-- dump date 20140619_000406 -- class Genbank::misc_feature -- table misc_feature_note -- id note 295405000001 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3666 295405000002 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 295405000003 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 295405000004 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 295405000005 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 295405000006 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 295405000007 P-loop; other site 295405000008 Magnesium ion binding site [ion binding]; other site 295405000009 Domain of unknown function (DUF4134); Region: DUF4134; pfam13572 295405000010 Bacteroides conjugation system ATPase, TraG family; Region: Bac_Flav_CT_G; TIGR03783 295405000011 Bacteroides conjugative transposon TraJ protein; Region: Bac_Flav_CT_J; TIGR03782 295405000012 Bacteroides conjugative transposon TraK protein; Region: Bac_Flav_CT_K; TIGR03781 295405000013 Bacteroides conjugative transposon TraM protein; Region: Bac_Flav_CT_M; TIGR03779 295405000014 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 295405000015 Bacteroides conjugative transposon TraN protein; Region: Bac_Flav_CT_N; TIGR03780 295405000016 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 295405000017 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 295405000018 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 295405000019 ligand binding site [chemical binding]; other site 295405000020 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 295405000021 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 295405000022 non-specific DNA binding site [nucleotide binding]; other site 295405000023 salt bridge; other site 295405000024 sequence-specific DNA binding site [nucleotide binding]; other site 295405000025 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 295405000026 Peptidase family M23; Region: Peptidase_M23; pfam01551 295405000027 Protein of unknown function (DUF4099); Region: DUF4099; pfam13351 295405000028 Protein of unknown function (DUF3945); Region: DUF3945; pfam13101 295405000029 Protein of unknown function (DUF3945); Region: DUF3945; pfam13101 295405000030 Protein of unknown function (DUF3991); Region: DUF3991; pfam13154 295405000031 Toprim-like; Region: Toprim_2; pfam13155 295405000032 Bacterial PH domain; Region: DUF304; cl01348 295405000033 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 295405000034 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 295405000035 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 295405000036 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 295405000037 IHF - DNA interface [nucleotide binding]; other site 295405000038 IHF dimer interface [polypeptide binding]; other site 295405000039 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 295405000040 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 295405000041 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 295405000042 non-specific DNA binding site [nucleotide binding]; other site 295405000043 salt bridge; other site 295405000044 sequence-specific DNA binding site [nucleotide binding]; other site 295405000045 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 295405000046 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 295405000047 Initiator Replication protein; Region: Rep_3; pfam01051 295405000048 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 295405000049 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 295405000050 Outer membrane efflux protein; Region: OEP; pfam02321 295405000051 Outer membrane efflux protein; Region: OEP; pfam02321 295405000052 LanC-like proteins. LanC is the cyclase enzyme of the lanthionine synthetase. Lanthionine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as a precursor peptide and then post-translationally modified to contain...; Region: LanC_like; cl04955 295405000053 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 295405000054 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 295405000055 active site 295405000056 Erythromycin esterase; Region: Erythro_esteras; cl17110 295405000057 Erythromycin esterase; Region: Erythro_esteras; cl17110 295405000058 Erythromycin esterase; Region: Erythro_esteras; cl17110 295405000059 Erythromycin esterase; Region: Erythro_esteras; cl17110 295405000060 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405000061 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 295405000062 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 295405000063 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 295405000064 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405000065 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 295405000066 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39B; cd02418 295405000067 putative active site [active] 295405000068 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 295405000069 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405000070 Walker A/P-loop; other site 295405000071 ATP binding site [chemical binding]; other site 295405000072 Q-loop/lid; other site 295405000073 ABC transporter signature motif; other site 295405000074 Walker B; other site 295405000075 D-loop; other site 295405000076 H-loop/switch region; other site 295405000077 Domain of unknown function (DUF4294); Region: DUF4294; pfam14127 295405000078 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 295405000079 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 295405000080 FeS/SAM binding site; other site 295405000081 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 295405000082 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405000083 Sulfatase; Region: Sulfatase; pfam00884 295405000084 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 295405000085 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405000086 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 295405000087 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 295405000088 N-terminal plug; other site 295405000089 ligand-binding site [chemical binding]; other site 295405000090 putative transporter; Provisional; Region: PRK11660 295405000091 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 295405000092 Sulfate transporter family; Region: Sulfate_transp; pfam00916 295405000093 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 295405000094 Rubrerythrin [Energy production and conversion]; Region: COG1592 295405000095 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 295405000096 binuclear metal center [ion binding]; other site 295405000097 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 295405000098 iron binding site [ion binding]; other site 295405000099 L-aspartate oxidase; Provisional; Region: PRK09077 295405000100 L-aspartate oxidase; Provisional; Region: PRK06175 295405000101 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 295405000102 Domain of unknown function (DUF1200); Region: DUF1200; pfam06713 295405000103 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion]; Region: Lpd; COG1249 295405000104 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 295405000105 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 295405000106 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 295405000107 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 295405000108 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 295405000109 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 295405000110 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14329 295405000111 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 295405000112 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 295405000113 FeS/SAM binding site; other site 295405000114 TRAM domain; Region: TRAM; pfam01938 295405000115 Alpha-L-fucosidase; Region: Alpha_L_fucos; smart00812 295405000116 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 295405000117 beta-D-glucuronidase; Provisional; Region: PRK10150 295405000118 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405000119 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405000120 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405000121 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405000122 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 295405000123 DNA binding site [nucleotide binding] 295405000124 NVEALA protein; Region: NVEALA; pfam14055 295405000125 NVEALA protein; Region: NVEALA; pfam14055 295405000126 phosphodiesterase; Provisional; Region: PRK12704 295405000127 NVEALA protein; Region: NVEALA; pfam14055 295405000128 NVEALA protein; Region: NVEALA; pfam14055 295405000129 ent-kaur-16-ene synthase; Region: PLN02279 295405000130 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 295405000131 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 295405000132 NVEALA protein; Region: NVEALA; pfam14055 295405000133 putative Zn-ribbon RNA-binding protein; Provisional; Region: PRK14890 295405000134 Methyltransferase domain; Region: Methyltransf_23; pfam13489 295405000135 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 295405000136 S-adenosylmethionine binding site [chemical binding]; other site 295405000137 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 295405000138 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 295405000139 O-Antigen ligase; Region: Wzy_C; cl04850 295405000140 Protein of unknown function (DUF3098); Region: DUF3098; pfam11297 295405000141 Bacitracin resistance protein BacA; Region: BacA; pfam02673 295405000142 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 295405000143 tRNA pseudouridine(55) synthase; Region: TruB; TIGR00431 295405000144 RNA binding site [nucleotide binding]; other site 295405000145 active site 295405000146 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 295405000147 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 295405000148 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 295405000149 catalytic center binding site [active] 295405000150 ATP binding site [chemical binding]; other site 295405000151 S-adenosylmethionine synthetase; Validated; Region: PRK05250 295405000152 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 295405000153 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 295405000154 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 295405000155 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 295405000156 Domain of unknown function (DUF4271); Region: DUF4271; pfam14093 295405000157 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 295405000158 active site 295405000159 ribonuclease P; Reviewed; Region: rnpA; PRK01903 295405000160 Haemolytic domain; Region: Haemolytic; pfam01809 295405000161 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 295405000162 active site 295405000163 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 295405000164 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 295405000165 active site 295405000166 HIGH motif; other site 295405000167 dimer interface [polypeptide binding]; other site 295405000168 KMSKS motif; other site 295405000169 Uncharacterized protein related to the periplasmic component of the Tol biopolymer transport system [Function unknown]; Region: COG4946 295405000170 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 295405000171 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 295405000172 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 295405000173 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 295405000174 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 295405000175 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 295405000176 protein binding site [polypeptide binding]; other site 295405000177 Tricorn protease; serine protease family S41; Region: Peptidase_S41_TRI; cd07562 295405000178 Domain interface; other site 295405000179 Peptide binding site; other site 295405000180 Active site tetrad [active] 295405000181 arylsulfatase; Provisional; Region: PRK13759 295405000182 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405000183 5-keto-4-deoxyuronate isomerase; Provisional; Region: PRK00924 295405000184 gluconate 5-dehydrogenase; Provisional; Region: PRK07097 295405000185 gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs; Region: Ga5DH-like_SDR_c; cd05347 295405000186 NADP binding site [chemical binding]; other site 295405000187 homodimer interface [polypeptide binding]; other site 295405000188 active site 295405000189 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 295405000190 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 295405000191 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 295405000192 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 295405000193 NodB motif; other site 295405000194 active site 295405000195 catalytic site [active] 295405000196 metal binding site [ion binding]; metal-binding site 295405000197 Protein of unknown function (DUF2723); Region: DUF2723; pfam11028 295405000198 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 295405000199 The C-terminal domain of uncharacterized bacterial proteins; Region: Bvu_2165_C_like; cd12843 295405000200 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 295405000201 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 295405000202 Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding...; Region: ZntC; cd01018 295405000203 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 295405000204 putative metal binding residues [ion binding]; other site 295405000205 S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_30; cl17711 295405000206 Predicted membrane protein [Function unknown]; Region: COG1238 295405000207 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 295405000208 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 295405000209 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 295405000210 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 295405000211 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 295405000212 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 295405000213 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 295405000214 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 295405000215 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 295405000216 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 295405000217 serine O-acetyltransferase; Region: cysE; TIGR01172 295405000218 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 295405000219 trimer interface [polypeptide binding]; other site 295405000220 active site 295405000221 substrate binding site [chemical binding]; other site 295405000222 CoA binding site [chemical binding]; other site 295405000223 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 295405000224 binding surface 295405000225 TPR motif; other site 295405000226 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405000227 Histidine kinase; Region: His_kinase; pfam06580 295405000228 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 295405000229 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 295405000230 active site 295405000231 phosphorylation site [posttranslational modification] 295405000232 intermolecular recognition site; other site 295405000233 dimerization interface [polypeptide binding]; other site 295405000234 LytTr DNA-binding domain; Region: LytTR; smart00850 295405000235 Family of unknown function (DUF3836); Region: DUF3836; pfam12930 295405000236 DNA polymerase I; Provisional; Region: PRK05755 295405000237 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 295405000238 active site 295405000239 metal binding site 1 [ion binding]; metal-binding site 295405000240 putative 5' ssDNA interaction site; other site 295405000241 metal binding site 3; metal-binding site 295405000242 metal binding site 2 [ion