other site 908937003530 undecaprenyl pyrophosphate synthase; Provisional; Region: PRK14838 908937003531 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 908937003532 catalytic residue [active] 908937003533 putative FPP diphosphate binding site; other site 908937003534 putative FPP binding hydrophobic cleft; other site 908937003535 dimer interface [polypeptide binding]; other site 908937003536 putative IPP diphosphate binding site; other site 908937003537 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 908937003538 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 908937003539 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 908937003540 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 908937003541 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 908937003542 Surface antigen; Region: Bac_surface_Ag; pfam01103 908937003543 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 908937003544 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 908937003545 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 908937003546 glutamate racemase; Provisional; Region: PRK00865 908937003547 Ribosome-binding factor A; Region: RBFA; pfam02033 908937003548 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 908937003549 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 908937003550 FtsX-like permease family; Region: FtsX; pfam02687 908937003551 Alpha-L-rhamnosidase N-terminal domain; Region: Bac_rhamnosid_N; pfam08531 908937003552 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; pfam05592 908937003553 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 908937003554 substrate binding site [chemical binding]; other site 908937003555 active site 908937003556 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 908937003557 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 908937003558 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 908937003559 active site 908937003560 HIGH motif; other site 908937003561 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 908937003562 active site 908937003563 KMSKS motif; other site 908937003564 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 908937003565 tRNA binding surface [nucleotide binding]; other site 908937003566 anticodon binding site; other site 908937003567 desulfoferrodoxin; Region: dfx_rbo; TIGR00320 908937003568 Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small; Region: DSRD; cl00018 908937003569 Superoxide reductase-like (SORL) domain, class I; SORL-domains are present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals...; Region: SORL_Dfx_classI; cd03171 908937003570 non-heme iron binding site [ion binding]; other site 908937003571 dimer interface [polypeptide binding]; other site 908937003572 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 908937003573 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 908937003574 dimer interface [polypeptide binding]; other site 908937003575 phosphorylation site [posttranslational modification] 908937003576 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 908937003577 ATP binding site [chemical binding]; other site 908937003578 Mg2+ binding site [ion binding]; other site 908937003579 G-X-G motif; other site 908937003580 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 908937003581 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 908937003582 active site 908937003583 phosphorylation site [posttranslational modification] 908937003584 intermolecular recognition site; other site 908937003585 dimerization interface [polypeptide binding]; other site 908937003586 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 908937003587 DNA binding site [nucleotide binding] 908937003588 gluconate 5-dehydrogenase; Provisional; Region: PRK07097 908937003589 gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs; Region: Ga5DH-like_SDR_c; cd05347 908937003590 NADP binding site [chemical binding]; other site 908937003591 homodimer interface [polypeptide binding]; other site 908937003592 active site 908937003593 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 908937003594 IHF dimer interface [polypeptide binding]; other site 908937003595 IHF - DNA interface [nucleotide binding]; other site 908937003596 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 908937003597 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; Region: EEP-2; cd09084 908937003598 putative catalytic site [active] 908937003599 putative metal binding site [ion binding]; other site 908937003600 putative phosphate binding site [ion binding]; other site 908937003601 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 908937003602 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 908937003603 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 908937003604 Protein export membrane protein; Region: SecD_SecF; pfam02355 908937003605 Melibiase; Region: Melibiase; pfam02065 908937003606 Melibiase; Region: Melibiase; pfam02065 908937003607 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937003608 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937003609 SusD family; Region: SusD; pfam07980 908937003610 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937003611 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937003612 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937003613 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 908937003614 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 908937003615 putative substrate translocation pore; other site 908937003616 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 908937003617 dimer interface [polypeptide binding]; other site 908937003618 active site 908937003619 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 908937003620 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 908937003621 nucleotide binding site [chemical binding]; other site 908937003622 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 908937003623 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 908937003624 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 908937003625 Alpha-L-rhamnosidase N-terminal domain; Region: Bac_rhamnosid_N; pfam08531 908937003626 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; pfam05592 908937003627 Transcriptional regulators [Transcription]; Region: PurR; COG1609 908937003628 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 908937003629 DNA binding site [nucleotide binding] 908937003630 domain linker motif; other site 908937003631 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 908937003632 dimerization interface [polypeptide binding]; other site 908937003633 ligand binding site [chemical binding]; other site 908937003634 Uncharacterized proteins of the AP superfamily [General function prediction only]; Region: COG1524 908937003635 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 908937003636 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2859 908937003637 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 908937003638 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 908937003639 active site 908937003640 HIGH motif; other site 908937003641 dimer interface [polypeptide binding]; other site 908937003642 KMSKS motif; other site 908937003643 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 908937003644 RNA binding surface [nucleotide binding]; other site 908937003645 Haemolytic domain; Region: Haemolytic; pfam01809 908937003646 ribonuclease P; Reviewed; Region: rnpA; PRK01903 908937003647 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 908937003648 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 908937003649 active site 908937003650 Domain of unknown function (DUF4271); Region: DUF4271; pfam14093 908937003651 S-adenosylmethionine synthetase; Validated; Region: PRK05250 908937003652 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 908937003653 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 908937003654 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 908937003655 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 908937003656 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 908937003657 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 908937003658 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 908937003659 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 908937003660 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 908937003661 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 908937003662 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 908937003663 active site 908937003664 Int/Topo IB signature motif; other site 908937003665 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 908937003666 Dehydroquinase class II; Region: DHquinase_II; pfam01220 908937003667 active site 908937003668 trimer interface [polypeptide binding]; other site 908937003669 dimer interface [polypeptide binding]; other site 908937003670 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 908937003671 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 908937003672 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 908937003673 Phage major tail protein 2; Region: Phage_tail_2; cl11463 908937003674 Phage head-tail joining protein; Region: Phage_H_T_join; cl11461 908937003675 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 908937003676 oligomerization interface [polypeptide binding]; other site 908937003677 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 908937003678 Phage capsid family; Region: Phage_capsid; pfam05065 908937003679 Caudovirus prohead protease; Region: Peptidase_U35; pfam04586 908937003680 Phage-related protein [Function unknown]; Region: COG4695 908937003681 Phage portal protein; Region: Phage_portal; pfam04860 908937003682 Phage terminase, small subunit; Region: Terminase_4; pfam05119 908937003683 Helix-turn-helix domain; Region: HTH_36; pfam13730 908937003684 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 908937003685 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 908937003686 active site 908937003687 catalytic residues [active] 908937003688 DNA binding site [nucleotide binding] 908937003689 Int/Topo IB signature motif; other site 908937003690 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937003691 active site 908937003692 HIGH motif; other site 908937003693 nucleotide binding site [chemical binding]; other site 908937003694 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 908937003695 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937003696 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 908937003697 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937003698 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937003699 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937003700 active site 908937003701 KMSKS motif; other site 908937003702 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 908937003703 tRNA binding surface [nucleotide binding]; other site 908937003704 Anticodon-binding domain of tRNA; Region: Anticodon_1; pfam08264 908937003705 Uncharacterized conserved protein [Function unknown]; Region: COG1284 908937003706 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 908937003707 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 908937003708 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 908937003709 active site 908937003710 dimerization interface [polypeptide binding]; other site 908937003711 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 908937003712 N-terminal domain of Chondroitin polymerase functions as a GalNAc transferase; Region: GT2_Chondriotin_Pol_N; cd06420 908937003713 Substrate binding site; other site 908937003714 metal-binding site 908937003715 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 908937003716 Domain of unknown function (DUF4294); Region: DUF4294; pfam14127 908937003717 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 908937003718 active site 908937003719 NTP binding site [chemical binding]; other site 908937003720 metal binding triad [ion binding]; metal-binding site 908937003721 antibiotic binding site [chemical binding]; other site 908937003722 ribonuclease R; Region: RNase_R; TIGR02063 908937003723 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 908937003724 RNB domain; Region: RNB; pfam00773 908937003725 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 908937003726 RNA binding site [nucleotide binding]; other site 908937003727 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 908937003728 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 908937003729 NAD(P) binding site [chemical binding]; other site 908937003730 active site 908937003731 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 908937003732 active site 908937003733 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 908937003734 active site 908937003735 DNA binding site [nucleotide binding] 908937003736 Int/Topo IB signature motif; other site 908937003737 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the...; Region: INT_Tn4399; cd01185 908937003738 Int/Topo IB signature motif; other site 908937003739 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 908937003740 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 908937003741 Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]; Region: {ManC}; COG0662 908937003742 Helix-turn-helix domain; Region: HTH_18; pfam12833 908937003743 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937003744 Helix-turn-helix domain; Region: HTH_17; pfam12728 908937003745 Helix-turn-helix domain; Region: HTH_17; pfam12728 908937003746 Virulence-associated protein E; Region: VirE; pfam05272 908937003747 DNA primase (bacterial type) [DNA replication, recombination, and repair]; Region: DnaG; COG0358 908937003748 Toprim-like; Region: Toprim_2; pfam13155 908937003749 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 908937003750 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 908937003751 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14329 908937003752 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 908937003753 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 908937003754 FeS/SAM binding site; other site 908937003755 TRAM domain; Region: TRAM; pfam01938 908937003756 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 908937003757 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 908937003758 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 908937003759 Walker A/P-loop; other site 908937003760 ATP binding site [chemical binding]; other site 908937003761 Q-loop/lid; other site 908937003762 ABC transporter signature motif; other site 908937003763 Walker B; other site 908937003764 D-loop; other site 908937003765 H-loop/switch region; other site 908937003766 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 908937003767 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 908937003768 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 908937003769 putative acyl-acceptor binding pocket; other site 908937003770 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 908937003771 Bacterial Ig-like domain; Region: Big_5; pfam13205 908937003772 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; cl01930 908937003773 GH3 auxin-responsive promoter; Region: GH3; pfam03321 908937003774 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 908937003775 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 908937003776 alpha-galactosidase; Region: PLN02808; cl17638 908937003777 NPCBM/NEW2 domain; Region: NPCBM; cl07060 908937003778 NPCBM/NEW2 domain; Region: NPCBM; cl07060 908937003779 NPCBM/NEW2 domain; Region: NPCBM; cl07060 908937003780 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 908937003781 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 908937003782 dimerization interface [polypeptide binding]; other site 908937003783 active site 908937003784 metal binding site [ion binding]; metal-binding site 908937003785 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 908937003786 dsRNA binding site [nucleotide binding]; other site 908937003787 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 908937003788 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 908937003789 dimer interface [polypeptide binding]; other site 908937003790 active site 908937003791 acyl carrier protein; Provisional; Region: acpP; PRK00982 908937003792 Protein of unknown function (DUF4254); Region: DUF4254; pfam14063 908937003793 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 908937003794 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 908937003795 putative active site [active] 908937003796 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 908937003797 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 908937003798 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 908937003799 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 908937003800 putative active site [active] 908937003801 Putative lipopolysaccharide-modifying enzyme; Region: CAP10; smart00672 908937003802 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 908937003803 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 908937003804 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 908937003805 active site 908937003806 catalytic tetrad [active] 908937003807 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional; Region: PRK02048 908937003808 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 908937003809 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 908937003810 AIR carboxylase; Region: AIRC; cl00310 908937003811 PAP2 superfamily; Region: PAP2; pfam01569 908937003812 active site 908937003813 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 908937003814 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 908937003815 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 908937003816 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 908937003817 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 908937003818 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 908937003819 NAD-dependent deacetylase; Provisional; Region: PRK00481 908937003820 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 908937003821 NAD+ binding site [chemical binding]; other site 908937003822 substrate binding site [chemical binding]; other site 908937003823 Zn binding site [ion binding]; other site 908937003824 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 908937003825 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 908937003826 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 908937003827 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 908937003828 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 908937003829 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 908937003830 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 908937003831 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 908937003832 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 908937003833 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 908937003834 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 908937003835 putative DNA binding site [nucleotide binding]; other site 908937003836 putative Zn2+ binding site [ion binding]; other site 908937003837 AsnC family; Region: AsnC_trans_reg; pfam01037 908937003838 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 908937003839 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 908937003840 conserved cys residue [active] 908937003841 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 908937003842 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 908937003843 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]; Region: COG2355 908937003844 active site 908937003845 dimer interface [polypeptide binding]; other site 908937003846 M28 Zn-Peptidases; Region: M28_like_6; cd08656 908937003847 Peptidase family M28; Region: Peptidase_M28; pfam04389 908937003848 metal binding site [ion binding]; metal-binding site 908937003849 Virulence-associated protein E; Region: VirE; pfam05272 908937003850 Domain of unknown function (DUF386); Region: DUF386; cl01047 908937003851 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 908937003852 MutS domain I; Region: MutS_I; pfam01624 908937003853 MutS domain II; Region: MutS_II; pfam05188 908937003854 MutS domain III; Region: MutS_III; pfam05192 908937003855 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 908937003856 Walker A/P-loop; other site 908937003857 ATP binding site [chemical binding]; other site 908937003858 Q-loop/lid; other site 908937003859 ABC transporter signature motif; other site 908937003860 Walker B; other site 908937003861 D-loop; other site 908937003862 H-loop/switch region; other site 908937003863 AAA domain; Region: AAA_14; pfam13173 908937003864 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 908937003865 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 908937003866 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 908937003867 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 908937003868 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937003869 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 908937003870 Pectate lyase; Region: Pec_lyase_C; cl01593 908937003871 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 908937003872 Interdomain contacts; other site 908937003873 Cytokine receptor motif; other site 908937003874 Fn3 associated; Region: Fn3_assoc; pfam13287 908937003875 Fn3 associated; Region: Fn3_assoc; pfam13287 908937003876 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 908937003877 Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]; Region: sufE; COG2166 908937003878 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 908937003879 Peptidase family U32; Region: Peptidase_U32; pfam01136 908937003880 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 908937003881 active site 908937003882 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 908937003883 active site 908937003884 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 908937003885 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 908937003886 active site 908937003887 HIGH motif; other site 908937003888 dimer interface [polypeptide binding]; other site 908937003889 KMSKS motif; other site 908937003890 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 908937003891 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 908937003892 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 908937003893 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 908937003894 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 908937003895 GTP-binding protein YchF; Reviewed; Region: PRK09601 908937003896 YchF GTPase; Region: YchF; cd01900 908937003897 G1 box; other site 908937003898 GTP/Mg2+ binding site [chemical binding]; other site 908937003899 Switch I region; other site 908937003900 G2 box; other site 908937003901 Switch II region; other site 908937003902 G3 box; other site 908937003903 G4 box; other site 908937003904 G5 box; other site 908937003905 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 908937003906 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 908937003907 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 908937003908 Acyltransferase family; Region: Acyl_transf_3; pfam01757 908937003909 Uncharacterized virulence-associated protein D [Function unknown]; Region: VapD; COG3309 908937003910 DNA polymerase I; Provisional; Region: PRK05755 908937003911 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 908937003912 active site 908937003913 metal binding site 1 [ion binding]; metal-binding site 908937003914 putative 5' ssDNA interaction site; other site 908937003915 metal binding site 3; metal-binding site 908937003916 metal binding site 2 [ion binding]; metal-binding site 908937003917 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 908937003918 putative DNA binding site [nucleotide binding]; other site 908937003919 putative metal binding site [ion binding]; other site 908937003920 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 908937003921 active site 908937003922 catalytic site [active] 908937003923 substrate binding site [chemical binding]; other site 908937003924 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 908937003925 active site 908937003926 DNA binding site [nucleotide binding] 908937003927 catalytic site [active] 908937003928 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 908937003929 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 908937003930 substrate binding pocket [chemical binding]; other site 908937003931 chain length determination region; other site 908937003932 substrate-Mg2+ binding site; other site 908937003933 catalytic residues [active] 908937003934 aspartate-rich region 1; other site 908937003935 active site lid residues [active] 908937003936 aspartate-rich region 2; other site 908937003937 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 908937003938 intersubunit interface [polypeptide binding]; other site 908937003939 active site 908937003940 catalytic residue [active] 908937003941 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain putative pyrophosphatase YpjD from Bacillus subtilis and its bacterial homologs; Region: NTP-PPase_BsYpjD; cd11531 908937003942 homodimer interface [polypeptide binding]; other site 908937003943 metal binding site [ion binding]; metal-binding site 908937003944 