binding]; metal-binding site 295405000243 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 295405000244 putative DNA binding site [nucleotide binding]; other site 295405000245 putative metal binding site [ion binding]; other site 295405000246 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 295405000247 active site 295405000248 catalytic site [active] 295405000249 substrate binding site [chemical binding]; other site 295405000250 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 295405000251 active site 295405000252 DNA binding site [nucleotide binding] 295405000253 catalytic site [active] 295405000254 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 295405000255 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 295405000256 substrate binding pocket [chemical binding]; other site 295405000257 chain length determination region; other site 295405000258 substrate-Mg2+ binding site; other site 295405000259 catalytic residues [active] 295405000260 aspartate-rich region 1; other site 295405000261 active site lid residues [active] 295405000262 aspartate-rich region 2; other site 295405000263 Protein of unknown function (DUF1266); Region: DUF1266; pfam06889 295405000264 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 295405000265 intersubunit interface [polypeptide binding]; other site 295405000266 active site 295405000267 catalytic residue [active] 295405000268 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 295405000269 homodimer interface [polypeptide binding]; other site 295405000270 metal binding site [ion binding]; metal-binding site 295405000271 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 295405000272 putative active site [active] 295405000273 dimerization interface [polypeptide binding]; other site 295405000274 putative tRNAtyr binding site [nucleotide binding]; other site 295405000275 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 295405000276 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 295405000277 GIY-YIG motif/motif A; other site 295405000278 active site 295405000279 catalytic site [active] 295405000280 putative DNA binding site [nucleotide binding]; other site 295405000281 metal binding site [ion binding]; metal-binding site 295405000282 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 295405000283 H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Region: H3TH_StructSpec-5'-nucleases; cl14815 295405000284 DNA binding site [nucleotide binding] 295405000285 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 295405000286 active site 295405000287 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 295405000288 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 295405000289 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 295405000290 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405000291 PcfK-like protein; Region: PcfK; pfam14058 295405000292 PcfJ-like protein; Region: PcfJ; pfam14284 295405000293 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 295405000294 catalytic residue [active] 295405000295 Domain of unknown function, B. Theta Gene description (DUF3872); Region: DUF3872; pfam12988 295405000296 CHC2 zinc finger; Region: zf-CHC2; cl17510 295405000297 Toprim-like; Region: Toprim_2; pfam13155 295405000298 active site 295405000299 metal binding site [ion binding]; metal-binding site 295405000300 Conjugative transposon protein TraO; Region: TraO; pfam10626 295405000301 Bacteroides conjugative transposon TraN protein; Region: Bac_Flav_CT_N; TIGR03780 295405000302 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 295405000303 Bacteroides conjugative transposon TraM protein; Region: Bac_Flav_CT_M; TIGR03779 295405000304 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 295405000305 Protein of unknown function (DUF3989); Region: DUF3989; pfam13150 295405000306 Bacteroides conjugative transposon TraK protein; Region: Bac_Flav_CT_K; TIGR03781 295405000307 Bacteroides conjugative transposon TraJ protein; Region: Bac_Flav_CT_J; TIGR03782 295405000308 Domain of unknown function (DUF4141); Region: DUF4141; pfam13605 295405000309 Domain of unknown function, B. Theta Gene description (DUF3876); Region: DUF3876; pfam12992 295405000310 Bacteroides conjugation system ATPase, TraG family; Region: Bac_Flav_CT_G; TIGR03783 295405000311 Domain of unknown function, B. Theta Gene description (DUF3875); Region: DUF3875; pfam12991 295405000312 C2 domain; Region: C2; cl14603 295405000313 Domain of unknown function (DUF4133); Region: DUF4133; pfam13571 295405000314 Domain of unknown function (DUF4134); Region: DUF4134; pfam13572 295405000315 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 295405000316 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 295405000317 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 295405000318 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 295405000319 P-loop; other site 295405000320 Magnesium ion binding site [ion binding]; other site 295405000321 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 295405000322 YWFCY protein; Region: YWFCY; pfam14293 295405000323 AAA-like domain; Region: AAA_10; pfam12846 295405000324 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 295405000325 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 295405000326 AAA domain; Region: AAA_14; pfam13173 295405000327 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 295405000328 HTH domain; Region: HTH_11; cl17392 295405000329 RteC protein; Region: RteC; pfam09357 295405000330 RibD C-terminal domain; Region: RibD_C; cl17279 295405000331 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 295405000332 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 295405000333 active site 295405000334 phosphorylation site [posttranslational modification] 295405000335 intermolecular recognition site; other site 295405000336 dimerization interface [polypeptide binding]; other site 295405000337 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 295405000338 Walker A motif; other site 295405000339 ATP binding site [chemical binding]; other site 295405000340 Walker B motif; other site 295405000341 arginine finger; other site 295405000342 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 295405000343 Response regulator receiver domain; Region: Response_reg; pfam00072 295405000344 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 295405000345 active site 295405000346 phosphorylation site [posttranslational modification] 295405000347 intermolecular recognition site; other site 295405000348 dimerization interface [polypeptide binding]; other site 295405000349 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405000350 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 295405000351 dimer interface [polypeptide binding]; other site 295405000352 phosphorylation site [posttranslational modification] 295405000353 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 295405000354 ATP binding site [chemical binding]; other site 295405000355 Mg2+ binding site [ion binding]; other site 295405000356 G-X-G motif; other site 295405000357 Methyltransferase domain; Region: Methyltransf_26; pfam13659 295405000358 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 295405000359 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 295405000360 helicase superfamily c-terminal domain; Region: HELICc; smart00490 295405000361 ATP-binding site [chemical binding]; other site 295405000362 Domain of unknown function (DUF1896); Region: DUF1896; pfam08989 295405000363 DNA topoisomerase III; Provisional; Region: PRK07726 295405000364 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 295405000365 active site 295405000366 putative interdomain interaction site [polypeptide binding]; other site 295405000367 putative metal-binding site [ion binding]; other site 295405000368 putative nucleotide binding site [chemical binding]; other site 295405000369 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 295405000370 domain I; other site 295405000371 DNA binding groove [nucleotide binding] 295405000372 phosphate binding site [ion binding]; other site 295405000373 domain II; other site 295405000374 domain III; other site 295405000375 nucleotide binding site [chemical binding]; other site 295405000376 catalytic site [active] 295405000377 domain IV; other site 295405000378 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 295405000379 Protein of unknown function (DUF4099); Region: DUF4099; pfam13351 295405000380 Protein of unknown function (DUF3945); Region: DUF3945; pfam13101 295405000381 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405000382 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405000383 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405000384 Talin, middle domain; Region: Talin_middle; pfam09141 295405000385 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405000386 Virulence protein [General function prediction only]; Region: COG3943 295405000387 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 295405000388 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 295405000389 Int/Topo IB signature motif; other site 295405000390 Peptidase C10 family; Region: Peptidase_C10; pfam01640 295405000391 Uncharacterized protein family UPF0054; Region: UPF0054; pfam02130 295405000392 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 295405000393 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 295405000394 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 295405000395 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 295405000396 A new structural DNA glycosylase; Region: AlkD_like; cd06561 295405000397 active site 295405000398 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 295405000399 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 295405000400 Walker A motif; other site 295405000401 ATP binding site [chemical binding]; other site 295405000402 Walker B motif; other site 295405000403 arginine finger; other site 295405000404 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 295405000405 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 295405000406 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 295405000407 Domain of unknown function (DUF389); Region: DUF389; pfam04087 295405000408 Peptidase S46; Region: Peptidase_S46; pfam10459 295405000409 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 295405000410 EamA-like transporter family; Region: EamA; pfam00892 295405000411 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 295405000412 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 295405000413 ATP binding site [chemical binding]; other site 295405000414 Mg++ binding site [ion binding]; other site 295405000415 motif III; other site 295405000416 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 295405000417 nucleotide binding region [chemical binding]; other site 295405000418 ATP-binding site [chemical binding]; other site 295405000419 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 295405000420 RNA binding site [nucleotide binding]; other site 295405000421 Tyrosine phosphatase family; Region: Y_phosphatase3; pfam13350 295405000422 Tyrosine phosphatase family; Region: Y_phosphatase2; pfam03162 295405000423 Tyrosine phosphatase family C-terminal region; Region: Y_phosphatase3C; pfam13348 295405000424 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 295405000425 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 295405000426 putative substrate binding site [chemical binding]; other site 295405000427 putative ATP binding site [chemical binding]; other site 295405000428 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 295405000429 putative active site [active] 295405000430 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 295405000431 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 295405000432 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 295405000433 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 295405000434 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 295405000435 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 295405000436 Coenzyme A binding pocket [chemical binding]; other site 295405000437 mannonate dehydratase; Provisional; Region: PRK03906 295405000438 mannonate dehydratase; Region: uxuA; TIGR00695 295405000439 D-mannonate oxidoreductase; Provisional; Region: PRK08277 295405000440 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405000441 NAD(P) binding site [chemical binding]; other site 295405000442 active site 295405000443 WbqC-like protein family; Region: WbqC; pfam08889 295405000444 Signal peptidase I [Intracellular trafficking and secretion]; Region: LepB; COG0681 295405000445 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 295405000446 Catalytic site [active] 295405000447 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 295405000448 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 295405000449 Signal peptidase I [Intracellular trafficking and secretion]; Region: LepB; COG0681 295405000450 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 295405000451 dihydrodipicolinate reductase; Provisional; Region: PRK00048 295405000452 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 295405000453 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 295405000454 Protein of unknown function (DUF2851); Region: DUF2851; pfam11013 295405000455 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 295405000456 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 295405000457 FMN binding site [chemical binding]; other site 295405000458 active site 295405000459 catalytic residues [active] 295405000460 substrate binding site [chemical binding]; other site 295405000461 DOMON-like type 9 carbohydrate binding module; Region: CBM9_like_3; cd09620 295405000462 putative ligand binding site [chemical binding]; other site 295405000463 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK12461 295405000464 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 295405000465 active site 295405000466 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 295405000467 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 295405000468 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405000469 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 295405000470 E3 interaction surface; other site 295405000471 lipoyl attachment site [posttranslational modification]; other site 295405000472 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405000473 beta-D-galactosidase; Reviewed; Region: lacZ; PRK09525 295405000474 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405000475 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405000476 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405000477 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 295405000478 Bacterial Ig-like domain; Region: Big_5; pfam13205 295405000479 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 295405000480 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 295405000481 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 295405000482 CoenzymeA binding site [chemical binding]; other site 295405000483 subunit interaction site [polypeptide binding]; other site 295405000484 PHB binding site; other site 295405000485 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 295405000486 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 295405000487 active site 295405000488 HIGH motif; other site 295405000489 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 295405000490 KMSKS motif; other site 295405000491 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 295405000492 tRNA binding surface [nucleotide binding]; other site 295405000493 anticodon binding site; other site 295405000494 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 295405000495 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 295405000496 active site 295405000497 motif I; other site 295405000498 motif II; other site 295405000499 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 295405000500 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 295405000501 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 295405000502 active site 295405000503 phosphorylation site [posttranslational modification] 295405000504 intermolecular recognition site; other site 295405000505 dimerization interface [polypeptide binding]; other site 295405000506 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 295405000507 DNA binding site [nucleotide binding] 295405000508 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405000509 His Kinase A (phosphoacceptor) domain; Region: HisKA; smart00388 295405000510 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 295405000511 ATP binding site [chemical binding]; other site 295405000512 Mg2+ binding site [ion binding]; other site 295405000513 G-X-G motif; other site 295405000514 Arylsulfatase regulator (Fe-S oxidoreductase) [General function prediction only]; Region: AslB; COG0641 295405000515 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 295405000516 FeS/SAM binding site; other site 295405000517 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 295405000518 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 295405000519 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405000520 cyclically-permuted mutarotase family protein; Region: mutarot_permut; TIGR03548 295405000521 Galactose oxidase, central domain; Region: Kelch_3; cl02701 295405000522 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405000523 Galactose oxidase, central domain; Region: Kelch_3; pfam13415 295405000524 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 295405000525 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 295405000526 active site 295405000527 phosphorylation site [posttranslational modification] 295405000528 intermolecular recognition site; other site 295405000529 dimerization interface [polypeptide binding]; other site 295405000530 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 295405000531 DNA binding site [nucleotide binding] 295405000532 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 295405000533 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 295405000534 dimerization interface [polypeptide binding]; other site 295405000535 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 295405000536 dimer interface [polypeptide binding]; other site 295405000537 phosphorylation site [posttranslational modification] 295405000538 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 295405000539 ATP binding site [chemical binding]; other site 295405000540 Mg2+ binding site [ion binding]; other site 295405000541 G-X-G motif; other site 295405000542 magnesium-transporting ATPase; Provisional; Region: PRK15122 295405000543 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 295405000544 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 295405000545 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 295405000546 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 295405000547 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 295405000548 Carbohydrate-selective porin, OprB family; Region: OprB; cl17816 295405000549 Bacterial SNF2 helicase associated; Region: SNF2_assoc; pfam08455 295405000550 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 295405000551 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 295405000552 putative Mg++ binding site [ion binding]; other site 295405000553 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 295405000554 nucleotide binding region [chemical binding]; other site 295405000555 ATP-binding site [chemical binding]; other site 295405000556 tRNA-specific 2-thiouridylase MnmA; Provisional; Region: mnmA; PRK14665 295405000557 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 295405000558 Ligand Binding Site [chemical binding]; other site 295405000559 GH3 auxin-responsive promoter; Region: GH3; pfam03321 295405000560 6-phosphofructokinase; Provisional; Region: PRK03202 295405000561 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 295405000562 active site 295405000563 ADP/pyrophosphate binding site [chemical binding]; other site 295405000564 dimerization interface [polypeptide binding]; other site 295405000565 allosteric effector site; other site 295405000566 fructose-1,6-bisphosphate binding site; other site 295405000567 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 295405000568 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 295405000569 dimerization interface [polypeptide binding]; other site 295405000570 active site 295405000571 metal binding site [ion binding]; metal-binding site 295405000572 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 295405000573 dsRNA binding site [nucleotide binding]; other site 295405000574 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 295405000575 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 295405000576 dimer interface [polypeptide binding]; other site 295405000577 active site 295405000578 acyl carrier protein; Provisional; Region: acpP; PRK00982 295405000579 Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]; Region: PurN; COG0299 295405000580 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 295405000581 active site 295405000582 substrate binding site [chemical binding]; other site 295405000583 cosubstrate binding site; other site 295405000584 catalytic site [active] 295405000585 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 295405000586 D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains; Region: ErythrP_dh; cd12158 295405000587 ligand binding site [chemical binding]; other site 295405000588 NAD binding site [chemical binding]; other site 295405000589 catalytic site [active] 295405000590 homodimer interface [polypeptide binding]; other site 295405000591 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 295405000592 active site 295405000593 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 295405000594 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 295405000595 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 295405000596 Ligand binding site; other site 295405000597 metal-binding site 295405000598 Putative lipopolysaccharide-modifying enzyme; Region: CAP10; smart00672 295405000599 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 295405000600 N-terminal domain of Chondroitin polymerase functions as a GalNAc transferase; Region: GT2_Chondriotin_Pol_N; cd06420 295405000601 Substrate binding site; other site 295405000602 metal-binding site 295405000603 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 295405000604 active site 295405000605 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 295405000606 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 295405000607 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 295405000608 Walker A/P-loop; other site 295405000609 ATP binding site [chemical binding]; other site 295405000610 Q-loop/lid; other site 295405000611 ABC transporter signature motif; other site 295405000612 Walker B; other site 295405000613 D-loop; other site 295405000614 H-loop/switch region; other site 295405000615 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]; Region: COG3341 295405000616 Caulimovirus viroplasmin; Region: Cauli_VI; pfam01693 295405000617 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 295405000618 active site 295405000619 RNA/DNA hybrid binding site [nucleotide binding]; other site 295405000620 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_4; cd02140 295405000621 dimer interface [polypeptide binding]; other site 295405000622 FMN binding site [chemical binding]; other site 295405000623 shikimate kinase; Reviewed; Region: aroK; PRK00131 295405000624 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 295405000625 ADP binding site [chemical binding]; other site 295405000626 magnesium binding site [ion binding]; other site 295405000627 putative shikimate binding site; other site 295405000628 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 295405000629 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 295405000630 Sel1-like repeats; Region: SEL1; smart00671 295405000631 Sel1-like repeats; Region: SEL1; smart00671 295405000632 Sel1-like repeats; Region: SEL1; smart00671 295405000633 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 295405000634 Sel1-like repeats; Region: SEL1; smart00671 295405000635 Sel1-like repeats; Region: SEL1; smart00671 295405000636 Sel1-like repeats; Region: SEL1; smart00671 295405000637 HSP90 family protein; Provisional; Region: PRK14083 295405000638 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 295405000639 ATP binding site [chemical binding]; other site 295405000640 Mg2+ binding site [ion binding]; other site 295405000641 G-X-G motif; other site 295405000642 arginine decarboxylase; Provisional; Region: PRK05354 295405000643 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 295405000644 dimer interface [polypeptide binding]; other site 295405000645 active site 295405000646 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 295405000647 catalytic residues [active] 295405000648 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 295405000649 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 295405000650 nucleotide binding site [chemical binding]; other site 295405000651 N-acetyl-L-glutamate binding site [chemical binding]; other site 295405000652 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 295405000653 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405000654 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 295405000655 DNA binding residues [nucleotide binding] 295405000656 Domain of unknown function (DUF4252); Region: DUF4252; pfam14060 295405000657 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 295405000658 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 295405000659 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 295405000660 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 295405000661 Protein of unknown function DUF45; Region: DUF45; pfam01863 295405000662 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 295405000663 NVEALA protein; Region: NVEALA; pfam14055 295405000664 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 295405000665 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 295405000666 DNA-binding site [nucleotide binding]; DNA binding site 295405000667 Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability; Region: PBP1_FucR_like; cd06276 295405000668 putative dimerization interface [polypeptide binding]; other site 295405000669 putative ligand binding site [chemical binding]; other site 295405000670 L-fucose isomerase; Provisional; Region: fucI; PRK10991 295405000671 L-fucose isomerase (FucIase); FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose during glycolysis). L-fucose (or 6-deoxy-L-galactose) is found in blood group...; Region: L-fucose_isomerase; cd03556 295405000672 hexamer (dimer of trimers) interface [polypeptide binding]; other site 295405000673 trimer interface [polypeptide binding]; other site 295405000674 substrate binding site [chemical binding]; other site 295405000675 Mn binding site [ion binding]; other site 295405000676 L-1,2-propanediol oxidoreductase; Provisional; Region: PRK10624 295405000677 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 295405000678 dimer interface [polypeptide binding]; other site 295405000679 active site 295405000680 metal binding site [ion binding]; metal-binding site 295405000681 Class II Aldolase and Adducin N-terminal domain; Region: Aldolase_II; pfam00596 295405000682 active site 295405000683 intersubunit interface [polypeptide binding]; other site 295405000684 Zn2+ binding site [ion binding]; other site 295405000685 L-rhamnulose kinases; a subfamily of the FGGY family of carbohydrate kinases; Region: FGGY_RhuK; cd07771 295405000686 N- and C-terminal domain interface [polypeptide binding]; other site 295405000687 rhamnulokinase; Region: rhamnulo_kin; TIGR02627 295405000688 active site 295405000689 putative catalytic site [active] 295405000690 metal binding site [ion binding]; metal-binding site 295405000691 ATP binding site [chemical binding]; other site 295405000692 carbohydrate binding site [chemical binding]; other site 295405000693 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 295405000694 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 295405000695 putative substrate translocation pore; other site 295405000696 hypothetical protein; Validated; Region: PRK02001 295405000697 Uncharacterized BCR, YhbC family COG0779; Region: DUF150; pfam02576 295405000698 heptamer interface [polypeptide binding]; other site 295405000699 Sm1 motif; other site 295405000700 hexamer interface [polypeptide binding]; other site 295405000701 RNA binding site [nucleotide binding]; other site 295405000702 Sm2 motif; other site 295405000703 transcription termination factor NusA; Region: NusA; TIGR01953 295405000704 NusA N-terminal domain; Region: NusA_N; pfam08529 295405000705 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 295405000706 RNA binding site [nucleotide binding]; other site 295405000707 homodimer interface [polypeptide binding]; other site 295405000708 NusA-like KH domain; Region: KH_5; pfam13184 295405000709 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 295405000710 G-X-X-G motif; other site 295405000711 translation initiation factor IF-2; Region: IF-2; TIGR00487 295405000712 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 295405000713 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 295405000714 G1 box; other site 295405000715 putative GEF interaction site [polypeptide binding]; other site 295405000716 GTP/Mg2+ binding site [chemical binding]; other site 295405000717 Switch I region; other site 295405000718 G2 box; other site 295405000719 G3 box; other site 295405000720 Switch II region; other site 295405000721 G4 box; other site 295405000722 G5 box; other site 295405000723 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 295405000724 Translation-initiation factor 2; Region: IF-2; pfam11987 295405000725 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 295405000726 Colicin V production protein; Region: Colicin_V; pfam02674 295405000727 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 295405000728 putative ABC transporter; Region: ycf24; CHL00085 295405000729 FeS assembly ATPase SufC; Region: sufC; TIGR01978 295405000730 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 295405000731 Walker A/P-loop; other site 295405000732 ATP binding site [chemical binding]; other site 295405000733 Q-loop/lid; other site 295405000734 ABC transporter signature motif; other site 295405000735 Walker B; other site 295405000736 D-loop; other site 295405000737 H-loop/switch region; other site 295405000738 Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]; Region: SufB; COG0719 295405000739 FeS assembly protein SufD; Region: sufD; TIGR01981 295405000740 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 295405000741 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 295405000742 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 295405000743 catalytic residue [active] 295405000744 hypothetical protein; Provisional; Region: PRK02877 295405000745 alpha-galactosidase; Region: PLN02808; cl17638 295405000746 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 295405000747 Ca binding site [ion binding]; other site 295405000748 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405000749 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405000750 SusD family; Region: SusD; pfam07980 