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 908937003945 putative active site [active] 908937003946 dimerization interface [polypeptide binding]; other site 908937003947 putative tRNAtyr binding site [nucleotide binding]; other site 908937003948 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 908937003949 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 908937003950 GIY-YIG motif/motif A; other site 908937003951 active site 908937003952 catalytic site [active] 908937003953 putative DNA binding site [nucleotide binding]; other site 908937003954 metal binding site [ion binding]; metal-binding site 908937003955 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 908937003956 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 908937003957 active site 908937003958 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 908937003959 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 908937003960 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 908937003961 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 908937003962 succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family; Region: sdhC_b558_fam; TIGR02046 908937003963 Succinate:quinone oxidoreductase (SQR)-like Type B subfamily 2, transmembrane subunit; composed of proteins with similarity to the SQRs of Geobacter metallireducens and Corynebacterium glutamicum. SQR catalyzes the oxidation of succinate to fumarate...; Region: SQR_TypeB_2_TM; cd03498 908937003964 putative Iron-sulfur protein interface [polypeptide binding]; other site 908937003965 proximal heme binding site [chemical binding]; other site 908937003966 distal heme binding site [chemical binding]; other site 908937003967 putative dimer interface [polypeptide binding]; other site 908937003968 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07573 908937003969 L-aspartate oxidase; Provisional; Region: PRK06175 908937003970 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 908937003971 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated; Region: PRK07570 908937003972 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 908937003973 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 908937003974 Methyltransferase domain; Region: Methyltransf_26; pfam13659 908937003975 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 908937003976 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 908937003977 ATP binding site [chemical binding]; other site 908937003978 Mg2+ binding site [ion binding]; other site 908937003979 G-X-G motif; other site 908937003980 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second...; Region: TopoII_MutL_Trans; cl02783 908937003981 ATP binding site [chemical binding]; other site 908937003982 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 908937003983 active site 908937003984 putative metal-binding site [ion binding]; other site 908937003985 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 908937003986 GxxExxY protein; Region: GxxExxY; TIGR04256 908937003987 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 908937003988 C-terminal peptidase (prc); Region: prc; TIGR00225 908937003989 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 908937003990 protein binding site [polypeptide binding]; other site 908937003991 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 908937003992 Catalytic dyad [active] 908937003993 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 908937003994 Uncharacterized protein family UPF0054; Region: UPF0054; pfam02130 908937003995 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 908937003996 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937003997 active site 908937003998 nucleotide binding site [chemical binding]; other site 908937003999 HIGH motif; other site 908937004000 KMSKS motif; other site 908937004001 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 908937004002 Rhamnogalacturonan lyase of the polysaccharide lyase family 11; Region: RGL11; cd10318 908937004003 metal binding site [ion binding]; metal-binding site 908937004004 active site 908937004005 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 908937004006 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 908937004007 FMN binding site [chemical binding]; other site 908937004008 active site 908937004009 catalytic residues [active] 908937004010 substrate binding site [chemical binding]; other site 908937004011 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 908937004012 DNA protecting protein DprA; Region: dprA; TIGR00732 908937004013 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 908937004014 active site 908937004015 Protein of unknown function (DUF2851); Region: DUF2851; pfam11013 908937004016 Carbohydrate binding domain; Region: CBM_4_9; pfam02018 908937004017 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; cl01412 908937004018 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; cl01412 908937004019 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 908937004020 active site 908937004021 Fasciclin domain; Region: Fasciclin; cl02663 908937004022 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937004023 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937004024 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937004025 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937004026 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937004027 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937004028 SusD family; Region: SusD; pfam07980 908937004029 Fasciclin domain; Region: Fasciclin; cl02663 908937004030 Fasciclin domain; Region: Fasciclin; cl02663 908937004031 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 908937004032 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937004033 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937004034 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937004035 Glycosyl hydrolase catalytic core; Region: Glyco_hydro_cc; pfam11790 908937004036 Lipocalin-like domain; Region: Lipocalin_6; pfam13944 908937004037 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 908937004038 Putative glycoside hydrolase xylanase; Region: Xylanase; pfam13201 908937004039 Dihydrodipicolinate reductase [Amino acid transport and metabolism]; Region: DapB; COG0289 908937004040 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 908937004041 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 908937004042 Signal peptidase I [Intracellular trafficking and secretion]; Region: LepB; COG0681 908937004043 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 908937004044 Catalytic site [active] 908937004045 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 908937004046 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 908937004047 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 908937004048 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 908937004049 WbqC-like protein family; Region: WbqC; pfam08889 908937004050 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 908937004051 FMN binding site [chemical binding]; other site 908937004052 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 908937004053 dimer interface [polypeptide binding]; other site 908937004054 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 908937004055 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 908937004056 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 908937004057 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 908937004058 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 908937004059 putative substrate binding site [chemical binding]; other site 908937004060 putative ATP binding site [chemical binding]; other site 908937004061 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 908937004062 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 908937004063 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 908937004064 catalytic residues [active] 908937004065 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 908937004066 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 908937004067 ATP binding site [chemical binding]; other site 908937004068 Mg++ binding site [ion binding]; other site 908937004069 motif III; other site 908937004070 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 908937004071 nucleotide binding region [chemical binding]; other site 908937004072 ATP-binding site [chemical binding]; other site 908937004073 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 908937004074 RNA binding site [nucleotide binding]; other site 908937004075 Replication initiation factor; Region: Rep_trans; pfam02486 908937004076 Domain of unknown function (DUF334); Region: DUF334; pfam03904 908937004077 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 908937004078 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 908937004079 DnaA N-terminal domain; Region: DnaA_N; pfam11638 908937004080 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 908937004081 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 908937004082 Walker A motif; other site 908937004083 ATP binding site [chemical binding]; other site 908937004084 Walker B motif; other site 908937004085 arginine finger; other site 908937004086 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 908937004087 DnaA box-binding interface [nucleotide binding]; other site 908937004088 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 908937004089 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 908937004090 Carbohydrate binding domain; Region: CBM_4_9; pfam02018 908937004091 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; smart00813 908937004092 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; cl01412 908937004093 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 908937004094 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 908937004095 dimer interface [polypeptide binding]; other site 908937004096 putative anticodon binding site; other site 908937004097 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 908937004098 motif 1; other site 908937004099 active site 908937004100 motif 2; other site 908937004101 motif 3; other site 908937004102 Domain of unknown function (DUF4332); Region: DUF4332; pfam14229 908937004103 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GpsA; COG0240 908937004104 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 908937004105 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 908937004106 glucose-6-phosphate isomerase; Provisional; Region: pgi; PRK14097 908937004107 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 908937004108 active site 908937004109 dimer interface [polypeptide binding]; other site 908937004110 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 908937004111 dimer interface [polypeptide binding]; other site 908937004112 active site 908937004113 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 908937004114 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 908937004115 motif II; other site 908937004116 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 908937004117 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 908937004118 CRISPR-associated helicase Cas3; Region: cas3_core; TIGR01587 908937004119 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 908937004120 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-C; cd09651 908937004121 CRISPR-associated protein (Cas_Cas5); Region: Cas_Cas5d; pfam09704 908937004122 CRISPR/Cas system-associated protein Cas8c; Region: Cas8c_I-C; cd09757 908937004123 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cl01465 908937004124 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 908937004125 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 908937004126 Domain of unknown function (DUF4270); Region: DUF4270; pfam14092 908937004127 Starch synthase catalytic domain; Region: Glyco_transf_5; pfam08323 908937004128 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06549 908937004129 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 908937004130 carboxyltransferase (CT) interaction site; other site 908937004131 biotinylation site [posttranslational modification]; other site 908937004132 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 908937004133 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 908937004134 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 908937004135 fumarate hydratase; Provisional; Region: PRK15389 908937004136 Tartrate dehydratase alpha subunit/Fumarate hydratase class I, N-terminal domain [Energy production and conversion]; Region: TtdA; COG1951 908937004137 Fumarase C-terminus; Region: Fumerase_C; pfam05683 908937004138 ADP-glucose pyrophosphorylase [Carbohydrate transport and metabolism]; Region: GlgC; COG0448 908937004139 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 908937004140 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 908937004141 HflX GTPase family; Region: HflX; cd01878 908937004142 G1 box; other site 908937004143 GTP/Mg2+ binding site [chemical binding]; other site 908937004144 Switch I region; other site 908937004145 G2 box; other site 908937004146 G3 box; other site 908937004147 Switch II region; other site 908937004148 G4 box; other site 908937004149 G5 box; other site 908937004150 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 908937004151 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 908937004152 active site 908937004153 trimer interface [polypeptide binding]; other site 908937004154 allosteric site; other site 908937004155 active site lid [active] 908937004156 hexamer (dimer of trimers) interface [polypeptide binding]; other site 908937004157 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 908937004158 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 908937004159 Part of AAA domain; Region: AAA_19; pfam13245 908937004160 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 908937004161 active site 908937004162 catalytic site [active] 908937004163 substrate binding site [chemical binding]; other site 908937004164 Family description; Region: UvrD_C_2; pfam13538 908937004165 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 908937004166 GxxExxY protein; Region: GxxExxY; TIGR04256 908937004167 OPT oligopeptide transporter protein; Region: OPT; pfam03169 908937004168 putative oligopeptide transporter, OPT family; Region: TIGR00733 908937004169 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 908937004170 Clp amino terminal domain; Region: Clp_N; pfam02861 908937004171 Clp amino terminal domain; Region: Clp_N; pfam02861 908937004172 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 908937004173 Walker A motif; other site 908937004174 ATP binding site [chemical binding]; other site 908937004175 Walker B motif; other site 908937004176 arginine finger; other site 908937004177 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 908937004178 Walker A motif; other site 908937004179 ATP binding site [chemical binding]; other site 908937004180 Walker B motif; other site 908937004181 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 908937004182 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 908937004183 LytB protein; Region: LYTB; cl00507 908937004184 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 908937004185 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 908937004186 MG2 domain; Region: A2M_N; pfam01835 908937004187 Alpha-2-macroglobulin family; Region: A2M; pfam00207 908937004188 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 908937004189 glutamine synthetase, type I; Region: GlnA; TIGR00653 908937004190 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 908937004191 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 908937004192 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 908937004193 Class I aldolases; Region: Aldolase_Class_I; cl17187 908937004194 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 908937004195 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 908937004196 cytidylate kinase; Provisional; Region: cmk; PRK00023 908937004197 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 908937004198 CMP-binding site; other site 908937004199 The sites determining sugar specificity; other site 908937004200 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 908937004201 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 908937004202 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 908937004203 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 908937004204 substrate binding pocket [chemical binding]; other site 908937004205 chain length determination region; other site 908937004206 substrate-Mg2+ binding site; other site 908937004207 catalytic residues [active] 908937004208 aspartate-rich region 1; other site 908937004209 active site lid residues [active] 908937004210 aspartate-rich region 2; other site 908937004211 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 908937004212 active site 908937004213 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 908937004214 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 908937004215 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 908937004216 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 908937004217 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 908937004218 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 908937004219 putative DNA binding site [nucleotide binding]; other site 908937004220 putative Zn2+ binding site [ion binding]; other site 908937004221 AsnC family; Region: AsnC_trans_reg; pfam01037 908937004222 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 908937004223 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 908937004224 folate binding site [chemical binding]; other site 908937004225 NADP+ binding site [chemical binding]; other site 908937004226 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 908937004227 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 908937004228 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; pfam13636 908937004229 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 908937004230 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937004231 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 908937004232 DNA binding residues [nucleotide binding] 908937004233 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 908937004234 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 908937004235 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 908937004236 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 908937004237 putative active site; other site 908937004238 catalytic triad [active] 908937004239 putative dimer interface [polypeptide binding]; other site 908937004240 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 908937004241 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 908937004242 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 908937004243 metal-binding site [ion binding] 908937004244 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 908937004245 Glycosyl hydrolase family 53; Region: Glyco_hydro_53; cl06672 908937004246 Glycosyl hydrolases family 35; Region: Glyco_hydro_35; pfam01301 908937004247 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937004248 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937004249 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937004250 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937004251 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 908937004252 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 908937004253 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 908937004254 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 908937004255 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 908937004256 dimer interface [polypeptide binding]; other site 908937004257 phosphorylation site [posttranslational modification] 908937004258 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 908937004259 ATP binding site [chemical binding]; other site 908937004260 Mg2+ binding site [ion binding]; other site 908937004261 G-X-G motif; other site 908937004262 Helix-turn-helix domain; Region: HTH_18; pfam12833 908937004263 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937004264 Uncharacterized conserved protein [Function unknown]; Region: COG2966 908937004265 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 908937004266 Protein of unknown function (DUF3815); Region: DUF3815; pfam12821 908937004267 putative transporter; Validated; Region: PRK03818 908937004268 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 908937004269 TrkA-C domain; Region: TrkA_C; pfam02080 908937004270 AspT/YidE/YbjL antiporter duplication domain; Region: YidE_YbjL_dupl; TIGR01625 908937004271 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 908937004272 Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain; Region: NAGLU_N; pfam12971 908937004273 Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain; Region: NAGLU; pfam05089 908937004274 Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain; Region: NAGLU_C; pfam12972 908937004275 Pectate lyase superfamily protein; Region: Pectate_lyase_3; pfam12708 908937004276 Right handed beta helix region; Region: Beta_helix; pfam13229 908937004277 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 908937004278 CoenzymeA binding site [chemical binding]; other site 908937004279 subunit interaction site [polypeptide binding]; other site 908937004280 PHB binding site; other site 908937004281 aminodeoxychorismate synthase, component I, clade 2; Region: PabB-clade2; TIGR01824 908937004282 chorismate binding enzyme; Region: Chorismate_bind; cl10555 908937004283 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylic-acid synthase; Region: menD; TIGR00173 908937004284 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 908937004285 dimer interface [polypeptide binding]; other site 908937004286 tetramer interface [polypeptide binding]; other site 908937004287 PYR/PP interface [polypeptide binding]; other site 908937004288 TPP binding site [chemical binding]; other site 908937004289 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 908937004290 TPP-binding site [chemical binding]; other site 908937004291 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 908937004292 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 908937004293 substrate binding site [chemical binding]; other site 908937004294 oxyanion hole (OAH) forming residues; other site 908937004295 trimer interface [polypeptide binding]; other site 908937004296 GxxExxY protein; Region: GxxExxY; TIGR04256 908937004297 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 908937004298 o-succinylbenzoate synthase; Region: menC_gamma/gm+; TIGR01927 908937004299 active site 908937004300 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 908937004301 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 908937004302 acyl-activating enzyme (AAE) consensus motif; other site 908937004303 AMP binding site [chemical binding]; other site 908937004304 active site 908937004305 CoA binding site [chemical binding]; other site 908937004306 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 908937004307 active site 908937004308 dimer interface [polypeptide binding]; other site 908937004309 metal binding site [ion binding]; metal-binding site 908937004310 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937004311 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 908937004312 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937004313 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 908937004314 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 908937004315 N-terminal plug; other site 908937004316 ligand-binding site [chemical binding]; other site 908937004317 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 908937004318 RNA binding surface [nucleotide binding]; other site 908937004319 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 908937004320 putative active site [active] 908937004321 catalytic residue [active] 908937004322 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 908937004323 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 908937004324 5S rRNA interface [nucleotide binding]; other site 908937004325 CTC domain interface [polypeptide binding]; other site 908937004326 L16 interface [polypeptide binding]; other site 908937004327 transcription antitermination factor NusB; Region: nusB; TIGR01951 908937004328 Preprotein translocase subunit; Region: YajC; pfam02699 908937004329 YbbR-like protein; Region: YbbR; pfam07949 908937004330 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 908937004331 dephospho-CoA kinase; Provisional; Region: coaE; PRK14731 908937004332 CoA-binding site [chemical binding]; other site 908937004333 ATP-binding [chemical binding]; other site 908937004334 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 908937004335 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 908937004336 putative dimer interface [polypeptide binding]; other site 908937004337 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 908937004338 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 908937004339 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 908937004340 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 908937004341 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 908937004342 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]; Region: COG5016 908937004343 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 908937004344 active site 908937004345 metal binding site [ion binding]; metal-binding site 908937004346 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 908937004347 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 908937004348 Zn2+ binding site [ion binding]; other site 908937004349 Mg2+ binding site [ion binding]; other site 908937004350 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 908937004351 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 908937004352 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 908937004353 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 908937004354 catalytic residue [active] 908937004355 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 908937004356 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 908937004357 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937004358 homodimer interface [polypeptide binding]; other site 908937004359 catalytic residue [active] 908937004360 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 908937004361 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 908937004362 TrkA-C domain; Region: TrkA_C; pfam02080 908937004363 TrkA-C domain; Region: TrkA_C; pfam02080 908937004364 peptidase T; Region: peptidase-T; TIGR01882 908937004365 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 908937004366 metal binding site [ion binding]; metal-binding site 908937004367 dimer interface [polypeptide binding]; other site 908937004368 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 908937004369 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 908937004370 Coenzyme A binding pocket [chemical binding]; other site 908937004371 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 908937004372 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 908937004373 Domain of unknown function (DUF303); Region: DUF303; pfam03629 908937004374 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 908937004375 Domain of unknown function DUF20; Region: UPF0118; pfam01594 908937004376 thymidine kinase; Provisional; Region: PRK04296 908937004377 Diphthamide biosynthesis methyltransferase [Translation, ribosomal structure and biogenesis]; Region: DPH5; COG1798 908937004378 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 908937004379 putative SAM binding site [chemical binding]; other site 908937004380 putative homodimer interface [polypeptide binding]; other site 908937004381 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 908937004382 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 908937004383 nucleoside/Zn binding site; other site 908937004384 dimer interface [polypeptide binding]; other site 908937004385 catalytic motif [active] 908937004386 hypothetical protein; Reviewed; Region: PRK12497 908937004387 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 908937004388 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 908937004389 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 908937004390 putative nucleotide binding site [chemical binding]; other site 908937004391 uridine monophosphate binding site [chemical binding]; other site 908937004392 homohexameric interface [polypeptide binding]; other site 908937004393 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 908937004394 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 908937004395 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937004396 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937004397 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937004398 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937004399 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937004400 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937004401 SusD family; Region: SusD; pfam07980 908937004402 Alpha-L-fucosidase; Region: Alpha_L_fucos; smart00812 908937004403 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 908937004404 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 908937004405 Y-family of DNA polymerases; Region: PolY; cl12025 908937004406 active site 908937004407 DNA binding site [nucleotide binding] 908937004408 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 908937004409 catalytic triad [active] 908937004410 conserved cis-peptide bond; other site 908937004411 Protein of unknown function (DUF328); Region: DUF328; pfam03883 908937004412 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]; Region: COG4545 908937004413 seryl-tRNA synthetase; Provisional; Region: PRK05431 908937004414 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 908937004415 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 908937004416 dimer interface [polypeptide binding]; other site 908937004417 active site 908937004418 motif 1; other site 908937004419 motif 2; other site 908937004420 motif 3; other site 908937004421 putative bifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta; Provisional; Region: PRK12778 908937004422 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)...; Region: DHOD_e_trans_like1; cd06219 908937004423 FAD binding pocket [chemical binding]; other site 908937004424 FAD binding motif [chemical binding]; other site 908937004425 phosphate binding motif [ion binding]; other site 908937004426 beta-alpha-beta structure motif; other site 908937004427 NAD binding pocket [chemical binding]; other site 908937004428 Iron coordination center [ion binding]; other site 908937004429 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 908937004430 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 908937004431 Protein of unknown function (DUF2968); Region: DUF2968; pfam11180 908937004432 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 908937004433 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 908937004434 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 908937004435 trmE is a tRNA modification GTPase; Region: trmE; cd04164 908937004436 G1 box; other site 908937004437 GTP/Mg2+ binding site [chemical binding]; other site 908937004438 Switch I region; other site 908937004439 G2 box; other site 908937004440 Switch II region; other site 908937004441 G3 box; other site 908937004442 G4 box; other site 908937004443 G5 box; other site 908937004444 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 908937004445 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 908937004446 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 908937004447 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 908937004448 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 908937004449 Protein of unknwon function (DUF2893); Region: DUF2893; pfam11459 908937004450 Helix-turn-helix domain; Region: HTH_17; pfam12728 908937004451 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 908937004452 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 908937004453 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 908937004454 Walker A motif; other site 908937004455 ATP binding site [chemical binding]; other site 908937004456 Walker B motif; other site 908937004457 arginine finger; other site 908937004458 Spi protease inhibitor; Region: Inhibitor_I69; pfam13734 908937004459 Peptidase C10 family; Region: Peptidase_C10; pfam01640 908937004460 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 908937004461 DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]; Region: NUC1; COG1864 908937004462 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 908937004463 active site 908937004464 substrate binding site [chemical binding]; other site 908937004465 Mg2+ binding site [ion binding]; other site 908937004466 Phosphomannose isomerase [Carbohydrate transport and metabolism]; Region: ManA; COG1482 908937004467 Alpha-Mannosidase Binding Domain of Atg19/34; Region: ABD; cl15429 908937004468 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 908937004469 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 908937004470 Substrate binding site; other site 908937004471 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 908937004472 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 908937004473 NAD binding site [chemical binding]; other site 908937004474 substrate binding site [chemical binding]; other site 908937004475 homodimer interface [polypeptide binding]; other site 908937004476 active site 908937004477 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 908937004478 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 908937004479 catalytic triad [active] 908937004480 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 908937004481 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 908937004482 catalytic residues [active] 908937004483 MarR family; Region: MarR_2; pfam12802 908937004484 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 908937004485 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of...; Region: Band_7_flotillin; cd03399 908937004486 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 908937004487 active site 908937004488 xanthine permease; Region: pbuX; TIGR03173 908937004489 probable metal-binding protein; Region: matur_matur; TIGR03853 908937004490 Rhamnogalacturonan lyase of the polysaccharide lyase family 11; Region: RGL11; cd10318 908937004491 metal binding site [ion binding]; metal-binding site 908937004492 active site 908937004493 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937004494 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 908937004495 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 908937004496 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937004497 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 908937004498 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 908937004499 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 908937004500 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 908937004501 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 908937004502 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 908937004503 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 908937004504 catalytic residues [active] 908937004505 Alginate Lyase A1-III; enzymatically depolymerizes alginate, a complex copolymer of beta-D-mannuronate and alpha-L-guluronate, by cleaving the beta-(1,4) glycosidic bond; Region: AlgLyase; cl00179 908937004506 Glycosyl hydrolases family 28; Region: Glyco_hydro_28; pfam00295 908937004507 Glycosyl Hydrolase Family 88; Region: Glyco_hydro_88; pfam07470 908937004508 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 908937004509 S-adenosylmethionine binding site [chemical binding]; other site 908937004510 Domain of unknown function DUF59; Region: DUF59; pfam01883 908937004511 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 908937004512 Walker A motif; other site 908937004513 cell division ATPase MinD, archaeal; Region: minD_arch; TIGR01969 908937004514 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 908937004515 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 908937004516 ATP binding site [chemical binding]; other site 908937004517 Mg++ binding site [ion binding]; other site 908937004518 motif III; other site 908937004519 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 908937004520 nucleotide binding region [chemical binding]; other site 908937004521 ATP-binding site [chemical binding]; other site 908937004522 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 908937004523 binding surface 908937004524 TPR motif; other site 908937004525 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 908937004526 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 908937004527 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 908937004528 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 908937004529 ligand binding site [chemical binding]; other site 908937004530 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 908937004531 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 908937004532 DNA binding residues [nucleotide binding] 908937004533 dimerization interface [polypeptide binding]; other site 908937004534 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937004535 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 908937004536 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 908937004537 motif II; other site 908937004538 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 908937004539 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 908937004540 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 908937004541 active site 908937004542 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 908937004543 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 908937004544 active site 908937004545 nucleophile elbow; other site 908937004546 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 908937004547 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 908937004548 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]; Region: COG1924 908937004549 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 908937004550 CoA enzyme activase uncharacterized domain (DUF2229); Region: DUF2229; cl17855 908937004551 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 908937004552 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3581 908937004553 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 908937004554 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 908937004555 dimerization interface [polypeptide binding]; other site 908937004556 DPS ferroxidase diiron center [ion binding]; other site 908937004557 ion pore; other site 908937004558 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 908937004559 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 908937004560 catalytic residue [active] 908937004561 TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then...; Region: AhpF_NTD_C; cd03026 908937004562 catalytic residues [active] 908937004563 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 908937004564 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 908937004565 peroxiredoxin; Region: AhpC; TIGR03137 908937004566 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 908937004567 dimer interface [polypeptide binding]; other site 908937004568 decamer (pentamer of dimers) interface [polypeptide binding]; other site 908937004569 catalytic triad [active] 908937004570 peroxidatic and resolving cysteines [active] 908937004571 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 908937004572 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 908937004573 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 908937004574 Transcriptional regulator [Transcription]; Region: LysR; COG0583 908937004575 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 908937004576 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 908937004577 dimerization interface [polypeptide binding]; other site 908937004578 serine O-acetyltransferase; Region: cysE; TIGR01172 908937004579 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 908937004580 trimer interface [polypeptide binding]; other site 908937004581 active site 908937004582 substrate binding site [chemical binding]; other site 908937004583 CoA binding site [chemical binding]; other site 908937004584 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 908937004585 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 908937004586 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 908937004587 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 908937004588 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 908937004589 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 908937004590 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 908937004591 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 908937004592 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 908937004593 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 908937004594 Predicted membrane protein [Function unknown]; Region: COG1238 908937004595 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 908937004596 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 908937004597 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 908937004598 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 908937004599 active site 908937004600 dimer interface [polypeptide binding]; other site 908937004601 motif 1; other site 908937004602 motif 2; other site 908937004603 motif 3; other site 908937004604 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 908937004605 anticodon binding site; other site 908937004606 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 908937004607 TPR motif; other site 908937004608 TPR repeat; Region: TPR_11; pfam13414 908937004609 binding surface 908937004610 TPR repeat; Region: TPR_11; pfam13414 908937004611 TPR repeat; Region: TPR_11; pfam13414 908937004612 TPR repeat; Region: TPR_11; pfam13414 908937004613 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 908937004614 binding surface 908937004615 TPR motif; other site 908937004616 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 908937004617 TPR motif; other site 908937004618 TPR repeat; Region: TPR_11; pfam13414 908937004619 binding surface 908937004620 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 908937004621 TPR motif; other site 908937004622 TPR repeat; Region: TPR_11; pfam13414 908937004623 binding surface 908937004624 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 908937004625 active site 908937004626 catalytic residues [active] 908937004627 metal binding site [ion binding]; metal-binding site 908937004628 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 908937004629 Sporulation related domain; Region: SPOR; pfam05036 908937004630 Transposase; Region: DEDD_Tnp_IS110; pfam01548 908937004631 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 908937004632 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 908937004633 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 908937004634 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 908937004635 active site 908937004636 substrate binding site [chemical binding]; other site 908937004637 metal binding site [ion binding]; metal-binding site 908937004638 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 908937004639 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 908937004640 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 908937004641 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 908937004642 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 908937004643 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 908937004644 Substrate binding site; other site 908937004645 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 908937004646 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937004647 Walker A/P-loop; other site 908937004648 ATP binding site [chemical binding]; other site 908937004649 Q-loop/lid; other site 908937004650 ABC transporter signature motif; other site 908937004651 Walker B; other site 908937004652 D-loop; other site 908937004653 H-loop/switch region; other site 908937004654 ABC transporter; Region: ABC_tran_2; pfam12848 908937004655 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 908937004656 GrpE; Region: GrpE; pfam01025 908937004657 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 908937004658 dimer interface [polypeptide binding]; other site 908937004659 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 908937004660 chaperone protein DnaJ; Provisional; Region: PRK14289 908937004661 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 908937004662 HSP70 interaction site [polypeptide binding]; other site 908937004663 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 908937004664 Zn binding sites [ion binding]; other site 908937004665 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 908937004666 dimer interface [polypeptide binding]; other site 908937004667 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 908937004668 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 908937004669 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 908937004670 active site 908937004671 catalytic residues [active] 908937004672 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 908937004673 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 908937004674 putative substrate translocation pore; other site 908937004675 Galactokinase [Carbohydrate transport and metabolism]; Region: GalK; COG0153 908937004676 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 908937004677 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 908937004678 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 908937004679 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 908937004680 active site 908937004681 catalytic residues [active] 908937004682 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 908937004683 Na binding site [ion binding]; other site 908937004684 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 908937004685 nudix motif; other site 908937004686 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 908937004687 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 908937004688 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 908937004689 intersubunit interface [polypeptide binding]; other site 908937004690 active site 908937004691 Zn2+ binding site [ion binding]; other site 908937004692 L-arabinose isomerase; Provisional; Region: PRK02929 908937004693 L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose...; Region: L-fuc_L-ara-isomerases; cl00947 908937004694 hexamer (dimer of trimers) interface [polypeptide binding]; other site 908937004695 trimer interface [polypeptide binding]; other site 908937004696 substrate binding site [chemical binding]; other site 908937004697 Mn binding site [ion binding]; other site 908937004698 L-ribulokinase-like proteins; a subfamily of the FGGY family of carbohydrate kinases; Region: FGGY_L-RBK_like; cd07778 908937004699 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 908937004700 putative N- and C-terminal domain interface [polypeptide binding]; other site 908937004701 putative active site [active] 908937004702 MgATP binding site [chemical binding]; other site 908937004703 catalytic site [active] 908937004704 metal binding site [ion binding]; metal-binding site 908937004705 putative carbohydrate binding site [chemical binding]; other site 908937004706 Alpha-L-arabinofuranosidase [Carbohydrate transport and metabolism]; Region: AbfA; COG3534 908937004707 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; pfam06964 908937004708 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 908937004709 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 908937004710 TPP-binding site [chemical binding]; other site 908937004711 dimer interface [polypeptide binding]; other site 908937004712 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 908937004713 PYR/PP interface [polypeptide binding]; other site 908937004714 dimer interface [polypeptide binding]; other site 908937004715 TPP binding site [chemical binding]; other site 908937004716 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 908937004717 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 908937004718 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 908937004719 IHF - DNA interface [nucleotide binding]; other site 908937004720 IHF dimer interface [polypeptide binding]; other site 908937004721 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 908937004722 Part of AAA domain; Region: AAA_19; pfam13245 908937004723 Family description; Region: UvrD_C_2; pfam13538 908937004724 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 908937004725 Transglycosylase; Region: Transgly; cl17702 908937004726 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 908937004727 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 908937004728 ligand binding site [chemical binding]; other site 908937004729 prolyl-tRNA synthetase; Provisional; Region: PRK08661 908937004730 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_arch_euk; cd00778 908937004731 dimer interface [polypeptide binding]; other site 908937004732 motif 1; other site 908937004733 active site 908937004734 motif 2; other site 908937004735 motif 3; other site 908937004736 ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in...; Region: ProRS_anticodon_zinc; cd00862 908937004737 anticodon binding site; other site 908937004738 zinc-binding site [ion binding]; other site 908937004739 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 908937004740 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 908937004741 hexamer interface [polypeptide binding]; other site 908937004742 ligand binding site [chemical binding]; other site 908937004743 putative active site [active] 908937004744 NAD(P) binding site [chemical binding]; other site 908937004745 Domain of unknown function (DUF4250); Region: DUF4250; pfam14056 908937004746 Glutamine Amidotransferase (GATase_I) involved in pyridoxine biosynthesis; Region: GATase1_PB; cd01749 908937004747 predicted active site [active] 908937004748 catalytic triad [active] 908937004749 pyridoxal 5'-phosphate synthase, synthase subunit Pdx1; Region: TIGR00343 908937004750 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 908937004751 active site 908937004752 multimer interface [polypeptide binding]; other site 908937004753 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 