295405000751 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405000752 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405000753 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405000754 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405000755 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 295405000756 FecR protein; Region: FecR; pfam04773 295405000757 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405000758 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405000759 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405000760 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 295405000761 DNA binding residues [nucleotide binding] 295405000762 Galactose oxidase, central domain; Region: Kelch_3; cl02701 295405000763 Galactose oxidase, central domain; Region: Kelch_3; cl02701 295405000764 Arylsulfatase regulator (Fe-S oxidoreductase) [General function prediction only]; Region: AslB; COG0641 295405000765 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 295405000766 FeS/SAM binding site; other site 295405000767 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 295405000768 Rhodopirellula transposase DDE domain; Region: DDE_Tnp_ISAZ013; pfam07592 295405000769 Alpha-galactosidase [Carbohydrate transport and metabolism]; Region: GalA; COG3345 295405000770 Melibiase; Region: Melibiase; pfam02065 295405000771 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 295405000772 Inorganic H+ pyrophosphatase; Region: H_PPase; pfam03030 295405000773 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 295405000774 RNA/DNA hybrid binding site [nucleotide binding]; other site 295405000775 active site 295405000776 uncharacterized bacterial subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB family; Region: EcCorA_ZntB-like_u2; cd12827 295405000777 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 295405000778 Cl binding site [ion binding]; other site 295405000779 oligomer interface [polypeptide binding]; other site 295405000780 phosphoglyceromutase; Provisional; Region: PRK05434 295405000781 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: pgm_bpd_ind; TIGR01307 295405000782 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405000783 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 295405000784 dimer interface [polypeptide binding]; other site 295405000785 phosphorylation site [posttranslational modification] 295405000786 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 295405000787 ATP binding site [chemical binding]; other site 295405000788 Mg2+ binding site [ion binding]; other site 295405000789 G-X-G motif; other site 295405000790 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405000791 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 295405000792 dimer interface [polypeptide binding]; other site 295405000793 phosphorylation site [posttranslational modification] 295405000794 Protein of unknown function (DUF3109); Region: DUF3109; pfam11307 295405000795 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 295405000796 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 295405000797 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 295405000798 ATP binding site [chemical binding]; other site 295405000799 Mg2+ binding site [ion binding]; other site 295405000800 G-X-G motif; other site 295405000801 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 295405000802 anchoring element; other site 295405000803 dimer interface [polypeptide binding]; other site 295405000804 ATP binding site [chemical binding]; other site 295405000805 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 295405000806 active site 295405000807 putative metal-binding site [ion binding]; other site 295405000808 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 295405000809 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 295405000810 Recombination protein O N terminal; Region: RecO_N; pfam11967 295405000811 DNA repair protein RecO; Region: reco; TIGR00613 295405000812 Recombination protein O C terminal; Region: RecO_C; pfam02565 295405000813 Yqey-like protein; Region: YqeY; pfam09424 295405000814 cell division protein FtsZ; Validated; Region: PRK09330 295405000815 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 295405000816 nucleotide binding site [chemical binding]; other site 295405000817 SulA interaction site; other site 295405000818 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 295405000819 Cell division protein FtsA; Region: FtsA; smart00842 295405000820 Cell division protein FtsA; Region: FtsA; pfam14450 295405000821 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 295405000822 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 295405000823 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 295405000824 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 295405000825 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 295405000826 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 295405000827 active site 295405000828 homodimer interface [polypeptide binding]; other site 295405000829 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 295405000830 UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]; Region: MurD; COG0771 295405000831 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 295405000832 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 295405000833 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 295405000834 Mg++ binding site [ion binding]; other site 295405000835 putative catalytic motif [active] 295405000836 putative substrate binding site [chemical binding]; other site 295405000837 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 295405000838 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 295405000839 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 295405000840 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 295405000841 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 295405000842 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 295405000843 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 295405000844 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 295405000845 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 295405000846 MraW methylase family; Region: Methyltransf_5; cl17771 295405000847 cell division protein MraZ; Reviewed; Region: PRK00326 295405000848 MraZ protein; Region: MraZ; pfam02381 295405000849 MraZ protein; Region: MraZ; pfam02381 295405000850 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 295405000851 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 295405000852 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405000853 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 295405000854 DNA binding residues [nucleotide binding] 295405000855 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 295405000856 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 295405000857 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 295405000858 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 295405000859 putative acyl-acceptor binding pocket; other site 295405000860 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 295405000861 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 295405000862 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 295405000863 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 295405000864 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 295405000865 trimer interface [polypeptide binding]; other site 295405000866 active site 295405000867 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 295405000868 binding surface 295405000869 TPR motif; other site 295405000870 Tetratricopeptide repeat; Region: TPR_16; pfam13432 295405000871 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 295405000872 binding surface 295405000873 TPR motif; other site 295405000874 Tetratricopeptide repeat; Region: TPR_16; pfam13432 295405000875 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 295405000876 TPR motif; other site 295405000877 binding surface 295405000878 TPR repeat; Region: TPR_11; pfam13414 295405000879 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 295405000880 binding surface 295405000881 TPR motif; other site 295405000882 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405000883 Domain of unknown function (DUF4292); Region: DUF4292; pfam14125 295405000884 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 295405000885 Peptidase family M23; Region: Peptidase_M23; pfam01551 295405000886 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 295405000887 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 295405000888 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405000889 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 295405000890 dimer interface [polypeptide binding]; other site 295405000891 phosphorylation site [posttranslational modification] 295405000892 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 295405000893 ATP binding site [chemical binding]; other site 295405000894 Mg2+ binding site [ion binding]; other site 295405000895 G-X-G motif; other site 295405000896 Response regulator receiver domain; Region: Response_reg; pfam00072 295405000897 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 295405000898 active site 295405000899 phosphorylation site [posttranslational modification] 295405000900 intermolecular recognition site; other site 295405000901 dimerization interface [polypeptide binding]; other site 295405000902 Protein kinase C-related kinase homology region 1 (HR1) domain that binds Rho family small GTPases; Region: HR1; cl00087 295405000903 Mga helix-turn-helix domain; Region: Mga; pfam05043 295405000904 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405000905 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405000906 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 295405000907 active site 295405000908 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 295405000909 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 295405000910 domain in bacterial beta-glucosidases other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins; Region: PA14; smart00758 295405000911 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 295405000912 Glycosyl hydrolase family 76; Region: Glyco_hydro_76; pfam03663 295405000913 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405000914 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405000915 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405000916 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 295405000917 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 295405000918 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 295405000919 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 295405000920 active site 295405000921 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405000922 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405000923 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405000924 Domain of unknown function (DUF1793); Region: DUF1793; pfam08760 295405000925 N-terminal catalytic domain of endoplasmic reticulum(ER)/cytosolic class II alpha-mannosidases; glycoside hydrolase family 38 (GH38); Region: GH38N_AMII_ER_cytosolic; cd10789 295405000926 active site 295405000927 catalytic site [active] 295405000928 Alpha mannosidase, middle domain; Region: Alpha-mann_mid; smart00872 295405000929 Glycosyl hydrolases family 38 C-terminal domain; Region: Glyco_hydro_38C; pfam07748 295405000930 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405000931 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405000932 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405000933 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405000934 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405000935 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405000936 SusD family; Region: SusD; pfam07980 295405000937 Protein of unknown function (DUF3823); Region: DUF3823; pfam12866 295405000938 Glycosyl hydrolase family 43; Region: GH43_ABN_2; cd08999 295405000939 putative substrate binding site [chemical binding]; other site 295405000940 active site 295405000941 Glycosyl hydrolase family 76; Region: Glyco_hydro_76; pfam03663 295405000942 Domain of unknown function (DUF1793); Region: DUF1793; pfam08760 295405000943 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 295405000944 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 295405000945 Uncharacterized conserved protein [Function unknown]; Region: COG3538 295405000946 Protein of unknown function (DUF1237); Region: DUF1237; pfam06824 295405000947 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 295405000948 active site 295405000949 catalytic residues [active] 295405000950 Predicted membrane protein [Function unknown]; Region: COG2311 295405000951 Protein of unknown function (DUF418); Region: DUF418; pfam04235 295405000952 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 295405000953 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 295405000954 active site 295405000955 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405000956 sugar binding site [chemical binding]; other site 295405000957 Carbohydrate Binding Module 6 (CBM6); many are appended to glycoside hydrolase (GH) family 11 and GH43 xylanase domains; Region: CBM6_xylanase-like; cd04084 295405000958 metal binding site [ion binding]; metal-binding site 295405000959 ligand binding site [chemical binding]; other site 295405000960 Glycosyl hydrolase family 43; Region: GH43_bXyl_2; cd08991 295405000961 active site 295405000962 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 295405000963 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 295405000964 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 295405000965 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 295405000966 ligand binding site [chemical binding]; other site 295405000967 flexible hinge region; other site 295405000968 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405000969 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 295405000970 DNA-binding site [nucleotide binding]; DNA binding site 295405000971 Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability; Region: PBP1_FucR_like; cd06276 295405000972 Transcriptional regulators [Transcription]; Region: PurR; COG1609 295405000973 putative dimerization interface [polypeptide binding]; other site 295405000974 putative ligand binding site [chemical binding]; other site 295405000975 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 295405000976 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 295405000977 Domain of Unknown Function (DUF1080); Region: DUF1080; pfam06439 295405000978 Carbohydrate binding domain; Region: CBM_4_9; pfam02018 295405000979 Alpha-L-arabinofuranosidase [Carbohydrate transport and metabolism]; Region: AbfA; COG3534 295405000980 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; smart00813 295405000981 Alpha-L-rhamnosidase N-terminal domain; Region: Bac_rhamnosid_N; pfam08531 295405000982 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; pfam05592 295405000983 M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases; Region: M20_ArgE_DapE_like5; cd05651 295405000984 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 295405000985 metal binding site [ion binding]; metal-binding site 295405000986 dimer interface [polypeptide binding]; other site 295405000987 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 295405000988 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 295405000989 acyl-activating enzyme (AAE) consensus motif; other site 295405000990 putative AMP binding site [chemical binding]; other site 295405000991 putative active site [active] 295405000992 putative CoA binding site [chemical binding]; other site 295405000993 This domain is found in peptide chain release factors; Region: PCRF; smart00937 295405000994 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 295405000995 RF-1 domain; Region: RF-1; pfam00472 295405000996 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 295405000997 CYTH-like Clostridium thermocellum TTM-like subgroup 1; Region: CYTH-like_CthTTM-like_1; cd07891 295405000998 putative active site [active] 295405000999 putative metal binding residues [ion binding]; other site 295405001000 signature motif; other site 295405001001 putative dimer interface [polypeptide binding]; other site 295405001002 putative phosphate binding site [ion binding]; other site 295405001003 Predicted membrane protein [Function unknown]; Region: COG3174 295405001004 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 295405001005 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001006 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405001007 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 295405001008 Uncharacterized protein conserved in bacteria (DUF2264); Region: DUF2264; pfam10022 295405001009 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405001010 beta-D-glucuronidase; Provisional; Region: PRK10150 295405001011 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405001012 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405001013 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 295405001014 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 295405001015 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 295405001016 active site 295405001017 Sulfatase; Region: Sulfatase; cl17466 295405001018 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 295405001019 Glycosyl Hydrolase Family 88; Region: Glyco_hydro_88; pfam07470 295405001020 Heparinase II/III-like protein; Region: Hepar_II_III; pfam07940 295405001021 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405001022 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405001023 SusD family; Region: SusD; pfam07980 295405001024 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001025 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001026 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405001027 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405001028 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405001029 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405001030 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 295405001031 dimer interface [polypeptide binding]; other site 295405001032 phosphorylation site [posttranslational modification] 295405001033 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 295405001034 ATP binding site [chemical binding]; other site 295405001035 Mg2+ binding site [ion binding]; other site 295405001036 G-X-G motif; other site 295405001037 Response regulator receiver domain; Region: Response_reg; pfam00072 295405001038 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 295405001039 active site 295405001040 phosphorylation site [posttranslational modification] 295405001041 intermolecular recognition site; other site 295405001042 dimerization interface [polypeptide binding]; other site 295405001043 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405001044 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405001045 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 295405001046 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 295405001047 Members of the SGNH-hydrolase superfamily, 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_like_7; cd04502 295405001048 active site 295405001049 catalytic triad [active] 295405001050 oxyanion hole [active] 295405001051 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5368 295405001052 Putative glucoamylase; Region: Glycoamylase; pfam10091 295405001053 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 295405001054 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 295405001055 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 295405001056 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405001057 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405001058 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001059 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001060 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405001061 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 295405001062 non-specific DNA binding site [nucleotide binding]; other site 295405001063 salt bridge; other site 295405001064 sequence-specific DNA binding site [nucleotide binding]; other site 295405001065 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 295405001066 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 295405001067 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001068 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001069 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405001070 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405001071 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405001072 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405001073 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405001074 Interphotoreceptor retinoid-binding protein; serine protease family S41; Region: Peptidase_S41_IRBP; cd07563 295405001075 active site triad [active] 295405001076 Protein of unknown function (DUF3316); Region: DUF3316; pfam11777 295405001077 DNA topoisomerase IV subunit A; Provisional; Region: PRK12758 295405001078 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 295405001079 CAP-like domain; other site 295405001080 active site 295405001081 primary dimer interface [polypeptide binding]; other site 295405001082 glycyl-tRNA synthetase; Provisional; Region: PRK04173 295405001083 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 295405001084 motif 1; other site 295405001085 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 295405001086 active site 295405001087 motif 2; other site 295405001088 motif 3; other site 295405001089 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for...; Region: HGTP_anticodon; cl00266 295405001090 anticodon binding site; other site 295405001091 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 295405001092 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405001093 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 295405001094 binding surface 295405001095 TPR motif; other site 295405001096 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405001097 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405001098 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_ox_2; pfam12900 295405001099 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 295405001100 cytochrome c nitrate reductase, small subunit; Region: cytochr_NrfH; TIGR03153 295405001101 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; PRK11125 295405001102 ResB-like family; Region: ResB; pfam05140 295405001103 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 295405001104 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 295405001105 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 295405001106 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 295405001107 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 295405001108 ligand binding site [chemical binding]; other site 295405001109 flexible hinge region; other site 295405001110 putative switch regulator; other site 295405001111 non-specific DNA interactions [nucleotide binding]; other site 295405001112 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 295405001113 DNA binding site [nucleotide binding] 295405001114 sequence specific DNA binding site [nucleotide binding]; other site 295405001115 putative cAMP binding site [chemical binding]; other site 295405001116 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 295405001117 Beta-lactamase; Region: Beta-lactamase; cl17358 295405001118 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 295405001119 active site 295405001120 catalytic triad [active] 295405001121 oxyanion hole [active] 295405001122 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: murQ; PRK05441 295405001123 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 295405001124 putative active site [active] 295405001125 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 295405001126 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 295405001127 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 295405001128 FAD binding domain; Region: FAD_binding_4; pfam01565 295405001129 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 295405001130 Protein of unknown function (DUF1343); Region: DUF1343; pfam07075 295405001131 muropeptide transporter; Reviewed; Region: ampG; PRK11902 295405001132 muropeptide transporter; Validated; Region: ampG; cl17669 295405001133 Stage II sporulation protein; Region: SpoIID; pfam08486 295405001134 SpoIID/LytB domain; Region: SpoIID_LytB; TIGR02669 295405001135 GDP-L-galactose-hexose-1-phosphate guanyltransferase; Provisional; Region: PLN03103 295405001136 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 295405001137 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 295405001138 active site 295405001139 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 295405001140 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 295405001141 active site 295405001142 metal binding site [ion binding]; metal-binding site 295405001143 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 295405001144 Trp docking motif [polypeptide binding]; other site 295405001145 PQQ-like domain; Region: PQQ_2; pfam13360 295405001146 active site 295405001147 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 295405001148 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; cl02713 295405001149 active site 295405001150 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 295405001151 Interdomain contacts; other site 295405001152 Cytokine receptor motif; other site 295405001153 Na(+)/iodide (NIS) and Na(+)/multivitamin (SMVT) cotransporters, and related proteins; solute binding domain; Region: SLC5sbd_NIS-like; cd10326 295405001154 Na binding site [ion binding]; other site 295405001155 Protein of unknown function (DUF1343); Region: DUF1343; pfam07075 295405001156 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405001157 SusD family; Region: SusD; pfam07980 295405001158 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001159 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001160 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405001161 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405001162 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 295405001163 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 295405001164 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 295405001165 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 295405001166 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 295405001167 The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria and archea . Na+/H+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na+ /H+ exchange activity is also crucial...; Region: Na_H_Antiporter_C; cd01988 295405001168 Ligand Binding Site [chemical binding]; other site 295405001169 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 295405001170 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 295405001171 putative ATP binding site [chemical binding]; other site 295405001172 putative substrate interface [chemical binding]; other site 295405001173 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 295405001174 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 295405001175 Walker A/P-loop; other site 295405001176 ATP binding site [chemical binding]; other site 295405001177 Q-loop/lid; other site 295405001178 ABC transporter signature motif; other site 295405001179 Walker B; other site 295405001180 D-loop; other site 295405001181 H-loop/switch region; other site 295405001182 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 295405001183 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 295405001184 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 295405001185 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 295405001186 Na2 binding site [ion binding]; other site 295405001187 putative substrate binding site 1 [chemical binding]; other site 295405001188 Na binding site 1 [ion binding]; other site 295405001189 putative substrate binding site 2 [chemical binding]; other site 295405001190 Predicted integral membrane protein [Function unknown]; Region: COG5652 295405001191 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 295405001192 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 295405001193 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 295405001194 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 295405001195 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 295405001196 Major Facilitator Superfamily; Region: MFS_1; pfam07690 295405001197 putative substrate translocation pore; other site 295405001198 DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and...; Region: DOPA_deC_like; cd06450 295405001199 tyrosine decarboxylase MnfA; Region: tyr_de_CO2_Arch; TIGR03812 295405001200 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405001201 catalytic residue [active] 295405001202 glutaminase; Reviewed; Region: PRK12356 295405001203 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 295405001204 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405001205 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 295405001206 dimer interface [polypeptide binding]; other site 295405001207 phosphorylation site [posttranslational modification] 295405001208 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 295405001209 ATP binding site [chemical binding]; other site 295405001210 Mg2+ binding site [ion binding]; other site 295405001211 G-X-G motif; other site 295405001212 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 295405001213 dihydropteroate synthase; Region: DHPS; TIGR01496 295405001214 substrate binding pocket [chemical binding]; other site 295405001215 dimer interface [polypeptide binding]; other site 295405001216 inhibitor binding site; inhibition site 295405001217 TIGR00159 family protein; Region: TIGR00159 295405001218 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 295405001219 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 295405001220 NVEALA protein; Region: NVEALA; pfam14055 295405001221 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 295405001222 Predicted acetyltransferase involved in intracellular survival and related acetyltransferases [General function prediction only]; Region: Eis; COG4552 295405001223 Acetyltransferase (GNAT) domain; Region: Acetyltransf_9; pfam13527 295405001224 Uncharacterized conserved protein (DUF2156); Region: DUF2156; pfam09924 295405001225 LrgB-like family; Region: LrgB; pfam04172 295405001226 Putative effector of murein hydrolase LrgA [General function prediction only]; Region: COG1380 295405001227 Domain of unknown function (DUF4384); Region: DUF4384; pfam14326 295405001228 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 295405001229 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 295405001230 propionate/acetate kinase; Provisional; Region: PRK12379 295405001231 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cl15837 295405001232 dimer interface [polypeptide binding]; other site 295405001233 Alkaline phosphatase homologues; Region: alkPPc; smart00098 295405001234 active site 295405001235 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cl15837 295405001236 FeS assembly SUF system protein; Region: SUF_assoc; TIGR02945 295405001237 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 