908937004754 substrate binding site [chemical binding]; other site 908937004755 dimer interface [polypeptide binding]; other site 908937004756 ATP binding site [chemical binding]; other site 908937004757 Helix-turn-helix domain; Region: HTH_18; pfam12833 908937004758 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 908937004759 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 908937004760 glutaminase active site [active] 908937004761 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 908937004762 dimer interface [polypeptide binding]; other site 908937004763 active site 908937004764 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 908937004765 dimer interface [polypeptide binding]; other site 908937004766 active site 908937004767 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 908937004768 Domain of unknown function (DUF4359); Region: DUF4359; pfam14271 908937004769 Glycosyl hydrolase family 67 N-terminus; Region: Glyco_hydro_67N; pfam03648 908937004770 Uncharacterized protein family UPF0027; Region: UPF0027; cl17455 908937004771 Glycosyl hydrolase family 67 middle domain; Region: Glyco_hydro_67M; pfam07488 908937004772 Glycosyl hydrolase family 67 C-terminus; Region: Glyco_hydro_67C; pfam07477 908937004773 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 908937004774 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_1; cd09000 908937004775 inhibitor binding site; inhibition site 908937004776 active site 908937004777 Two component regulator propeller; Region: Reg_prop; pfam07494 908937004778 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 908937004779 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 908937004780 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 908937004781 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 908937004782 dimer interface [polypeptide binding]; other site 908937004783 phosphorylation site [posttranslational modification] 908937004784 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 908937004785 ATP binding site [chemical binding]; other site 908937004786 Mg2+ binding site [ion binding]; other site 908937004787 G-X-G motif; other site 908937004788 Response regulator receiver domain; Region: Response_reg; pfam00072 908937004789 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 908937004790 active site 908937004791 phosphorylation site [posttranslational modification] 908937004792 intermolecular recognition site; other site 908937004793 dimerization interface [polypeptide binding]; other site 908937004794 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937004795 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937004796 Glycosyl hydrolase family 43, includes arabinoxylan arabinofuranohydrolase, beta-xylosidase, endo-1,4-beta-xylanase, alpha-L-arabinofuranosidase; Region: GH43_AXH_like; cd08990 908937004797 substrate binding site [chemical binding]; other site 908937004798 active site 908937004799 Glycosyl hydrolase family 10; Region: Glyco_hydro_10; pfam00331 908937004800 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 908937004801 MFS/sugar transport protein; Region: MFS_2; pfam13347 908937004802 Domain of unknown function (DUF303); Region: DUF303; pfam03629 908937004803 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 908937004804 Domain of unknown function (DUF303); Region: DUF303; pfam03629 908937004805 O-Glycosyl hydrolase [Cell envelope biogenesis, outer membrane]; Region: COG5520 908937004806 O-Glycosyl hydrolase family 30; Region: Glyco_hydro_30; pfam02055 908937004807 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937004808 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937004809 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937004810 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937004811 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 908937004812 Fasciclin domain; Region: Fasciclin; cl02663 908937004813 Fasciclin domain; Region: Fasciclin; pfam02469 908937004814 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937004815 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937004816 SusD family; Region: SusD; pfam07980 908937004817 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937004818 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937004819 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937004820 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937004821 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 908937004822 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_2; cd09001 908937004823 active site 908937004824 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 908937004825 D-xylulose kinase; Region: XylB; TIGR01312 908937004826 nucleotide binding site [chemical binding]; other site 908937004827 xylose isomerase; Provisional; Region: PRK05474 908937004828 xylose isomerase; Region: xylose_isom_A; TIGR02630 908937004829 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 908937004830 TrkA-C domain; Region: TrkA_C; pfam02080 908937004831 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 908937004832 RNA polymerase sigma factor, cyanobacterial RpoD-like family; Region: Sig70-cyanoRpoD; TIGR02997 908937004833 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937004834 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 908937004835 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 908937004836 DNA binding residues [nucleotide binding] 908937004837 Phosphotransferase enzyme family; Region: APH; pfam01636 908937004838 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; cl17270 908937004839 DOMON-like type 9 carbohydrate binding module; Region: CBM9_like_3; cd09620 908937004840 putative ligand binding site [chemical binding]; other site 908937004841 Protein of unknown function (DUF1232); Region: DUF1232; pfam06803 908937004842 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 908937004843 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 908937004844 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 908937004845 protein binding site [polypeptide binding]; other site 908937004846 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 908937004847 protein binding site [polypeptide binding]; other site 908937004848 SynChlorMet cassette protein ScmC; Region: SCM_chp_ScmC; TIGR04249 908937004849 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cd06462 908937004850 Catalytic site [active] 908937004851 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 908937004852 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 908937004853 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 908937004854 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 908937004855 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 908937004856 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 908937004857 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937004858 Walker A/P-loop; other site 908937004859 ATP binding site [chemical binding]; other site 908937004860 Q-loop/lid; other site 908937004861 ABC transporter signature motif; other site 908937004862 Walker B; other site 908937004863 D-loop; other site 908937004864 H-loop/switch region; other site 908937004865 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 908937004866 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 908937004867 active site 908937004868 Pleckstrin homology-like domain; Region: PH-like; cl17171 908937004869 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 908937004870 Surface antigen; Region: Bac_surface_Ag; pfam01103 908937004871 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 908937004872 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 908937004873 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 908937004874 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 908937004875 active site 908937004876 motif I; other site 908937004877 motif II; other site 908937004878 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 908937004879 putative active site pocket [active] 908937004880 4-fold oligomerization interface [polypeptide binding]; other site 908937004881 metal binding residues [ion binding]; metal-binding site 908937004882 3-fold/trimer interface [polypeptide binding]; other site 908937004883 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 908937004884 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 908937004885 Toprim-like; Region: Toprim_2; pfam13155 908937004886 Histidine kinase; Region: His_kinase; pfam06580 908937004887 putative transposase OrfB; Reviewed; Region: PHA02517 908937004888 Integrase core domain; Region: rve; pfam00665 908937004889 Integrase core domain; Region: rve_3; pfam13683 908937004890 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937004891 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 908937004892 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937004893 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937004894 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cl00065 908937004895 Interdomain contacts; other site 908937004896 Cytokine receptor motif; other site 908937004897 Domain of unknown function (DUF4302); Region: DUF4302; pfam14135 908937004898 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937004899 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937004900 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937004901 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937004902 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 908937004903 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 908937004904 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 908937004905 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 908937004906 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 908937004907 DNA binding residues [nucleotide binding] 908937004908 dimerization interface [polypeptide binding]; other site 908937004909 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 908937004910 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 908937004911 active site 908937004912 Int/Topo IB signature motif; other site 908937004913 DNA binding site [nucleotide binding] 908937004914 Transposase; Region: DEDD_Tnp_IS110; pfam01548 908937004915 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 908937004916 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 908937004917 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 908937004918 Rab5-interacting protein (Rab5ip); Region: Rab5ip; pfam07019 908937004919 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 908937004920 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 908937004921 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 908937004922 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 908937004923 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 908937004924 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 908937004925 NAD(P) binding site [chemical binding]; other site 908937004926 active site 908937004927 Alpha-L-rhamnosidase N-terminal domain; Region: Bac_rhamnosid_N; pfam08531 908937004928 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; pfam05592 908937004929 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 908937004930 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 908937004931 Carboxylesterase family; Region: COesterase; pfam00135 908937004932 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 908937004933 substrate binding pocket [chemical binding]; other site 908937004934 catalytic triad [active] 908937004935 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 908937004936 Carboxylesterase family; Region: COesterase; pfam00135 908937004937 substrate binding pocket [chemical binding]; other site 908937004938 catalytic triad [active] 908937004939 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 908937004940 PA14 domain; Region: PA14; pfam07691 908937004941 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 908937004942 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 908937004943 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 908937004944 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 908937004945 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 908937004946 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937004947 Walker A/P-loop; other site 908937004948 ATP binding site [chemical binding]; other site 908937004949 Q-loop/lid; other site 908937004950 ABC transporter signature motif; other site 908937004951 Walker B; other site 908937004952 D-loop; other site 908937004953 H-loop/switch region; other site 908937004954 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 908937004955 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937004956 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 908937004957 Walker A/P-loop; other site 908937004958 ATP binding site [chemical binding]; other site 908937004959 Q-loop/lid; other site 908937004960 ABC transporter signature motif; other site 908937004961 Walker B; other site 908937004962 D-loop; other site 908937004963 H-loop/switch region; other site 908937004964 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 908937004965 Protein export membrane protein; Region: SecD_SecF; cl14618 908937004966 Sterol-sensing domain of SREBP cleavage-activation; Region: Sterol-sensing; pfam12349 908937004967 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 908937004968 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 908937004969 active site 908937004970 DNA binding site [nucleotide binding] 908937004971 Int/Topo IB signature motif; other site 908937004972 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 908937004973 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 908937004974 active site 908937004975 phosphorylation site [posttranslational modification] 908937004976 intermolecular recognition site; other site 908937004977 dimerization interface [polypeptide binding]; other site 908937004978 LytTr DNA-binding domain; Region: LytTR; smart00850 908937004979 Histidine kinase; Region: His_kinase; pfam06580 908937004980 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 908937004981 Mg2+ binding site [ion binding]; other site 908937004982 G-X-G motif; other site 908937004983 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 908937004984 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 908937004985 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 908937004986 Walker A/P-loop; other site 908937004987 ATP binding site [chemical binding]; other site 908937004988 Q-loop/lid; other site 908937004989 ABC transporter signature motif; other site 908937004990 Walker B; other site 908937004991 D-loop; other site 908937004992 H-loop/switch region; other site 908937004993 Outer membrane efflux protein; Region: OEP; pfam02321 908937004994 Outer membrane efflux protein; Region: OEP; pfam02321 908937004995 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 908937004996 Lumazine binding domain; Region: Lum_binding; pfam00677 908937004997 Lumazine binding domain; Region: Lum_binding; pfam00677 908937004998 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 908937004999 SdiA-regulated; Region: SdiA-regulated; cd09971 908937005000 putative active site [active] 908937005001 Uncharacterized protein family (UPF0014); Region: UPF0014; cl00424 908937005002 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 908937005003 Walker A/P-loop; other site 908937005004 ATP binding site [chemical binding]; other site 908937005005 ABC transporter; Region: ABC_tran; pfam00005 908937005006 Q-loop/lid; other site 908937005007 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 908937005008 DNA gyrase subunit A; Validated; Region: PRK05560 908937005009 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 908937005010 CAP-like domain; other site 908937005011 active site 908937005012 primary dimer interface [polypeptide binding]; other site 908937005013 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 908937005014 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 908937005015 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 908937005016 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 908937005017 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 908937005018 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 908937005019 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 908937005020 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 908937005021 active site 908937005022 phosphorylation site [posttranslational modification] 908937005023 intermolecular recognition site; other site 908937005024 Tetratricopeptide repeat; Region: TPR_12; pfam13424 908937005025 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 908937005026 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 908937005027 ATP binding site [chemical binding]; other site 908937005028 Mg2+ binding site [ion binding]; other site 908937005029 G-X-G motif; other site 908937005030 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]; Region: Eda; COG0800 908937005031 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 908937005032 active site 908937005033 intersubunit interface [polypeptide binding]; other site 908937005034 catalytic residue [active] 908937005035 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 908937005036 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 908937005037 substrate binding site [chemical binding]; other site 908937005038 ATP binding site [chemical binding]; other site 908937005039 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 908937005040 DNA binding site [nucleotide binding] 908937005041 domain linker motif; other site 908937005042 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 908937005043 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 908937005044 ligand binding site [chemical binding]; other site 908937005045 galactarate dehydratase; Region: galactar-dH20; TIGR03248 908937005046 Domains similar to fish antifreeze type III protein; Region: SAF_AH_GD; cd11613 908937005047 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 908937005048 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 908937005049 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 908937005050 Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues; Region: GH25_muramidase; cl10448 908937005051 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 908937005052 active site 908937005053 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 908937005054 Double zinc ribbon; Region: DZR; pfam12773 908937005055 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 908937005056 Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues; Region: GH25_muramidase; cl10448 908937005057 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 908937005058 active site 908937005059 diphosphate--fructose-6-phosphate 1-phosphotransferase; Provisional; Region: PRK07085 908937005060 pyrophosphate-dependent phosphofructokinase; Region: PLN02251 908937005061 active site 908937005062 ADP/pyrophosphate binding site [chemical binding]; other site 908937005063 dimerization interface [polypeptide binding]; other site 908937005064 allosteric effector site; other site 908937005065 fructose-1,6-bisphosphate binding site; other site 908937005066 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 908937005067 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 908937005068 putative acyl-acceptor binding pocket; other site 908937005069 Carbohydrate Binding Module 6 (CBM6); appended to several carbohydrate binding enzymes, including several glycoside hydrolase (GH) family 26 mannanase domains; Region: CBM6_mannanase-like; cd04086 908937005070 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 908937005071 Interdomain contacts; other site 908937005072 Cytokine receptor motif; other site 908937005073 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 908937005074 hypothetical protein; Provisional; Region: PRK00955 908937005075 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 908937005076 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 908937005077 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 908937005078 dimerization interface 3.5A [polypeptide binding]; other site 908937005079 active site 908937005080 EamA-like transporter family; Region: EamA; cl17759 908937005081 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 908937005082 dihydrodipicolinate synthase; Region: dapA; TIGR00674 908937005083 dimer interface [polypeptide binding]; other site 908937005084 active site 908937005085 catalytic residue [active] 908937005086 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 908937005087 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 908937005088 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937005089 D-xylose transporter XylE; Provisional; Region: xylE; PRK10077 908937005090 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 908937005091 putative substrate translocation pore; other site 908937005092 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 908937005093 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 908937005094 TPR motif; other site 908937005095 binding surface 908937005096 TPR repeat; Region: TPR_11; pfam13414 908937005097 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 908937005098 binding surface 908937005099 TPR motif; other site 908937005100 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937005101 Transposase; Region: DEDD_Tnp_IS110; pfam01548 908937005102 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 908937005103 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 908937005104 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 908937005105 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937005106 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 908937005107 active site 908937005108 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 908937005109 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 908937005110 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 908937005111 active site 908937005112 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 908937005113 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 908937005114 active site 908937005115 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 908937005116 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 908937005117 POT family; Region: PTR2; cl17359 908937005118 POT family; Region: PTR2; cl17359 908937005119 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 908937005120 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 908937005121 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 908937005122 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 908937005123 C-terminal domain of CHU protein family; Region: CHU_C; pfam13585 908937005124 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 908937005125 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 908937005126 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 908937005127 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 908937005128 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 908937005129 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 908937005130 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 908937005131 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 908937005132 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 908937005133 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 908937005134 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 908937005135 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 908937005136 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 908937005137 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 908937005138 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 908937005139 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 908937005140 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 908937005141 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; pfam00329 908937005142 NADH dehydrogenase subunit D; Validated; Region: PRK06075; cl17338 908937005143 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 908937005144 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl17194 908937005145 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 908937005146 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 908937005147 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 908937005148 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 908937005149 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 908937005150 putative active site [active] 908937005151 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 908937005152 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 908937005153 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 908937005154 putative active site [active] 908937005155 catalytic site [active] 908937005156 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 908937005157 putative active site [active] 908937005158 catalytic site [active] 908937005159 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 908937005160 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_2; cd09001 908937005161 active site 908937005162 Putative glucose uptake permease [Carbohydrate transport and metabolism]; Region: GlcU; COG4975 908937005163 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 908937005164 Putative esterase; Region: Esterase; pfam00756 908937005165 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; pfam03747 908937005166 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; pfam03747 908937005167 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; pfam03747 908937005168 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937005169 SusD family; Region: SusD; pfam07980 908937005170 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937005171 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937005172 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937005173 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 908937005174 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 908937005175 substrate binding site [chemical binding]; other site 908937005176 dimer interface [polypeptide binding]; other site 908937005177 ATP binding site [chemical binding]; other site 908937005178 Transcriptional regulators [Transcription]; Region: PurR; COG1609 908937005179 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 908937005180 DNA binding site [nucleotide binding] 908937005181 domain linker motif; other site 908937005182 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 908937005183 dimerization interface [polypeptide binding]; other site 908937005184 ligand binding site [chemical binding]; other site 908937005185 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 908937005186 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 908937005187 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 908937005188 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 908937005189 lipoyl attachment site [posttranslational modification]; other site 908937005190 glycine dehydrogenase subunit 1; Validated; Region: PRK00451 908937005191 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 908937005192 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 908937005193 catalytic residue [active] 908937005194 glycine dehydrogenase subunit 2; Validated; Region: PRK04366 908937005195 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 908937005196 catalytic residue [active] 908937005197 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion]; Region: Lpd; COG1249 908937005198 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 908937005199 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 908937005200 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 908937005201 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 908937005202 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 908937005203 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 908937005204 IgA Peptidase M64; Region: Peptidase_M64; pfam09471 908937005205 TPR repeat; Region: TPR_11; pfam13414 908937005206 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 908937005207 binding surface 908937005208 TPR motif; other site 908937005209 Flavodoxin domain; Region: Flavodoxin_5; cl17428 908937005210 Ferredoxin [Energy production and conversion]; Region: COG1146 908937005211 4Fe-4S binding domain; Region: Fer4; pfam00037 908937005212 M6 family metalloprotease domain; Region: M6dom_TIGR03296 908937005213 Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]; Region: {ManC}; COG0662 908937005214 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 908937005215 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 908937005216 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 908937005217 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 908937005218 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 908937005219 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 908937005220 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 908937005221 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 908937005222 motif II; other site 908937005223 The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is...; Region: CBM20; cl15347 908937005224 starch-binding site 2 [chemical binding]; other site 908937005225 starch-binding site 1 [chemical binding]; other site 908937005226 YceG-like family; Region: YceG; pfam02618 908937005227 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 908937005228 dimerization interface [polypeptide binding]; other site 908937005229 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 908937005230 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937005231 active site 908937005232 HIGH motif; other site 908937005233 nucleotide binding site [chemical binding]; other site 908937005234 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937005235 active site 908937005236 KMSKS motif; other site 908937005237 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 908937005238 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 908937005239 TPR motif; other site 908937005240 binding surface 908937005241 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 908937005242 binding surface 908937005243 TPR motif; other site 908937005244 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 908937005245 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 908937005246 SurA N-terminal domain; Region: SurA_N_2; pfam13623 908937005247 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 908937005248 PPIC-type PPIASE domain; Region: Rotamase_3; pfam13616 908937005249 Domain of unknown function DUF21; Region: DUF21; pfam01595 908937005250 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 908937005251 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 908937005252 Transporter associated domain; Region: CorC_HlyC; smart01091 908937005253 flagellar hook protein FlgE, epsilon proteobacterial; Region: flgE_epsilon; TIGR02489 908937005254 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 908937005255 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 908937005256 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK12901 908937005257 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 908937005258 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 908937005259 nucleotide binding region [chemical binding]; other site 908937005260 ATP-binding site [chemical binding]; other site 908937005261 SEC-C motif; Region: SEC-C; pfam02810 908937005262 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 908937005263 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 908937005264 Walker A/P-loop; other site 908937005265 ATP binding site [chemical binding]; other site 908937005266 Q-loop/lid; other site 908937005267 ABC transporter signature motif; other site 908937005268 Walker B; other site 908937005269 D-loop; other site 908937005270 H-loop/switch region; other site 908937005271 N-terminal Early set domain associated with the catalytic domain of esterase; Region: E_set_Esterase_N; cd02858 908937005272 Putative esterase; Region: Esterase; pfam00756 908937005273 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 908937005274 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 908937005275 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 908937005276 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 908937005277 Low molecular weight phosphatase family; Region: LMWPc; cd00115 908937005278 active site 908937005279 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 908937005280 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 908937005281 motif II; other site 908937005282 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 908937005283 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 908937005284 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 908937005285 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 908937005286 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 908937005287 D-alanyl-D-alanine carboxypeptidase, serine-type, PBP4 family; Region: PBP4; TIGR00666 908937005288 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 908937005289 Secretin and TonB N terminus short domain; Region: STN; pfam07660 908937005290 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937005291 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 908937005292 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 908937005293 Domain of unknown function (DUF4249); Region: DUF4249; pfam14054 908937005294 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 908937005295 FecR protein; Region: FecR; pfam04773 908937005296 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937005297 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 908937005298 Listeria/Bacterioides repeat; Region: List_Bact_rpt; TIGR02543 908937005299 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937005300 Protease prsW family; Region: PrsW-protease; pfam13367 908937005301 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 908937005302 homotrimer interaction site [polypeptide binding]; other site 908937005303 putative active site [active] 908937005304 thiamine monophosphate kinase; Provisional; Region: PRK05731 908937005305 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 908937005306 ATP binding site [chemical binding]; other site 908937005307 dimerization interface [polypeptide binding]; other site 908937005308 purine nucleoside phosphorylase; Provisional; Region: PRK08202 908937005309 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 908937005310 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 908937005311 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 908937005312 tandem repeat interface [polypeptide binding]; other site 908937005313 oligomer interface [polypeptide binding]; other site 908937005314 active site residues [active] 908937005315 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 908937005316 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 908937005317 tandem repeat interface [polypeptide binding]; other site 908937005318 oligomer interface [polypeptide binding]; other site 908937005319 active site residues [active] 908937005320 Probable polygalacturonase At3g15720; Region: PLN03003; cl14103 908937005321 Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are...; Region: Rhamnogalacturan_acetylesterase_like; cd01821 908937005322 active site 908937005323 catalytic triad [active] 908937005324 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 908937005325 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 908937005326 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 908937005327 Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes; Region: FA58C; cl12042 908937005328 Uncharacterized conserved protein [Function unknown]; Region: COG2461 908937005329 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 908937005330 phosphodiesterase; Provisional; Region: PRK12704 908937005331 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 908937005332 Zn2+ binding site [ion binding]; other site 908937005333 Mg2+ binding site [ion binding]; other site 908937005334 Transcriptional regulators [Transcription]; Region: PurR; COG1609 908937005335 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 908937005336 DNA binding site [nucleotide binding] 908937005337 domain linker motif; other site 908937005338 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 908937005339 dimerization interface [polypeptide binding]; other site 908937005340 ligand binding site [chemical binding]; other site 908937005341 Protein of unknown function (DUF4230); Region: DUF4230; pfam14014 908937005342 Protein of unknown function (DUF4230); Region: DUF4230; pfam14014 908937005343 DpnII restriction endonuclease; Region: DpnII; pfam04556 908937005344 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 908937005345 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 908937005346 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 908937005347 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 908937005348 active site 908937005349 metal binding site [ion binding]; metal-binding site 908937005350 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 908937005351 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 908937005352 ABC transporter; Region: ABC_tran_2; pfam12848 908937005353 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 908937005354 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 908937005355 G1 box; other site 908937005356 GTP/Mg2+ binding site [chemical binding]; other site 908937005357 Switch I region; other site 908937005358 G2 box; other site 908937005359 G3 box; other site 908937005360 Switch II region; other site 908937005361 G4 box; other site 908937005362 G5 box; other site 908937005363 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 908937005364 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937005365 active site 908937005366 HIGH motif; other site 908937005367 nucleotide binding site [chemical binding]; other site 908937005368 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 908937005369 active site 908937005370 KMSKS motif; other site 908937005371 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 908937005372 tRNA binding surface [nucleotide binding]; other site 908937005373 anticodon binding site; other site 908937005374 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 908937005375 lipoprotein signal peptidase; Provisional; Region: PRK14788 908937005376 Domain of unknown function (DUF4296); Region: DUF4296; pfam14129 908937005377 Peptidase family C69; Region: Peptidase_C69; cl17793 908937005378 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 908937005379 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 908937005380 active site 908937005381 metal binding site [ion binding]; metal-binding site 908937005382 homotetramer interface [polypeptide binding]; other site 908937005383 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 908937005384 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 908937005385 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937005386 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 908937005387 DNA binding residues [nucleotide binding] 908937005388 Alpha-galactosidase [Carbohydrate transport and metabolism]; Region: GalA; COG3345 908937005389 Melibiase; Region: Melibiase; pfam02065 908937005390 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 908937005391 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 908937005392 NAD(P) binding site [chemical binding]; other site 908937005393 homodimer interface [polypeptide binding]; other site 908937005394 substrate binding site [chemical binding]; other site 908937005395 active site 908937005396 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 908937005397 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 908937005398 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 908937005399 Xanthine/uracil permeases [Nucleotide transport and metabolism]; Region: UraA; COG2233 908937005400 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 908937005401 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 908937005402 FeS/SAM binding site; other site 908937005403 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 908937005404 Pyruvate formate lyase 1; Region: PFL1; cd01678 908937005405 coenzyme A binding site [chemical binding]; other site 908937005406 active site 908937005407 catalytic residues [active] 908937005408 glycine loop; other site 908937005409 Na(+)/iodide (NIS) and Na(+)/multivitamin (SMVT) cotransporters, and related proteins; solute binding domain; Region: SLC5sbd_NIS-like; cd10326 908937005410 Na binding site [ion binding]; other site 908937005411 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 908937005412 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937005413 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 908937005414 DNA binding residues [nucleotide binding] 908937005415 FecR protein; Region: FecR; pfam04773 908937005416 Secretin and TonB N terminus short domain; Region: STN; smart00965 908937005417 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937005418 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937005419 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937005420 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 908937005421 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 908937005422 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937005423 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937005424 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 908937005425 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 908937005426 catalytic residues [active] 908937005427 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 908937005428 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 908937005429 sequence-specific DNA binding site [nucleotide binding]; other site 908937005430 salt bridge; other site 908937005431 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 908937005432 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 908937005433 substrate binding site; other site 908937005434 tetramer interface; other site 908937005435 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 908937005436 Chain length determinant protein; Region: Wzz; pfam02706 908937005437 capsular exopolysaccharide family; Region: eps_fam; TIGR01007 908937005438 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 908937005439 Nucleotide binding site [chemical binding]; other site 908937005440 P loop; other site 908937005441 DTAP/Switch II; other site 908937005442 Switch I; other site 908937005443 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 908937005444 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 908937005445 putative active site [active] 908937005446 substrate binding site [chemical binding]; other site 908937005447 putative cosubstrate binding site; other site 908937005448 catalytic site [active] 908937005449 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 908937005450 substrate binding site [chemical binding]; other site 908937005451 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 908937005452 nucleotide binding site [chemical binding]; other site 908937005453 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 908937005454 putative voltage-gated ClC-type chloride channel ClcB; Provisional; Region: PRK01862 908937005455 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 908937005456 Cl- selectivity filter; other site 908937005457 Cl- binding residues [ion binding]; other site 908937005458 pore gating glutamate residue; other site 908937005459 dimer interface [polypeptide binding]; other site 908937005460 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC; Region: CBS_pair_SpoIVFB_EriC_assoc2; cd04613 908937005461 Peptidase M15; Region: Peptidase_M15_3; cl01194 908937005462 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937005463 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937005464 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937005465 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937005466 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 908937005467 Fasciclin domain; Region: Fasciclin; cl02663 908937005468 Fasciclin domain; Region: Fasciclin; pfam02469 908937005469 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937005470 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937005471 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937005472 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937005473 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937005474 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 908937005475 Fasciclin domain; Region: Fasciclin; cl02663 908937005476 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 908937005477 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 908937005478 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 908937005479 Glutamine amidotransferase class-I; Region: GATase; pfam00117 908937005480 glutamine binding [chemical binding]; other site 908937005481 catalytic triad [active] 908937005482 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 908937005483 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 908937005484 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 908937005485 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 908937005486 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 908937005487 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937005488 catalytic residue [active] 908937005489 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 908937005490 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 908937005491 substrate binding site [chemical binding]; other site 908937005492 active site 908937005493 catalytic residues [active] 908937005494 heterodimer interface [polypeptide binding]; other site 908937005495 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 908937005496 active site 908937005497 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 908937005498 active site 908937005499 ribulose/triose binding site [chemical binding]; other site 908937005500 phosphate binding site [ion binding]; other site 908937005501 substrate (anthranilate) binding pocket [chemical binding]; other site 908937005502 product (indole) binding pocket [chemical binding]; other site 908937005503 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 908937005504 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 908937005505 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 908937005506 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 908937005507 Endopygalactorunase [Cell envelope biogenesis, outer membrane]; Region: PGU1; COG5434 908937005508 Probable polygalacturonase At3g15720; Region: PLN03003; cl14103 908937005509 Glycosyl Hydrolase Family 88; Region: Glyco_hydro_88; pfam07470 908937005510 Protein of unknown function (DUF4199); Region: DUF4199; pfam13858 908937005511 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 908937005512 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 908937005513 Ligand binding site; other site 908937005514 Putative Catalytic site; other site 908937005515 DXD motif; other site 908937005516 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 908937005517 ApbE family; Region: ApbE; pfam02424 908937005518 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 908937005519 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 908937005520 ligand binding site [chemical binding]; other site 908937005521 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 908937005522 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937005523 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 908937005524 RmuC family; Region: RmuC; pfam02646 908937005525 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 908937005526 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 908937005527 Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues; Region: GH25_muramidase; cl10448 908937005528 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 908937005529 active site 908937005530 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]; Region: COG1933 908937005531 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 908937005532 Peptidase family U32; Region: Peptidase_U32; pfam01136 908937005533 Collagenase; Region: DUF3656; pfam12392 908937005534 homoserine O-succinyltransferase; Provisional; Region: PRK05368 908937005535 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 908937005536 proposed active site lysine [active] 908937005537 conserved cys residue [active] 908937005538 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 908937005539 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 908937005540 active site 908937005541 Zn binding site [ion binding]; other site 908937005542 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 908937005543 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 908937005544 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 908937005545 ABC transporter; Region: ABC_tran_2; pfam12848 908937005546 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 908937005547 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 908937005548 Surface antigen; Region: Bac_surface_Ag; pfam01103 908937005549 Family of unknown function (DUF490); Region: DUF490; pfam04357 908937005550 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 908937005551 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 908937005552 active site 908937005553 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 908937005554 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 908937005555 NAD(P) binding site [chemical binding]; other site 908937005556 homotetramer interface [polypeptide binding]; other site 908937005557 homodimer interface [polypeptide binding]; other site 908937005558 active site 908937005559 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 908937005560 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 908937005561 Uncharacterized protein conserved in bacteria [Function unknown]; Region: MmcQ; COG2315 908937005562 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 908937005563 AAA domain; Region: AAA_31; pfam13614 908937005564 P-loop; other site 908937005565 Magnesium ion binding site [ion binding]; other site 908937005566 DNA polymerase III subunits gamma and tau; Validated; Region: PRK07003 908937005567 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 908937005568 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937005569 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937005570 