295405001238 putative active site [active] 295405001239 putative metal binding site [ion binding]; other site 295405001240 hypothetical protein; Reviewed; Region: PRK00024 295405001241 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 295405001242 MPN+ (JAMM) motif; other site 295405001243 Zinc-binding site [ion binding]; other site 295405001244 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 295405001245 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 295405001246 active site 295405001247 elongation factor P; Validated; Region: PRK00529 295405001248 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 295405001249 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 295405001250 RNA binding site [nucleotide binding]; other site 295405001251 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 295405001252 RNA binding site [nucleotide binding]; other site 295405001253 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 295405001254 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 295405001255 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 295405001256 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 295405001257 RNA binding surface [nucleotide binding]; other site 295405001258 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 295405001259 active site 295405001260 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 295405001261 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 295405001262 ATP-grasp domain; Region: ATP-grasp_4; cl17255 295405001263 NigD-like protein; Region: NigD; pfam12667 295405001264 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 295405001265 active site residue [active] 295405001266 N-acetylornithine carbamoyltransferase; Reviewed; Region: PRK04523 295405001267 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 295405001268 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 295405001269 L,D-transpeptidase catalytic domain; Region: YkuD_2; pfam13645 295405001270 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 295405001271 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 295405001272 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 295405001273 putative catalytic cysteine [active] 295405001274 gamma-glutamyl kinase; Provisional; Region: PRK05429 295405001275 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 295405001276 nucleotide binding site [chemical binding]; other site 295405001277 homotetrameric interface [polypeptide binding]; other site 295405001278 putative phosphate binding site [ion binding]; other site 295405001279 putative allosteric binding site; other site 295405001280 PUA domain; Region: PUA; pfam01472 295405001281 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 295405001282 glutamate racemase; Provisional; Region: PRK00865 295405001283 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 295405001284 periplasmic chaperone; Provisional; Region: PRK10780 295405001285 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 295405001286 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 295405001287 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 295405001288 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 295405001289 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 295405001290 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 295405001291 Surface antigen; Region: Bac_surface_Ag; pfam01103 295405001292 undecaprenyl pyrophosphate synthase; Provisional; Region: PRK14838 295405001293 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 295405001294 catalytic residue [active] 295405001295 putative FPP diphosphate binding site; other site 295405001296 putative FPP binding hydrophobic cleft; other site 295405001297 dimer interface [polypeptide binding]; other site 295405001298 putative IPP diphosphate binding site; other site 295405001299 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 295405001300 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 295405001301 catalytic motif [active] 295405001302 Zn binding site [ion binding]; other site 295405001303 RibD C-terminal domain; Region: RibD_C; pfam01872 295405001304 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 295405001305 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 295405001306 S-adenosylmethionine binding site [chemical binding]; other site 295405001307 RecX family; Region: RecX; pfam02631 295405001308 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 295405001309 active site 295405001310 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 295405001311 hydrophobic ligand binding site; other site 295405001312 Lyase; Region: Lyase_1; pfam00206 295405001313 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 295405001314 active sites [active] 295405001315 tetramer interface [polypeptide binding]; other site 295405001316 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 295405001317 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 295405001318 catalytic residues [active] 295405001319 catalytic nucleophile [active] 295405001320 Recombinase; Region: Recombinase; pfam07508 295405001321 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 295405001322 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 295405001323 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; cd01120 295405001324 Walker A motif; other site 295405001325 ATP binding site [chemical binding]; other site 295405001326 Walker B motif; other site 295405001327 Helix-turn-helix domain; Region: HTH_28; pfam13518 295405001328 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 295405001329 non-specific DNA binding site [nucleotide binding]; other site 295405001330 salt bridge; other site 295405001331 sequence-specific DNA binding site [nucleotide binding]; other site 295405001332 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 295405001333 active site 295405001334 catalytic residues [active] 295405001335 DNA binding site [nucleotide binding] 295405001336 Int/Topo IB signature motif; other site 295405001337 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 295405001338 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 295405001339 active site 295405001340 nucleophile elbow; other site 295405001341 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 295405001342 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 295405001343 non-specific DNA binding site [nucleotide binding]; other site 295405001344 salt bridge; other site 295405001345 sequence-specific DNA binding site [nucleotide binding]; other site 295405001346 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 295405001347 Medium-chain acyl-CoA synthetase (MACS) of AAE_MA like; Region: MACS_AAE_MA_like; cd05970 295405001348 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 295405001349 active site 295405001350 acyl-activating enzyme (AAE) consensus motif; other site 295405001351 putative CoA binding site [chemical binding]; other site 295405001352 AMP binding site [chemical binding]; other site 295405001353 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 295405001354 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 295405001355 non-specific DNA binding site [nucleotide binding]; other site 295405001356 salt bridge; other site 295405001357 sequence-specific DNA binding site [nucleotide binding]; other site 295405001358 Cupin domain; Region: Cupin_2; pfam07883 295405001359 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 295405001360 Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]; Region: ProC; COG0345 295405001361 acetylornithine aminotransferase; Provisional; Region: PRK02627 295405001362 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 295405001363 inhibitor-cofactor binding pocket; inhibition site 295405001364 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405001365 catalytic residue [active] 295405001366 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 295405001367 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 295405001368 argininosuccinate synthase; Provisional; Region: PRK13820 295405001369 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 295405001370 ANP binding site [chemical binding]; other site 295405001371 Substrate Binding Site II [chemical binding]; other site 295405001372 Substrate Binding Site I [chemical binding]; other site 295405001373 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 295405001374 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 295405001375 Coenzyme A binding pocket [chemical binding]; other site 295405001376 Arginine repressor [Transcription]; Region: ArgR; COG1438 295405001377 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 295405001378 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 295405001379 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405001380 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 295405001381 dimer interface [polypeptide binding]; other site 295405001382 phosphorylation site [posttranslational modification] 295405001383 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 295405001384 ATP binding site [chemical binding]; other site 295405001385 Mg2+ binding site [ion binding]; other site 295405001386 G-X-G motif; other site 295405001387 putative glutamate/gamma-aminobutyrate antiporter; Region: put_Glu_GABA_T; TIGR03813 295405001388 Ion channel; Region: Ion_trans_2; pfam07885 295405001389 Malate/lactate dehydrogenases [Energy production and conversion]; Region: Mdh; COG0039 295405001390 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl17195 295405001391 NAD(P) binding site [chemical binding]; other site 295405001392 LDH/MDH dimer interface [polypeptide binding]; other site 295405001393 substrate binding site [chemical binding]; other site 295405001394 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 295405001395 S1 domain; Region: S1_2; pfam13509 295405001396 SmpA / OmlA family; Region: SmpA_OmlA; cl17115 295405001397 Transglycosylase; Region: Transgly; pfam00912 295405001398 MutS domain III; Region: MutS_III; pfam05192 295405001399 ATP-binding cassette domain of MutS-like homolog; Region: ABC_MutS-like; cd03283 295405001400 Walker A/P-loop; other site 295405001401 ATP binding site [chemical binding]; other site 295405001402 Q-loop/lid; other site 295405001403 ABC transporter signature motif; other site 295405001404 Walker B; other site 295405001405 D-loop; other site 295405001406 H-loop/switch region; other site 295405001407 Alpha-galactosidase [Carbohydrate transport and metabolism]; Region: GalA; COG3345 295405001408 Melibiase; Region: Melibiase; pfam02065 295405001409 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 295405001410 This family represents an uncharacterized glycosyl hydrolase family 31 (GH31) enzyme found in bacteria and eukaryotes that is related to the XylS xylosidase of Sulfolobus solfataricus. Alpha-xylosidases catalyze the release of an alpha-xylose residue...; Region: GH31_xylosidase_XylS-like; cd06595 295405001411 putative active site [active] 295405001412 putative catalytic site [active] 295405001413 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405001414 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405001415 SusD family; Region: SusD; pfam07980 295405001416 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405001417 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001418 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001419 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405001420 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405001421 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405001422 FecR protein; Region: FecR; pfam04773 295405001423 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405001424 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405001425 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 295405001426 DNA binding residues [nucleotide binding] 295405001427 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 295405001428 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405001429 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405001430 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405001431 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405001432 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 295405001433 FtsX-like permease family; Region: FtsX; pfam02687 295405001434 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405001435 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 295405001436 FtsX-like permease family; Region: FtsX; pfam02687 295405001437 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 295405001438 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 295405001439 Walker A/P-loop; other site 295405001440 ATP binding site [chemical binding]; other site 295405001441 Q-loop/lid; other site 295405001442 ABC transporter signature motif; other site 295405001443 Walker B; other site 295405001444 D-loop; other site 295405001445 H-loop/switch region; other site 295405001446 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 295405001447 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 295405001448 nucleotide binding site [chemical binding]; other site 295405001449 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 295405001450 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 295405001451 Escherichia coli UshA-like family, N-terminal metallophosphatase domain; Region: MPP_UshA_N_like; cd00845 295405001452 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 295405001453 active site 295405001454 metal binding site [ion binding]; metal-binding site 295405001455 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 295405001456 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 295405001457 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 295405001458 Beta-lactamase; Region: Beta-lactamase; cl17358 295405001459 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 295405001460 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 295405001461 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 295405001462 Beta-lactamase; Region: Beta-lactamase; cl17358 295405001463 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001464 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001465 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405001466 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405001467 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405001468 SusD family; Region: SusD; pfam07980 295405001469 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405001470 Sulfatase; Region: Sulfatase; pfam00884 295405001471 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 295405001472 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 295405001473 PS-10 peptidase S37; Region: Peptidase_S37; pfam05576 295405001474 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 295405001475 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 295405001476 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 295405001477 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 295405001478 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 295405001479 Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar...; Region: RHOD_Pyr_redox; cd01524 295405001480 active site residue [active] 295405001481 SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that...; Region: SirA_RHOD_Pry_redox; cd03420 295405001482 CPxP motif; other site 295405001483 DsrE/DsrF/DrsH-like family; Region: DrsE_2; pfam13686 295405001484 Aspartokinases [Amino acid transport and metabolism]; Region: LysC; COG0527 295405001485 AAK_AK-HSDH-like: Amino Acid Kinase Superfamily (AAK), AK-HSDH-like; this family includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK- homoserine dehydrogenase (HSDH). These aspartokinases are found in