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937005571 Alpha-L-fucosidase; Region: Alpha_L_fucos; smart00812 908937005572 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 908937005573 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG; TIGR02491 908937005574 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 908937005575 FeS/SAM binding site; other site 908937005576 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK07111 908937005577 ATP cone domain; Region: ATP-cone; pfam03477 908937005578 Class III ribonucleotide reductase; Region: RNR_III; cd01675 908937005579 effector binding site; other site 908937005580 active site 908937005581 Zn binding site [ion binding]; other site 908937005582 glycine loop; other site 908937005583 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 908937005584 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cd12082 908937005585 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 908937005586 classical (c) SDRs; Region: SDR_c; cd05233 908937005587 NAD(P) binding site [chemical binding]; other site 908937005588 active site 908937005589 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylic-acid synthase; Region: menD; TIGR00173 908937005590 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 908937005591 dimer interface [polypeptide binding]; other site 908937005592 tetramer interface [polypeptide binding]; other site 908937005593 PYR/PP interface [polypeptide binding]; other site 908937005594 TPP binding site [chemical binding]; other site 908937005595 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 908937005596 TPP-binding site [chemical binding]; other site 908937005597 serine O-acetyltransferase; Region: cysE; TIGR01172 908937005598 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 908937005599 trimer interface [polypeptide binding]; other site 908937005600 active site 908937005601 substrate binding site [chemical binding]; other site 908937005602 CoA binding site [chemical binding]; other site 908937005603 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 908937005604 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 908937005605 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 908937005606 Acyltransferase family; Region: Acyl_transf_3; pfam01757 908937005607 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 908937005608 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 908937005609 Probable Catalytic site; other site 908937005610 metal-binding site 908937005611 Photosystem I reaction centre subunit XI; Region: PsaL; cl03651 908937005612 Capsular polysaccharide synthesis protein; Region: Caps_synth; pfam05704 908937005613 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937005614 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 908937005615 active site 908937005616 nucleotide binding site [chemical binding]; other site 908937005617 HIGH motif; other site 908937005618 KMSKS motif; other site 908937005619 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 908937005620 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 908937005621 classical (c) SDRs; Region: SDR_c; cd05233 908937005622 NAD(P) binding site [chemical binding]; other site 908937005623 active site 908937005624 LicD family; Region: LicD; pfam04991 908937005625 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 908937005626 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_6; cd04955 908937005627 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 908937005628 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 908937005629 NADP binding site [chemical binding]; other site 908937005630 active site 908937005631 putative substrate binding site [chemical binding]; other site 908937005632 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 908937005633 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 908937005634 NADP-binding site; other site 908937005635 homotetramer interface [polypeptide binding]; other site 908937005636 substrate binding site [chemical binding]; other site 908937005637 homodimer interface [polypeptide binding]; other site 908937005638 active site 908937005639 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 908937005640 Virulence protein [General function prediction only]; Region: COG3943 908937005641 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 908937005642 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 908937005643 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_5; cd06153 908937005644 homotrimer interaction site [polypeptide binding]; other site 908937005645 putative active site [active] 908937005646 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_5; cd06153 908937005647 homotrimer interaction site [polypeptide binding]; other site 908937005648 putative active site [active] 908937005649 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 908937005650 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 908937005651 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 908937005652 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 908937005653 Protein of unknown function (DUF1111); Region: DUF1111; pfam06537 908937005654 Imelysin; Region: Peptidase_M75; pfam09375 908937005655 Imelysin; Region: Peptidase_M75; pfam09375 908937005656 Hemerythrin-like domain; Region: Hr-like; cd12108 908937005657 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 908937005658 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 908937005659 DNA binding residues [nucleotide binding] 908937005660 dimerization interface [polypeptide binding]; other site 908937005661 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 908937005662 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 908937005663 DNA binding residues [nucleotide binding] 908937005664 dimerization interface [polypeptide binding]; other site 908937005665 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 908937005666 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 908937005667 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 908937005668 G1 box; other site 908937005669 putative GEF interaction site [polypeptide binding]; other site 908937005670 GTP/Mg2+ binding site [chemical binding]; other site 908937005671 Switch I region; other site 908937005672 G2 box; other site 908937005673 G3 box; other site 908937005674 Switch II region; other site 908937005675 G4 box; other site 908937005676 G5 box; other site 908937005677 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 908937005678 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 908937005679 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 908937005680 NADP binding site [chemical binding]; other site 908937005681 active site 908937005682 putative substrate binding site [chemical binding]; other site 908937005683 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 908937005684 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 908937005685 active site residue [active] 908937005686 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 908937005687 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 908937005688 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 908937005689 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 908937005690 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 908937005691 23S rRNA binding site [nucleotide binding]; other site 908937005692 L21 binding site [polypeptide binding]; other site 908937005693 L13 binding site [polypeptide binding]; other site 908937005694 Fn3 associated; Region: Fn3_assoc; pfam13287 908937005695 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 908937005696 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 908937005697 substrate binding site [chemical binding]; other site 908937005698 hexamer interface [polypeptide binding]; other site 908937005699 metal binding site [ion binding]; metal-binding site 908937005700 RNA polymerase sigma factor; Provisional; Region: PRK12513 908937005701 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937005702 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 908937005703 DNA binding residues [nucleotide binding] 908937005704 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_ox_2; pfam12900 908937005705 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 908937005706 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 908937005707 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 908937005708 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 908937005709 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 908937005710 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 908937005711 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 908937005712 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 908937005713 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 908937005714 Glycogen debranching enzyme N terminal; Region: GDE_N; pfam12439 908937005715 glycogen debranching enzyme, archaeal type, putative; Region: gde_arch; TIGR01561 908937005716 Amylo-alpha-1,6-glucosidase; Region: GDE_C; pfam06202 908937005717 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 908937005718 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 908937005719 N-terminal catalytic domain of a thermoactive alpha-amylase from Methanococcus jannaschii and similar proteins; glycoside hydrolase family 57 (GH57); Region: GH57N_MJA1_like; cd10795 908937005720 Glycosyl hydrolase family 57; Region: Glyco_hydro_57; pfam03065 908937005721 putative active site [active] 908937005722 catalytic site [active] 908937005723 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 908937005724 Uncharacterized conserved protein [Function unknown]; Region: COG3379 908937005725 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 908937005726 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 908937005727 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 908937005728 active site 908937005729 catalytic triad [active] 908937005730 oxyanion hole [active] 908937005731 Rhamnogalacturonan lyase of the polysaccharide lyase family 11; Region: RGL11; cd10318 908937005732 metal binding site [ion binding]; metal-binding site 908937005733 active site 908937005734 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 908937005735 oligomerisation interface [polypeptide binding]; other site 908937005736 mobile loop; other site 908937005737 roof hairpin; other site 908937005738 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 908937005739 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 908937005740 ring oligomerisation interface [polypeptide binding]; other site 908937005741 ATP/Mg binding site [chemical binding]; other site 908937005742 stacking interactions; other site 908937005743 hinge regions; other site 908937005744 Phosphotransferase enzyme family; Region: APH; pfam01636 908937005745 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 908937005746 P-loop ATPase protein family; Region: ATP_bind_2; cl15794 908937005747 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; pfam00150 908937005748 N-terminal domain of cellobiose phosphorylase (CBP) and similar proteins; Region: GH94N_CBP_like; cd11754 908937005749 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 908937005750 catalytic domain interface [polypeptide binding]; other site 908937005751 homodimer interface [polypeptide binding]; other site 908937005752 putative active site [active] 908937005753 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 908937005754 MFS/sugar transport protein; Region: MFS_2; pfam13347 908937005755 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937005756 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937005757 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937005758 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 908937005759 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937005760 Starch-binding associating with outer membrane; Region: SusD-like_2; pfam12771 908937005761 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 908937005762 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 908937005763 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 908937005764 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 908937005765 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 908937005766 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 908937005767 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 908937005768 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 908937005769 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937005770 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937005771 Flavodoxin-like fold; Region: Flavodoxin_2; pfam02525 908937005772 maltose O-acetyltransferase; Provisional; Region: PRK10092 908937005773 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 908937005774 active site 908937005775 substrate binding site [chemical binding]; other site 908937005776 trimer interface [polypeptide binding]; other site 908937005777 CoA binding site [chemical binding]; other site 908937005778 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 908937005779 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937005780 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 908937005781 DNA binding residues [nucleotide binding] 908937005782 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 908937005783 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 908937005784 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937005785 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937005786 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937005787 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937005788 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 908937005789 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937005790 starch binding outer membrane protein SusD; Region: SusD; cd08977 908937005791 SusD family; Region: SusD; pfam07980 908937005792 putative alpha-glucosidase; Provisional; Region: PRK10658 908937005793 Galactose mutarotase-like; Region: Gal_mutarotas_2; pfam13802 908937005794 The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase; Region: GH31; cl11402 908937005795 active site 908937005796 catalytic site [active] 908937005797 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 908937005798 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 908937005799 inhibitor-cofactor binding pocket; inhibition site 908937005800 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937005801 catalytic residue [active] 908937005802 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 908937005803 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 908937005804 putative ADP-binding pocket [chemical binding]; other site 908937005805 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 908937005806 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 908937005807 active site 908937005808 catalytic tetrad [active] 908937005809 Sugar-transfer associated ATP-grasp; Region: ATPgrasp_ST; pfam14397 908937005810 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 908937005811 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 908937005812 dimer interface [polypeptide binding]; other site 908937005813 active site 908937005814 CoA binding pocket [chemical binding]; other site 908937005815 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 908937005816 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 908937005817 acyl-activating enzyme (AAE) consensus motif; other site 908937005818 AMP binding site [chemical binding]; other site 908937005819 active site 908937005820 CoA binding site [chemical binding]; other site 908937005821 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 908937005822 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 908937005823 classical (c) SDRs; Region: SDR_c; cd05233 908937005824 NAD(P) binding site [chemical binding]; other site 908937005825 active site 908937005826 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 908937005827 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 908937005828 dimer interface [polypeptide binding]; other site 908937005829 active site 908937005830 CoA binding pocket [chemical binding]; other site 908937005831 Phosphopantetheine attachment site; Region: PP-binding; cl09936 908937005832 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 908937005833 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 908937005834 putative trimer interface [polypeptide binding]; other site 908937005835 putative CoA binding site [chemical binding]; other site 908937005836 Bacterial sugar transferase; Region: Bac_transf; pfam02397 908937005837 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 908937005838 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 908937005839 putative ADP-binding pocket [chemical binding]; other site 908937005840 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 908937005841 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 908937005842 active site 908937005843 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 908937005844 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 908937005845 active site 908937005846 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 908937005847 Acyltransferase family; Region: Acyl_transf_3; pfam01757 908937005848 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 908937005849 active site 908937005850 Serine acetyltransferase [Amino acid transport and metabolism]; Region: CysE; COG1045 908937005851 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 908937005852 trimer interface [polypeptide binding]; other site 908937005853 active site 908937005854 substrate binding site [chemical binding]; other site 908937005855 CoA binding site [chemical binding]; other site 908937005856 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 908937005857 Glycosyl transferases group 1; Region: Glycos_transf_1; pfam00534 908937005858 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 908937005859 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 908937005860 metal-binding site 908937005861 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 908937005862 active site 908937005863 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 908937005864 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 908937005865 Acyltransferase family; Region: Acyl_transf_3; pfam01757 908937005866 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 908937005867 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 908937005868 Acyltransferase family; Region: Acyl_transf_3; pfam01757 908937005869 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 908937005870 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 908937005871 active site 908937005872 Domain of unknown function (DUF1919); Region: DUF1919; cl01628 908937005873 UDP-galactopyranose mutase [Cell envelope biogenesis, outer membrane]; Region: Glf; COG0562 908937005874 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 908937005875 UDP-galactopyranose mutase; Region: GLF; pfam03275 908937005876 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 908937005877 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 908937005878 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cl00233 908937005879 catalytic center binding site [active] 908937005880 ATP binding site [chemical binding]; other site 908937005881 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 908937005882 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 908937005883 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 908937005884 active site 908937005885 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937005886 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937005887 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937005888 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 908937005889 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937005890 SusD family; Region: SusD; pfam07980 908937005891 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 908937005892 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 908937005893 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 908937005894 Cleaved Adhesin Domain; Region: Cleaved_Adhesin; pfam07675 908937005895 Tandem repeat subunit of reelin and related proteins; Region: Reelin_subrepeat_like; cl15240 908937005896 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 908937005897 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 908937005898 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 908937005899 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 908937005900 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 908937005901 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 908937005902 Uncharacterized conserved protein [Function unknown]; Region: COG3538 908937005903 Protein of unknown function (DUF1237); Region: DUF1237; pfam06824 908937005904 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 908937005905 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 908937005906 nucleophile elbow; other site 908937005907 Transposase; Region: DEDD_Tnp_IS110; pfam01548 908937005908 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 908937005909 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 908937005910 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 908937005911 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 908937005912 ABC-2 type transporter; Region: ABC2_membrane; cl17235 908937005913 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 908937005914 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 908937005915 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 908937005916 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 908937005917 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 908937005918 Walker A/P-loop; other site 908937005919 ATP binding site [chemical binding]; other site 908937005920 Q-loop/lid; other site 908937005921 ABC transporter signature motif; other site 908937005922 Walker B; other site 908937005923 D-loop; other site 908937005924 H-loop/switch region; other site 908937005925 ATP-binding cassette domain of the lipid transporters, subfamily A; Region: ABC_subfamily_A; cd03263 908937005926 Walker A/P-loop; other site 908937005927 ATP binding site [chemical binding]; other site 908937005928 Q-loop/lid; other site 908937005929 ABC transporter signature motif; other site 908937005930 Walker B; other site 908937005931 D-loop; other site 908937005932 H-loop/switch region; other site 908937005933 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 908937005934 HlyD family secretion protein; Region: HlyD_3; pfam13437 908937005935 Outer membrane efflux protein; Region: OEP; pfam02321 908937005936 Outer membrane efflux protein; Region: OEP; pfam02321 908937005937 Helix-turn-helix domain; Region: HTH_18; pfam12833 908937005938 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937005939 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 908937005940 EamA-like transporter family; Region: EamA; pfam00892 908937005941 Glycosyl hydrolase family 98; Region: Glyco_hydro_98M; pfam08306 908937005942 Glycosyl hydrolase family 98 C-terminal domain; Region: Glyco_hydro_98C; pfam08307 908937005943 Carbohydrate Binding Module family 35 (CBM35); appended mainly to enzymes that bind alpha-D-galactose (CBM35-Gal), including glycoside hydrolase (GH) families GH31 and GH43; Region: CBM35_galactosidase-like; cd04081 908937005944 O-Glycosyl hydrolase [Cell envelope biogenesis, outer membrane]; Region: COG5520 908937005945 aconitate hydratase, mitochondrial; Region: aconitase_mito; TIGR01340 908937005946 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 908937005947 substrate binding site [chemical binding]; other site 908937005948 ligand binding site [chemical binding]; other site 908937005949 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 908937005950 substrate binding site [chemical binding]; other site 908937005951 citrate synthase; Provisional; Region: PRK14032 908937005952 Citrate synthase; Region: Citrate_synt; pfam00285 908937005953 oxalacetate binding site [chemical binding]; other site 908937005954 citrylCoA binding site [chemical binding]; other site 908937005955 coenzyme A binding site [chemical binding]; other site 908937005956 catalytic triad [active] 908937005957 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 908937005958 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 908937005959 putative ATP binding site [chemical binding]; other site 908937005960 putative substrate interface [chemical binding]; other site 908937005961 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 908937005962 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 908937005963 FeS/SAM binding site; other site 908937005964 HemN C-terminal domain; Region: HemN_C; pfam06969 908937005965 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 908937005966 elongation factor G; Reviewed; Region: PRK12740 908937005967 G1 box; other site 908937005968 putative GEF interaction site [polypeptide binding]; other site 908937005969 GTP/Mg2+ binding site [chemical binding]; other site 908937005970 Switch I region; other site 908937005971 G2 box; other site 908937005972 G3 box; other site 908937005973 Switch II region; other site 908937005974 G4 box; other site 908937005975 G5 box; other site 908937005976 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 908937005977 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 908937005978 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 908937005979 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 908937005980 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 908937005981 dimer interface [polypeptide binding]; other site 908937005982 phosphorylation site [posttranslational modification] 908937005983 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 908937005984 ATP binding site [chemical binding]; other site 908937005985 Mg2+ binding site [ion binding]; other site 908937005986 G-X-G motif; other site 908937005987 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 908937005988 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 908937005989 active site 908937005990 phosphorylation site [posttranslational modification] 908937005991 intermolecular recognition site; other site 908937005992 dimerization interface [polypeptide binding]; other site 908937005993 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 908937005994 DNA binding site [nucleotide binding] 908937005995 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 908937005996 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 908937005997 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 908937005998 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 908937005999 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 908937006000 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 908937006001 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 908937006002 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 908937006003 Alpha amylase catalytic domain found in an uncharacterized protein family; Region: AmyAc_3; cd11349 908937006004 active site 908937006005 catalytic site [active] 908937006006 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 908937006007 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 908937006008 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 908937006009 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 908937006010 homodimer interface [polypeptide binding]; other site 908937006011 oligonucleotide binding site [chemical binding]; other site 908937006012 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 908937006013 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 908937006014 IHF - DNA interface [nucleotide binding]; other site 908937006015 IHF dimer interface [polypeptide binding]; other site 908937006016 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 908937006017 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 908937006018 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 908937006019 metal binding site [ion binding]; metal-binding site 908937006020 dimer interface [polypeptide binding]; other site 908937006021 heat shock protein 90; Provisional; Region: PRK05218 908937006022 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 908937006023 ATP binding site [chemical binding]; other site 908937006024 Mg2+ binding site [ion binding]; other site 908937006025 G-X-G motif; other site 908937006026 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 908937006027 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 908937006028 minor groove reading motif; other site 908937006029 helix-hairpin-helix signature motif; other site 908937006030 substrate binding pocket [chemical binding]; other site 908937006031 active site 908937006032 TIGR02453 family protein; Region: TIGR02453 908937006033 Clostripain family; Region: Peptidase_C11; pfam03415 908937006034 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 908937006035 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937006036 active site 908937006037 HIGH motif; other site 908937006038 nucleotide binding site [chemical binding]; other site 908937006039 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 908937006040 active site 908937006041 KMSKS motif; other site 908937006042 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 908937006043 tRNA binding surface [nucleotide binding]; other site 908937006044 anticodon binding site; other site 908937006045 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 908937006046 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 908937006047 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 908937006048 homodimer interface [polypeptide binding]; other site 908937006049 metal binding site [ion binding]; metal-binding site 908937006050 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 908937006051 homodimer interface [polypeptide binding]; other site 908937006052 active site 908937006053 putative chemical substrate binding site [chemical binding]; other site 908937006054 metal binding site [ion binding]; metal-binding site 908937006055 Lipocalin-like; Region: Lipocalin_3; pfam12702 908937006056 ribonuclease Z; Region: RNase_Z; TIGR02651 908937006057 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 908937006058 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 908937006059 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 908937006060 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 908937006061 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 908937006062 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 908937006063 DNA binding residues [nucleotide binding] 908937006064 Domain of unknown function (DUF4289); Region: DUF4289; pfam14121 908937006065 Domain of unknown function (DUF4289); Region: DUF4289; pfam14121 908937006066 Uncharacterized proteins similar to Bacteroides ovatus 4320; Region: Bacova_04320_like; cd12190 908937006067 excinuclease ABC subunit B; Provisional; Region: PRK05298 908937006068 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 908937006069 ATP binding site [chemical binding]; other site 908937006070 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 908937006071 nucleotide binding region [chemical binding]; other site 908937006072 ATP-binding site [chemical binding]; other site 908937006073 Ultra-violet resistance protein B; Region: UvrB; pfam12344 908937006074 UvrB/uvrC motif; Region: UVR; pfam02151 908937006075 Outer membrane lipoprotein; Region: YfiO; pfam13525 908937006076 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 908937006077 Domain of unknown function (DUF4293); Region: DUF4293; pfam14126 908937006078 altronate oxidoreductase; Provisional; Region: PRK03643 908937006079 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 908937006080 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 908937006081 pyruvate kinase; Provisional; Region: PRK05826 908937006082 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 908937006083 domain interfaces; other site 908937006084 active site 908937006085 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 908937006086 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937006087 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937006088 SusD family; Region: SusD; pfam07980 908937006089 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937006090 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937006091 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 908937006092 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 908937006093 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 908937006094 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937006095 catalytic residue [active] 908937006096 cofactor-independent phosphoglycerate mutase; Provisional; Region: PRK04200 908937006097 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: PhosphMutase; cl17294 908937006098 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 908937006099 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 908937006100 nucleotide binding site [chemical binding]; other site 908937006101 substrate binding site [chemical binding]; other site 908937006102 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 908937006103 dimer interface [polypeptide binding]; other site 908937006104 putative threonine allosteric regulatory site; other site 908937006105 ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase); Region: ACT_AK-like_2; cd04892 908937006106 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 908937006107 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 908937006108 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 908937006109 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 908937006110 NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]; Region: Lig; COG0272 908937006111 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cl03295 908937006112 nucleotide binding pocket [chemical binding]; other site 908937006113 K-X-D-G motif; other site 908937006114 catalytic site [active] 908937006115 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 908937006116 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 908937006117 Dimer interface [polypeptide binding]; other site 908937006118 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 908937006119 active site 908937006120 8-oxo-dGMP binding site [chemical binding]; other site 908937006121 nudix motif; other site 908937006122 metal binding site [ion binding]; metal-binding site 908937006123 pantothenate kinase; Provisional; Region: PRK13317 908937006124 pantothenate kinase, eukaryotic/staphyloccocal type; Region: panK_eukar; TIGR00555 908937006125 Peptidase family M49; Region: Peptidase_M49; pfam03571 908937006126 A new structural DNA glycosylase; Region: AlkD_like; cl11434 908937006127 active site 908937006128 MoxR-like ATPases [General function prediction only]; Region: COG0714 908937006129 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 908937006130 Walker A motif; other site 908937006131 ATP binding site [chemical binding]; other site 908937006132 Walker B motif; other site 908937006133 arginine finger; other site 908937006134 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 908937006135 Protein of unknown function DUF58; Region: DUF58; pfam01882 908937006136 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 908937006137 metal ion-dependent adhesion site (MIDAS); other site 908937006138 VWA BatA type: 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...; Region: vWA_BatA_type; cd01467 908937006139 metal ion-dependent adhesion site (MIDAS); other site 908937006140 Aerotolerance regulator N-terminal; Region: BatA; cl06567 908937006141 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 908937006142 metal ion-dependent adhesion site (MIDAS); other site 908937006143 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 908937006144 TPR motif; other site 908937006145 TPR repeat; Region: TPR_11; pfam13414 908937006146 binding surface 908937006147 TPR repeat; Region: TPR_11; pfam13414 908937006148 Oxygen tolerance; Region: BatD; pfam13584 908937006149 Tetratricopeptide repeat; Region: TPR_16; pfam13432 908937006150 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 908937006151 binding surface 908937006152 TPR motif; other site 908937006153 Bacterial SH3 domain homologues; Region: SH3b; smart00287 908937006154 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 908937006155 active site 908937006156 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 908937006157 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 908937006158 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 908937006159 Domain of unknown function (DUF2027); Region: DUF2027; pfam09640 908937006160 NAD synthetase; Reviewed; Region: nadE; PRK02628 908937006161 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 908937006162 multimer interface [polypeptide binding]; other site 908937006163 active site 908937006164 catalytic triad [active] 908937006165 protein interface 1 [polypeptide binding]; other site 908937006166 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 908937006167 homodimer interface [polypeptide binding]; other site 908937006168 NAD binding pocket [chemical binding]; other site 908937006169 ATP binding pocket [chemical binding]; other site 908937006170 Mg binding site [ion binding]; other site 908937006171 active-site loop [active] 908937006172 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 908937006173 ribosomal protein L33; Region: rpl33; CHL00104 908937006174 Domain of unknown function (DUF4295); Region: DUF4295; pfam14128 908937006175 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 908937006176 active site 908937006177 homodimer interface [polypeptide binding]; other site 908937006178 glucuronate isomerase; Reviewed; Region: PRK02925 908937006179 Glucuronate isomerase [Carbohydrate transport and metabolism]; Region: UxaC; COG1904 908937006180 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 908937006181 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 908937006182 amidophosphoribosyltransferase; Region: purF; TIGR01134 908937006183 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 908937006184 active site 908937006185 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 908937006186 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 908937006187 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 908937006188 catalytic site [active] 908937006189 subunit interface [polypeptide binding]; other site 908937006190 carbamoyl-phosphate synthase, large subunit; Region: CPSaseII_lrg; TIGR01369 908937006191 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 908937006192 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 908937006193 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 908937006194 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 908937006195 ATP-grasp domain; Region: ATP-grasp_4; cl17255 908937006196 Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain; Region: MGS_CPS_I_III; cd01423 908937006197 probable substrate binding site [chemical binding]; other site 908937006198 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 908937006199 homopentamer interface [polypeptide binding]; other site 908937006200 active site 908937006201 recombination protein F; Reviewed; Region: recF; PRK00064 908937006202 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937006203 Walker A/P-loop; other site 908937006204 ATP binding site [chemical binding]; other site 908937006205 Q-loop/lid; other site 908937006206 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937006207 ABC transporter signature motif; other site 908937006208 Walker B; other site 908937006209 D-loop; other site 908937006210 H-loop/switch region; other site 908937006211 Protein of unknown function (DUF721); Region: DUF721; pfam05258 908937006212 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 908937006213 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 908937006214 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 908937006215 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 908937006216 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 908937006217 protein binding site [polypeptide binding]; other site 908937006218 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 908937006219 Catalytic dyad [active] 908937006220 Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the...; Region: deoxycytidylate_deaminase; cd01286 908937006221 catalytic motif [active] 908937006222 Zn binding site [ion binding]; other site 908937006223 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 908937006224 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 908937006225 active site 908937006226 Zn binding site [ion binding]; other site 908937006227 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 908937006228 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 908937006229 Substrate binding site; other site 908937006230 metal-binding site 908937006231 GMP synthase; Reviewed; Region: guaA; PRK00074 908937006232 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 908937006233 AMP/PPi binding site [chemical binding]; other site 908937006234 candidate oxyanion hole; other site 908937006235 catalytic triad [active] 908937006236 potential glutamine specificity residues [chemical binding]; other site 908937006237 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 908937006238 ATP Binding subdomain [chemical binding]; other site 908937006239 Ligand Binding sites [chemical binding]; other site 908937006240 Dimerization subdomain; other site 908937006241 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 908937006242 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 908937006243 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 908937006244 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 908937006245 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 908937006246 homodimer interface [polypeptide binding]; other site 908937006247 substrate-cofactor binding pocket; other site 908937006248 pyridoxal 5'-phosphate binding site [chemical binding]; other site 908937006249 catalytic residue [active] 908937006250 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 908937006251 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 908937006252 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 908937006253 Bacterial Ig-like domain (group 1); Region: Big_1; cl17740 908937006254 Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms]; Region: MecR1; COG4219 908937006255 Penicillinase repressor; Region: Pencillinase_R; pfam03965 908937006256 Glycosyl hydrolase family 43; Region: GH43_6; cd08985 908937006257 active site 908937006258 an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; Region: DNA_pol_III_epsilon_like; cd06130 908937006259 active site 908937006260 catalytic site [active] 908937006261 substrate binding site [chemical binding]; other site 908937006262 Helix-turn-helix domain; Region: HTH_17; pfam12728 908937006263 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the...; Region: INT_Tn4399; cd01185 908937006264 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 908937006265 Int/Topo IB signature motif; other site 908937006266 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the...; Region: INT_Tn4399; cd01185 908937006267 Int/Topo IB signature motif; other site 908937006268 37-kD nucleoid-associated bacterial protein; Region: NA37; pfam04245 908937006269 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 908937006270 A new structural DNA glycosylase; Region: AlkD_like; cl11434 908937006271 active site 908937006272 intracellular protease, PfpI family; Region: PfpI; TIGR01382 908937006273 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_3; cd03140 908937006274 conserved cys residue [active] 908937006275 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 908937006276 hydrophobic ligand binding site; other site 908937006277 Protein of unknown function with HXXEE motif; Region: HXXEE; pfam13787 908937006278 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 908937006279 Helix-turn-helix domain; Region: HTH_18; pfam12833 908937006280 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937006281 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 908937006282 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 908937006283 RteC protein; Region: RteC; pfam09357 908937006284 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 908937006285 Transposase; Region: DEDD_Tnp_IS110; pfam01548 908937006286 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 908937006287 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 908937006288 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]; Region: COG1051 908937006289 nudix motif; other site 908937006290 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 908937006291 putative transposase OrfB; Reviewed; Region: PHA02517 908937006292 Integrase core domain; Region: rve; pfam00665 908937006293 Integrase core domain; Region: rve_3; pfam13683 908937006294 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 908937006295 active site 908937006296 Int/Topo IB signature motif; other site 908937006297 DNA binding site [nucleotide binding] 908937006298 Predicted ATPases [General function prediction only]; Region: COG1106 908937006299 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937006300 Walker A/P-loop; other site 908937006301 ATP binding site [chemical binding]; other site 908937006302 RloB-like protein; Region: RloB; pfam13707 908937006303 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 908937006304 active site 908937006305 NTP binding site [chemical binding]; other site 908937006306 metal binding triad [ion binding]; metal-binding site 908937006307 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cl17196 908937006308 ATP binding site [chemical binding]; other site 908937006309 Prokaryotic homologs of the JAB domain; Region: Prok-JAB; pfam14464 908937006310 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 908937006311 RteC protein; Region: RteC; pfam09357 908937006312 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 908937006313 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 908937006314 active site 908937006315 phosphorylation site [posttranslational modification] 908937006316 intermolecular recognition site; other site 908937006317 dimerization interface [polypeptide binding]; other site 908937006318 LytTr DNA-binding domain; Region: LytTR; smart00850 908937006319 Histidine kinase; Region: His_kinase; pfam06580 908937006320 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 908937006321 ATP binding site [chemical binding]; other site 908937006322 Mg2+ binding site [ion binding]; other site 908937006323 G-X-G motif; other site 908937006324 Histidine kinase; Region: His_kinase; pfam06580 908937006325 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 908937006326 Beta-lactamase; Region: Beta-lactamase; pfam00144 908937006327 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 908937006328 putative DNA binding site [nucleotide binding]; other site 908937006329 putative Zn2+ binding site [ion binding]; other site 908937006330 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 908937006331 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 908937006332 active site 908937006333 DNA binding site [nucleotide binding] 908937006334 Int/Topo IB signature motif; other site 908937006335 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the...; Region: INT_Tn4399; cd01185 908937006336 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 908937006337 Int/Topo IB signature motif; other site 908937006338 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 908937006339 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 908937006340 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 908937006341 AAA domain; Region: AAA_31; pfam13614 908937006342 P-loop; other site 908937006343 Magnesium ion binding site [ion binding]; other site 908937006344 Homeodomain-like domain; Region: HTH_23; cl17451 908937006345 Domain of unknown function (DUF4134); Region: DUF4134; pfam13572 908937006346 Domain of unknown function (DUF3333); Region: DUF3333; pfam11812 908937006347 Bacteroides conjugation system ATPase, TraG family; Region: Bac_Flav_CT_G; TIGR03783 908937006348 Bacteroides conjugative transposon TraJ protein; Region: Bac_Flav_CT_J; TIGR03782 908937006349 Bacteroides conjugative transposon TraK protein; Region: Bac_Flav_CT_K; TIGR03781 908937006350 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 908937006351 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 908937006352 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 908937006353 TraX protein; Region: TraX; pfam05857 908937006354 Family description; Region: UvrD_C_2; pfam13538 908937006355 C2 domain; Region: C2; cl14603 908937006356 AAA domain; Region: AAA_21; pfam13304 908937006357 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937006358 ABC transporter signature motif; other site 908937006359 Walker B; other site 908937006360 D-loop; other site 908937006361 H-loop/switch region; other site 908937006362 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 908937006363 active site 908937006364 metal binding site [ion binding]; metal-binding site 908937006365 DEAD-like helicases superfamily; Region: DEXDc; smart00487 908937006366 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 908937006367 ATP binding site [chemical binding]; other site 908937006368 putative Mg++ binding site [ion binding]; other site 908937006369 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 908937006370 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 908937006371 nucleotide binding region [chemical binding]; other site 908937006372 ATP-binding site [chemical binding]; other site 908937006373 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]; Region: COG1205 908937006374 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 908937006375 ATP binding site [chemical binding]; other site 908937006376 putative Mg++ binding site [ion binding]; other site 908937006377 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 908937006378 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 908937006379 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 908937006380 non-specific DNA binding site [nucleotide binding]; other site 908937006381 salt bridge; other site 908937006382 sequence-specific DNA binding site [nucleotide binding]; other site 908937006383 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 908937006384 Peptidase family M23; Region: Peptidase_M23; pfam01551 908937006385 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 908937006386 Protein of unknown function (DUF4099); Region: DUF4099; pfam13351 908937006387 Protein of unknown function (DUF3945); Region: DUF3945; pfam13101 908937006388 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 908937006389 active site 908937006390 MutS domain I; Region: MutS_I; pfam01624 908937006391 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 908937006392 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 908937006393 Protein of unknown function (DUF3991); Region: DUF3991; pfam13154 908937006394 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 908937006395 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 908937006396 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 908937006397 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 908937006398 Phage major capsid protein, P2 family; Region: Phage_cap_P2; cl04947 908937006399 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 908937006400 AAA domain; Region: AAA_14; pfam13173 908937006401 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 908937006402 salt bridge; other site 908937006403 non-specific DNA binding site [nucleotide binding]; other site 908937006404 sequence-specific DNA binding site [nucleotide binding]; other site 908937006405 DNA primase, catalytic core; Region: dnaG; TIGR01391 908937006406 CHC2 zinc finger; Region: zf-CHC2; pfam01807 908937006407 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 908937006408 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 908937006409 active site 908937006410 metal binding site [ion binding]; metal-binding site 908937006411 interdomain interaction site; other site 908937006412 Helix-turn-helix domain; Region: HTH_17; pfam12728 908937006413 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 908937006414 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 908937006415 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; cl17315 908937006416 DNA binding residues [nucleotide binding] 908937006417 dimerization interface [polypeptide binding]; other site 908937006418 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 908937006419 Interdomain contacts; other site 908937006420 Cytokine receptor motif; other site 908937006421 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 908937006422 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 908937006423 Por secretion system C-terminal sorting domain; Region: Por_Secre_tail; TIGR04183 908937006424 Protein of unknown function (DUF3791); Region: DUF3791; pfam12668 908937006425 Protein of unknown function (DUF3990); Region: DUF3990; pfam13151 908937006426 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cd00397 908937006427 active site 908937006428 DNA binding site [nucleotide binding] 908937006429 Int/Topo IB signature motif; other site 908937006430 Bacteriophage CI repressor helix-turn-helix domain; Region: Phage_CI_repr; pfam07022 908937006431 Predicted transcriptional regulator [Transcription]; Region: COG2932 908937006432 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 908937006433 Catalytic site [active] 908937006434 AAA ATPase domain; Region: AAA_16; pfam13191 908937006435 AAA domain; Region: AAA_22; pfam13401 908937006436 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 908937006437 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 908937006438 Walker A motif; other site 908937006439 ATP binding site [chemical binding]; other site 908937006440 Walker B motif; other site 908937006441 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 908937006442 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 908937006443 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 908937006444 Protein of unknown function (DUF935); Region: DUF935; pfam06074 908937006445 Protein of unknown function (DUF1320); Region: DUF1320; cl01818 908937006446 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 908937006447 Putative ATPase subunit of terminase (gpP-like); Region: Terminase_5; pfam06056 908937006448 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 908937006449 amidase catalytic site [active] 908937006450 Zn binding residues [ion binding]; other site 908937006451 substrate binding site [chemical binding]; other site 908937006452 Protein of unknown function (DUF2586); Region: DUF2586; pfam10758 908937006453 Phage-related minor tail protein; Region: PhageMin_Tail; pfam10145 908937006454 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 908937006455 Phage Tail Collar Domain; Region: Collar; pfam07484 908937006456 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 908937006457 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 908937006458 P-loop; other site 908937006459 Magnesium ion binding site [ion binding]; other site 908937006460 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 908937006461 Magnesium ion binding site [ion binding]; other site 908937006462 AAA domain; Region: AAA_21; pfam13304 908937006463 RloB-like protein; Region: RloB; pfam13707 908937006464 PcfK-like protein; Region: PcfK; pfam14058 908937006465 Antirestriction protein (ArdA); Region: ArdA; cl01953 908937006466 PcfJ-like protein; Region: PcfJ; pfam14284 908937006467 Domain of unknown function, B. Theta Gene description (DUF3872); Region: DUF3872; pfam12988 908937006468 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 908937006469 catalytic residue [active] 908937006470 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 908937006471 S-adenosylmethionine binding site [chemical binding]; other site 908937006472 Methyltransferase domain; Region: Methyltransf_26; pfam13659 908937006473 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 908937006474 PcfJ-like protein; Region: PcfJ; pfam14284 908937006475 Domain of unknown function (DUF1896); Region: DUF1896; pfam08989 908937006476 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the...; Region: INT_Tn4399; cd01185 908937006477 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 908937006478 Int/Topo IB signature motif; other site 908937006479 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 908937006480 active site 908937006481 DNA binding site [nucleotide binding] 908937006482 Int/Topo IB signature motif; other site 908937006483 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 908937006484 putative DNA binding site [nucleotide binding]; other site 908937006485 putative Zn2+ binding site [ion binding]; other site 908937006486 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 908937006487 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 908937006488 Beta-lactamase; Region: Beta-lactamase; pfam00144 908937006489 Histidine kinase; Region: His_kinase; pfam06580 908937006490 GDSL-like Lipase/Acylhydrolase family; Region: Lipase_GDSL_2; pfam13472 908937006491 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 908937006492 Phage Tail Collar Domain; Region: Collar; pfam07484 908937006493 Phage-related minor tail protein; Region: PhageMin_Tail; pfam10145 908937006494 Protein of unknown function (DUF2586); Region: DUF2586; pfam10758 908937006495 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 908937006496 amidase catalytic site [active] 908937006497 Zn binding residues [ion binding]; other site 908937006498 substrate binding site [chemical binding]; other site 908937006499 Putative ATPase subunit of terminase (gpP-like); Region: Terminase_5; pfam06056 908937006500 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 908937006501 Protein of unknown function (DUF1320); Region: DUF1320; cl01818 908937006502 Protein of unknown function (DUF935); Region: DUF935; pfam06074 908937006503 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 908937006504 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 908937006505 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 908937006506 AAA ATPase domain; Region: AAA_16; pfam13191 908937006507 AAA domain; Region: AAA_22; pfam13401 908937006508 Bacteriophage CI repressor helix-turn-helix domain; Region: Phage_CI_repr; pfam07022 908937006509 Predicted transcriptional regulator [Transcription]; Region: COG2932 908937006510 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 908937006511 Catalytic site [active] 908937006512 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 908937006513 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 908937006514 active site 908937006515 phosphorylation site [posttranslational modification] 908937006516 intermolecular recognition site; other site 908937006517 dimerization interface [polypeptide binding]; other site 908937006518 LytTr DNA-binding domain; Region: LytTR; smart00850 908937006519 RteC protein; Region: RteC; pfam09357 908937006520 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 908937006521 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 908937006522 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 908937006523 active site 908937006524 DNA binding site [nucleotide binding] 908937006525 Int/Topo IB signature motif; other site 908937006526 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 908937006527 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 908937006528 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 908937006529 CHC2 zinc finger; Region: zf-CHC2; cl17510 908937006530 Toprim-like; Region: Toprim_2; pfam13155 908937006531 AAA domain; Region: AAA_25; pfam13481 908937006532 Protein of unknown function (DUF3853); Region: DUF3853; pfam12964 908937006533 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 908937006534 non-specific DNA binding site [nucleotide binding]; other site 908937006535 salt bridge; other site 908937006536 sequence-specific DNA binding site [nucleotide binding]; other site 908937006537 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 908937006538 MutS domain III; Region: MutS_III; pfam05192 908937006539 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 908937006540 Walker A/P-loop; other site 908937006541 ATP binding site [chemical binding]; other site 908937006542 Q-loop/lid; other site 908937006543 ABC transporter signature motif; other site 908937006544 Walker B; other site 908937006545 D-loop; other site 908937006546 H-loop/switch region; other site 908937006547 Smr domain; Region: Smr; pfam01713 908937006548 Sulfatase; Region: Sulfatase; cl17466 908937006549 PAP2_like_4 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_4; cd03395 908937006550 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 908937006551 active site 908937006552 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 908937006553 homodimer interaction site [polypeptide binding]; other site 908937006554 cofactor binding site; other site 908937006555 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 908937006556 Sec-independent protein secretion pathway components [Intracellular trafficking and secretion]; Region: TatA; COG1826 908937006557 Endopygalactorunase [Cell envelope biogenesis, outer membrane]; Region: PGU1; COG5434 908937006558 Probable polygalacturonase At3g15720; Region: PLN03003; cl14103 908937006559 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 908937006560 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 908937006561 6-phosphofructokinase; Provisional; Region: PRK03202 908937006562 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 908937006563 active site 908937006564 ADP/pyrophosphate binding site [chemical binding]; other site 908937006565 dimerization interface [polypeptide binding]; other site 908937006566 allosteric effector site; other site 908937006567 fructose-1,6-bisphosphate binding site; other site 908937006568 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 908937006569 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 908937006570 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 908937006571 alpha subunit interaction interface [polypeptide binding]; other site 908937006572 Walker A motif; other site 908937006573 ATP binding site [chemical binding]; other site 908937006574 Walker B motif; other site 908937006575 inhibitor binding site; inhibition site 908937006576 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 908937006577 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 908937006578 gamma subunit interface [polypeptide binding]; other site 908937006579 LBP interface [polypeptide binding]; other site 908937006580 ATP synthase A chain; Region: ATP-synt_A; cl00413 908937006581 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 908937006582 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 908937006583 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl17210 908937006584 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13429 908937006585 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 908937006586 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 908937006587 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 908937006588 beta subunit interaction interface [polypeptide binding]; other site 908937006589 Walker A motif; other site 908937006590 ATP binding site [chemical binding]; other site 908937006591 Walker B motif; other site 908937006592 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 908937006593 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 908937006594 core domain interface [polypeptide binding]; other site 908937006595 delta subunit interface [polypeptide binding]; other site 908937006596 epsilon subunit interface [polypeptide binding]; other site 908937006597 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 908937006598 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 908937006599 transmembrane helices; other site 908937006600 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 908937006601 Glycosyl Hydrolase Family 88; Region: Glyco_hydro_88; pfam07470 908937006602 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 908937006603 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 908937006604 dimer interface [polypeptide binding]; other site 908937006605 anticodon binding site; other site 908937006606 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 908937006607 homodimer interface [polypeptide binding]; other site 908937006608 motif 1; other site 908937006609 active site 908937006610 motif 2; other site 908937006611 GAD domain; Region: GAD; pfam02938 908937006612 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 908937006613 motif 3; other site 908937006614 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 908937006615 active site 908937006616 putative catalytic site [active] 908937006617 DNA binding site [nucleotide binding] 908937006618 putative phosphate binding site [ion binding]; other site 908937006619 metal binding site A [ion binding]; metal-binding site 908937006620 AP binding site [nucleotide binding]; other site 908937006621 metal binding site B [ion binding]; metal-binding site 908937006622 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 908937006623 homodecamer interface [polypeptide binding]; other site 908937006624 GTP cyclohydrolase I; Provisional; Region: PLN03044 908937006625 active site 908937006626 putative catalytic site residues [active] 908937006627 zinc binding site [ion binding]; other site 908937006628 GTP-CH-I/GFRP interaction surface; other site 908937006629 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 908937006630 triosephosphate isomerase; Provisional; Region: PRK14565 908937006631 substrate binding site [chemical binding]; other site 908937006632 dimer interface [polypeptide binding]; other site 908937006633 catalytic triad [active] 908937006634 DoxX; Region: DoxX; pfam07681 908937006635 Domain of Unknown Function (DUF1599); Region: DUF1599; pfam07659 908937006636 Domain of Unknown Function (DUF1599); Region: DUF1599; pfam07659 908937006637 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 908937006638 tRNA adenylyltransferase; Region: tRNA_CCA_actino; TIGR02692 908937006639 active site 908937006640 NTP binding site [chemical binding]; other site 908937006641 metal binding triad [ion binding]; metal-binding site 908937006642 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 908937006643 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 908937006644 Zn2+ binding site [ion binding]; other site 908937006645 Mg2+ binding site [ion binding]; other site 908937006646 tRNA nucleotidyltransferase domain 2 putative; Region: tRNA_NucTran2_2; pfam13735 908937006647 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 908937006648 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 908937006649 HlyD family secretion protein; Region: HlyD_3; pfam13437 908937006650 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 908937006651 Protein export membrane protein; Region: SecD_SecF; cl14618 908937006652 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 908937006653 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK12461 908937006654 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 908937006655 putative trimer interface [polypeptide binding]; other site 908937006656 putative CoA binding site [chemical binding]; other site 908937006657 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 908937006658 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 908937006659 Coenzyme A binding pocket [chemical binding]; other site 908937006660 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 908937006661 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 908937006662 TPR motif; other site 908937006663 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 908937006664 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 908937006665 FeS/SAM binding site; other site 908937006666 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 908937006667 FtsX-like permease family; Region: FtsX; pfam02687 908937006668 Protein of unknown function (DUF3098); Region: DUF3098; pfam11297 908937006669 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 908937006670 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 908937006671 tRNA pseudouridine(55) synthase; Region: TruB; TIGR00431 908937006672 RNA binding site [nucleotide binding]; other site 908937006673 active site 908937006674 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 908937006675 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 908937006676 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 908937006677 catalytic center binding site [active] 908937006678 ATP binding site [chemical binding]; other site 908937006679 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 908937006680 16S/18S rRNA binding site [nucleotide binding]; other site 908937006681 S13e-L30e interaction site [polypeptide binding]; other site 908937006682 25S rRNA binding site [nucleotide binding]; other site 908937006683 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 908937006684 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 908937006685 G1 box; other site 908937006686 putative GEF interaction site [polypeptide binding]; other site 908937006687 GTP/Mg2+ binding site [chemical binding]; other site 908937006688 Switch I region; other site 908937006689 G2 box; other site 908937006690 G3 box; other site 908937006691 Switch II region; other site 908937006692 G4 box; other site 908937006693 G5 box; other site 908937006694 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 908937006695 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 908937006696 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 908937006697 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 908937006698 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 908937006699 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 908937006700 dimer interface [polypeptide binding]; other site 908937006701 phosphorylation site [posttranslational modification] 908937006702 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 908937006703 ATP binding site [chemical binding]; other site 908937006704 Mg2+ binding site [ion binding]; other site 908937006705 G-X-G motif; other site 908937006706 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 908937006707 Response regulator receiver domain; Region: Response_reg; pfam00072 908937006708 active site 908937006709 phosphorylation site [posttranslational modification] 908937006710 intermolecular recognition site; other site 908937006711 dimerization interface [polypeptide binding]; other site 908937006712 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 908937006713 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 908937006714 glycine betaine aldehyde dehydrogenase; Region: BADH; TIGR01804 908937006715 Four repeated domains in the Fasciclin I family of proteins, present in many other contexts; Region: FAS1; smart00554 908937006716 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 908937006717 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937006718 SusD family; Region: SusD; pfam07980 908937006719 Fasciclin domain; Region: Fasciclin; cl02663 908937006720 Fasciclin domain; Region: Fasciclin; cl02663 908937006721 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 908937006722 Cna protein B-type domain; Region: Cna_B_2; pfam13715 908937006723 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 908937006724 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937006725 starch binding outer membrane protein SusD; Region: SusD; cl17845 908937006726 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 908937006727 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 908937006728 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 908937006729 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 908937006730 GSCFA family; Region: GSCFA; pfam08885 908937006731 bifunctional fucokinase/L-fucose-1-P-guanylyltransferase; Provisional; Region: fkp; PRK13412 908937006732 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 908937006733 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 908937006734 L-fucose transporter; Provisional; Region: PRK10133; cl17665 908937006735 Ricin-type beta-trefoil lectin domain-like; Region: RicinB_lectin_2; pfam14200 908937006736 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 908937006737 Interdomain contacts; other site 908937006738 Cytokine receptor motif; other site 908937006739 Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of...; Region: LamG; cd00110 908937006740 Domain of unknown function (DUF373); Region: DUF373; cl12079 908937006741 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 908937006742 S-ribosylhomocysteinase; Provisional; Region: PRK02260 908937006743 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional; Region: PRK11930 908937006744 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 908937006745 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 908937006746 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 908937006747 active site 908937006748 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 908937006749 dimer interface [polypeptide binding]; other site 908937006750 substrate binding site [chemical binding]; other site 908937006751 catalytic residues [active] 908937006752 Phosphotransferase system, galactitol-specific IIC component [Carbohydrate transport and metabolism]; Region: GatC; COG3775 908937006753 PTS system sugar-specific permease component; Region: EIIC-GAT; cl04451 908937006754 5-keto-4-deoxyuronate isomerase; Provisional; Region: PRK00924 908937006755 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 908937006756 Major Facilitator Superfamily; Region: MFS_1; pfam07690 908937006757 putative substrate translocation pore; other site 908937006758 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 908937006759 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 908937006760 This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH as...; Region: NfsA_FRP; cd02146 908937006761 dimer interface [polypeptide binding]; other site 908937006762 FMN binding site [chemical binding]; other site 908937006763 NADPH bind site [chemical binding]; other site 908937006764 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 908937006765 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 908937006766 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 908937006767 active site 908937006768 dimer interface [polypeptide binding]; other site 908937006769 effector binding site; other site 908937006770 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 908937006771 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 908937006772 homooctamer interface [polypeptide binding]; other site 908937006773 active site 908937006774 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 908937006775 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 908937006776 active site 908937006777 metal binding site [ion binding]; metal-binding site 908937006778 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 908937006779 mce related protein; Region: MCE; pfam02470 908937006780 Domain of unknown function (DUF334); Region: DUF334; pfam03904 908937006781 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 908937006782 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 908937006783 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 908937006784 Replication initiation factor; Region: Rep_trans; pfam02486