such...; Region: AAK_AK-HSDH-like; cd04243 295405001486 putative catalytic residues [active] 295405001487 nucleotide binding site [chemical binding]; other site 295405001488 aspartate binding site [chemical binding]; other site 295405001489 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 295405001490 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 295405001491 dimer interface [polypeptide binding]; other site 295405001492 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 295405001493 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 295405001494 active site 295405001495 phosphorylation site [posttranslational modification] 295405001496 intermolecular recognition site; other site 295405001497 dimerization interface [polypeptide binding]; other site 295405001498 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 295405001499 Walker A motif; other site 295405001500 ATP binding site [chemical binding]; other site 295405001501 Walker B motif; other site 295405001502 arginine finger; other site 295405001503 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 295405001504 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 295405001505 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 295405001506 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 295405001507 Soluble P-type ATPase [General function prediction only]; Region: COG4087 295405001508 potassium-transporting ATPase subunit C; Provisional; Region: PRK14002 295405001509 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 295405001510 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 295405001511 Ligand Binding Site [chemical binding]; other site 295405001512 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 295405001513 dimerization interface [polypeptide binding]; other site 295405001514 PAS domain; Region: PAS; smart00091 295405001515 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 295405001516 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 295405001517 dimer interface [polypeptide binding]; other site 295405001518 phosphorylation site [posttranslational modification] 295405001519 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 295405001520 ATP binding site [chemical binding]; other site 295405001521 Mg2+ binding site [ion binding]; other site 295405001522 G-X-G motif; other site 295405001523 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405001524 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405001525 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 295405001526 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405001527 FecR protein; Region: FecR; pfam04773 295405001528 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405001529 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001530 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001531 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405001532 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405001533 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405001534 NigD-like protein; Region: NigD; pfam12667 295405001535 Lipocalin-like; Region: Lipocalin_3; pfam12702 295405001536 Predicted permeases [General function prediction only]; Region: COG0795 295405001537 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 295405001538 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 295405001539 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 295405001540 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 295405001541 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 295405001542 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 295405001543 dimerization interface [polypeptide binding]; other site 295405001544 active site 295405001545 aspartate aminotransferase; Provisional; Region: PRK05764 295405001546 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 295405001547 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405001548 homodimer interface [polypeptide binding]; other site 295405001549 catalytic residue [active] 295405001550 Alpha-L-rhamnosidase N-terminal domain; Region: Bac_rhamnosid_N; pfam08531 295405001551 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; pfam05592 295405001552 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 295405001553 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 295405001554 homoserine O-succinyltransferase; Provisional; Region: PRK05368 295405001555 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 295405001556 proposed active site lysine [active] 295405001557 conserved cys residue [active] 295405001558 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 295405001559 Peptidase family U32; Region: Peptidase_U32; pfam01136 295405001560 Collagenase; Region: DUF3656; pfam12392 295405001561 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405001562 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 295405001563 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 295405001564 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 295405001565 DNA binding residues [nucleotide binding] 295405001566 dimerization interface [polypeptide binding]; other site 295405001567 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 295405001568 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 295405001569 GxxExxY protein; Region: GxxExxY; TIGR04256 295405001570 DNA repair protein RadA; Provisional; Region: PRK11823 295405001571 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 295405001572 Walker A motif; other site 295405001573 ATP binding site [chemical binding]; other site 295405001574 Walker B motif; other site 295405001575 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 295405001576 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 295405001577 active site 295405001578 homodimer interface [polypeptide binding]; other site 295405001579 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 295405001580 AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli...; Region: AAK_AK-HSDH; cd04257 295405001581 putative catalytic residues [active] 295405001582 putative nucleotide binding site [chemical binding]; other site 295405001583 putative aspartate binding site [chemical binding]; other site 295405001584 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 295405001585 dimer interface [polypeptide binding]; other site 295405001586 putative threonine allosteric regulatory site; other site 295405001587 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 295405001588 putative threonine allosteric regulatory site; other site 295405001589 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 295405001590 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 295405001591 cofactor-independent phosphoglycerate mutase; Provisional; Region: PRK04200 295405001592 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: PhosphMutase; cl17294 295405001593 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 295405001594 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 295405001595 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405001596 catalytic residue [active] 295405001597 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 295405001598 EamA-like transporter family; Region: EamA; pfam00892 295405001599 EamA-like transporter family; Region: EamA; pfam00892 295405001600 Thiamine pyrophosphokinase; Region: TPK; cd07995 295405001601 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 295405001602 active site 295405001603 dimerization interface [polypeptide binding]; other site 295405001604 thiamine binding site [chemical binding]; other site 295405001605 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 295405001606 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405001607 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 295405001608 Conserved TM helix; Region: TM_helix; pfam05552 295405001609 Mechanosensitive ion channel; Region: MS_channel; pfam00924 295405001610 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405001611 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405001612 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 295405001613 DNA binding residues [nucleotide binding] 295405001614 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405001615 FecR protein; Region: FecR; pfam04773 295405001616 GatB domain; Region: GatB_Yqey; cl17694 295405001617 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405001618 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001619 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001620 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405001621 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 295405001622 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405001623 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405001624 SusD family; Region: SusD; pfam07980 295405001625 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405001626 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405001627 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405001628 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405001629 Glycosyl hydrolases family 35; Region: Glyco_hydro_35; pfam01301 295405001630 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405001631 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 295405001632 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_2; cd09001 295405001633 active site 295405001634 Domain of unknown function (DUF4374); Region: DUF4374; pfam14298 295405001635 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001636 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405001637 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 295405001638 O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3315 295405001639 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405001640 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405001641 Protein of unknown function (DUF581); Region: DUF581; pfam04570 295405001642 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 295405001643 active site 295405001644 TIGR02646 family protein; Region: TIGR02646 295405001645 TIGR02646 family protein; Region: TIGR02646 295405001646 Predicted ATP-binding protein involved in virulence [General function prediction only]; Region: COG3950 295405001647 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405001648 Walker A/P-loop; other site 295405001649 ATP binding site [chemical binding]; other site 295405001650 Domain of unknown function DUF87; Region: DUF87; pfam01935 295405001651 HerA helicase [Replication, recombination, and repair]; Region: COG0433 295405001652 DNA methylase; Region: N6_N4_Mtase; pfam01555 295405001653 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 295405001654 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405001655 RteC protein; Region: RteC; pfam09357 295405001656 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 295405001657 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 295405001658 motif II; other site 295405001659 maltose O-acetyltransferase; Provisional; Region: PRK10092 295405001660 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 295405001661 active site 295405001662 substrate binding site [chemical binding]; other site 295405001663 trimer interface [polypeptide binding]; other site 295405001664 CoA binding site [chemical binding]; other site 295405001665 Nitroreductase-like family 3. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_3; cd02139 295405001666 putative FMN binding site [chemical binding]; other site 295405001667 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 295405001668 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 295405001669 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405001670 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405001671 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405001672 Domain of unknown function, B. Theta Gene description (DUF3876); Region: DUF3876; pfam12992 295405001673 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405001674 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 295405001675 Int/Topo IB signature motif; other site 295405001676 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 295405001677 Domain of unknown function DUF20; Region: UPF0118; pfam01594 295405001678 thymidine kinase; Provisional; Region: PRK04296 295405001679 ribonuclease E; Reviewed; Region: rne; PRK10811 295405001680 Predicted methyltransferases [General function prediction only]; Region: COG0313 295405001681 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 295405001682 putative SAM binding site [chemical binding]; other site 295405001683 putative homodimer interface [polypeptide binding]; other site 295405001684 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 295405001685 HAD superfamily (subfamily IA) hydrolase, TIGR02254; Region: YjjG/YfnB 295405001686 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 295405001687 motif II; other site 295405001688 MarC family integral membrane protein; Region: MarC; pfam01914 295405001689 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405001690 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405001691 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001692 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001693 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405001694 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405001695 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 295405001696 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 295405001697 active site 295405001698 DNA binding site [nucleotide binding] 295405001699 Int/Topo IB signature motif; other site 295405001700 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001701 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405001702 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405001703 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405001704 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405001705 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405001706 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001707 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405001708 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 295405001709 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405001710 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405001711 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405001712 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 295405001713 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 295405001714 HflX GTPase family; Region: HflX; cd01878 295405001715 G1 box; other site 295405001716 GTP/Mg2+ binding site [chemical binding]; other site 295405001717 Switch I region; other site 295405001718 G2 box; other site 295405001719 G3 box; other site 295405001720 Switch II region; other site 295405001721 G4 box; other site 295405001722 G5 box; other site 295405001723 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 295405001724 putative trimer interface [polypeptide binding]; other site 295405001725 putative CoA binding site [chemical binding]; other site 295405001726 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_3; cd09602 295405001727 Zn binding site [ion binding]; other site 295405001728 fumarate hydratase; Provisional; Region: PRK15389 295405001729 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 295405001730 Fumarase C-terminus; Region: Fumerase_C; pfam05683 295405001731 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 295405001732 Acyltransferase family; Region: Acyl_transf_3; pfam01757 295405001733 Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain; Region: NAGLU_N; pfam12971 295405001734 Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain; Region: NAGLU; pfam05089 295405001735 Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain; Region: NAGLU_C; pfam12972 295405001736 amino acid transporter; Region: 2A0306; TIGR00909 295405001737 C-terminus of AA_permease; Region: AA_permease_C; pfam13906 295405001738 Outer membrane efflux protein; Region: OEP; pfam02321 295405001739 Outer membrane efflux protein; Region: OEP; pfam02321 295405001740 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 295405001741 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405001742 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405001743 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405001744 CAAX protease self-immunity; Region: Abi; pfam02517 295405001745 GTPase RsgA; Reviewed; Region: PRK00098 295405001746 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 295405001747 RNA binding site [nucleotide binding]; other site 295405001748 homodimer interface [polypeptide binding]; other site 295405001749 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 295405001750 GTPase/Zn-binding domain interface [polypeptide binding]; other site 295405001751 GTP/Mg2+ binding site [chemical binding]; other site 295405001752 G4 box; other site 295405001753 G5 box; other site 295405001754 G1 box; other site 295405001755 Switch I region; other site 295405001756 G2 box; other site 295405001757 G3 box; other site 295405001758 Switch II region; other site 295405001759 ribosome recycling factor; Reviewed; Region: frr; PRK00083 295405001760 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 295405001761 hinge region; other site 295405001762 Bacterial SH3 domain; Region: SH3_3; pfam08239 295405001763 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 295405001764 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 295405001765 Bacterial SH3 domain; Region: SH3_3; cl17532 295405001766 Nucleotide-binding domain of the HSP70 family; Region: HSP70_NBD; cd10170 295405001767 MreB/Mbl protein; Region: MreB_Mbl; pfam06723 295405001768 nucleotide binding site [chemical binding]; other site 295405001769 putative NEF/HSP70 interaction site [polypeptide binding]; other site 295405001770 SBD interface [polypeptide binding]; other site 295405001771 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 295405001772 putative nucleotide binding site [chemical binding]; other site 295405001773 uridine monophosphate binding site [chemical binding]; other site 295405001774 homohexameric interface [polypeptide binding]; other site 295405001775 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 295405001776 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 295405001777 glycosyl hydrolase family 16; Region: Glyco_hydrolase_16; cd00413 295405001778 active site 295405001779 catalytic residues [active] 295405001780 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 295405001781 binding surface 295405001782 TPR motif; other site 295405001783 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 295405001784 Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor; Region: ZnMc_pappalysin_like; cd04275 295405001785 active site 295405001786 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 295405001787 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 295405001788 Protein of unknown function (DUF419); Region: DUF419; pfam04237 295405001789 Uncharacterized protein family UPF0102; Region: UPF0102; cl00516 295405001790 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 295405001791 nucleoside/Zn binding site; other site 295405001792 dimer interface [polypeptide binding]; other site 295405001793 catalytic motif [active] 295405001794 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 295405001795 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 295405001796 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 295405001797 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 295405001798 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 295405001799 active site 295405001800 PHP Thumb interface [polypeptide binding]; other site 295405001801 metal binding site [ion binding]; metal-binding site 295405001802 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 295405001803 generic binding surface II; other site 295405001804 generic binding surface I; other site 295405001805 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 295405001806 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405001807 catalytic residues [active] 295405001808 RDD family; Region: RDD; pfam06271 295405001809 Integral membrane protein DUF95; Region: DUF95; pfam01944 295405001810 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 295405001811 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 295405001812 MoxR-like ATPases [General function prediction only]; Region: COG0714 295405001813 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 295405001814 Walker A motif; other site 295405001815 ATP binding site [chemical binding]; other site 295405001816 Walker B motif; other site 295405001817 arginine finger; other site 295405001818 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 295405001819 Protein of unknown function DUF58; Region: DUF58; pfam01882 295405001820 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 295405001821 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 295405001822 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 295405001823 ABC-ATPase subunit interface; other site 295405001824 dimer interface [polypeptide binding]; other site 295405001825 putative PBP binding regions; other site 295405001826 M28 Zn-Peptidases containing a PA domain insert and associated with a PDZ domain; Region: M28_like_PA_PDZ_associated; cd05663 295405001827 Peptidase family M28; Region: Peptidase_M28; pfam04389 295405001828 metal binding site [ion binding]; metal-binding site 295405001829 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 295405001830 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 295405001831 Galactose oxidase, central domain; Region: Kelch_3; cl02701 295405001832 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]; Region: COG3947 295405001833 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 295405001834 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 295405001835 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 295405001836 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 295405001837 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 295405001838 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001839 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001840 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405001841 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405001842 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405001843 SusD family; Region: SusD; pfam07980 295405001844 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 295405001845 Coagulation factor 5/8 C-terminal domain, discoidin domain; Region: FA58C; smart00231 295405001846 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405001847 sugar binding site [chemical binding]; other site 295405001848 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 295405001849 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 295405001850 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405001851 Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific...; Region: RICIN; cd00161 295405001852 Ricin-type beta-trefoil; Region: RICIN; smart00458 295405001853 putative sugar binding sites [chemical binding]; other site 295405001854 Q-X-W motif; other site 295405001855 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 295405001856 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405001857 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405001858 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405001859 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 295405001860 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 295405001861 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 295405001862 hinge; other site 295405001863 active site 295405001864 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405001865 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405001866 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 295405001867 dimer interface [polypeptide binding]; other site 295405001868 phosphorylation site [posttranslational modification] 295405001869 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 295405001870 ATP binding site [chemical binding]; other site 295405001871 Mg2+ binding site [ion binding]; other site 295405001872 G-X-G motif; other site 295405001873 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 295405001874 Glycosyl hydrolase family 20 (GH20) catalytic domain of dispersin B (DspB), lacto-N-biosidase (LnbB) and related proteins. Dispersin B is a soluble beta-N-acetylglucosamidase found in bacteria that hydrolyzes the beta-1,6-linkages of PGA (poly-beta-(1,6)...; Region: GH20_DspB_LnbB-like; cd06564 295405001875 active site 295405001876 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 295405001877 Acyltransferase family; Region: Acyl_transf_3; pfam01757 295405001878 hypothetical protein; Region: PHA00684 295405001879 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 295405001880 active site 295405001881 dimer interface [polypeptide binding]; other site 295405001882 metal binding site [ion binding]; metal-binding site 295405001883 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 295405001884 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 295405001885 cardiolipin synthase; Region: bac_cardiolipin; TIGR04265 295405001886 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 295405001887 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 295405001888 putative active site [active] 295405001889 catalytic site [active] 295405001890 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 295405001891 putative active site [active] 295405001892 catalytic site [active] 295405001893 Conserved hypothetical protein 95; Region: Cons_hypoth95; pfam03602 295405001894 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 295405001895 S-adenosylmethionine binding site [chemical binding]; other site 295405001896 Protein of unknown function (DUF3822); Region: DUF3822; pfam12864 295405001897 Psb28 protein; Region: Psb28; cl04326 295405001898 AAA domain; Region: AAA_30; pfam13604 295405001899 Family description; Region: UvrD_C_2; pfam13538 295405001900 Starch-binding associating with outer membrane; Region: SusD-like_2; pfam12771 295405001901 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405001902 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405001903 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405001904 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405001905 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001906 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405001907 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 295405001908 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 295405001909 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 295405001910 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 295405001911 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 295405001912 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405001913 FecR protein; Region: FecR; pfam04773 295405001914 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405001915 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405001916 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 295405001917 DNA binding residues [nucleotide binding] 295405001918 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 295405001919 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 295405001920 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 295405001921 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 295405001922 putative substrate translocation pore; other site 295405001923 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405001924 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405001925 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 295405001926 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 295405001927 motif 1; other site 295405001928 active site 295405001929 motif 2; other site 295405001930 motif 3; other site 295405001931 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 295405001932 DHHA1 domain; Region: DHHA1; pfam02272 295405001933 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 295405001934 Peptidase family M23; Region: Peptidase_M23; pfam01551 295405001935 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 295405001936 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 295405001937 DNA binding residues [nucleotide binding] 295405001938 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 295405001939 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 295405001940 Zn2+ binding site [ion binding]; other site 295405001941 Mg2+ binding site [ion binding]; other site 295405001942 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 295405001943 synthetase active site [active] 295405001944 NTP binding site [chemical binding]; other site 295405001945 metal binding site [ion binding]; metal-binding site 295405001946 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 295405001947 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 295405001948 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 295405001949 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 295405001950 N-acetyl-D-glucosamine binding site [chemical binding]; other site 295405001951 catalytic residue [active] 295405001952 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 295405001953 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 295405001954 ParB-like nuclease domain; Region: ParBc; pfam02195 295405001955 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 295405001956 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 295405001957 P-loop; other site 295405001958 Magnesium ion binding site [ion binding]; other site 295405001959 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 295405001960 Magnesium ion binding site [ion binding]; other site 295405001961 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 295405001962 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 295405001963 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 295405001964 NigD-like protein; Region: NigD; pfam12667 295405001965 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 295405001966 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 295405001967 FtsH Extracellular; Region: FtsH_ext; pfam06480 295405001968 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 295405001969 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 295405001970 Walker A motif; other site 295405001971 ATP binding site [chemical binding]; other site 295405001972 Walker B motif; other site 295405001973 arginine finger; other site 295405001974 Peptidase family M41; Region: Peptidase_M41; pfam01434 295405001975 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 295405001976 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 295405001977 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 295405001978 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 295405001979 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 295405001980 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 295405001981 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 295405001982 MgtE intracellular N domain; Region: MgtE_N; smart00924 295405001983 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 295405001984 Divalent cation transporter; Region: MgtE; pfam01769 295405001985 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 295405001986 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 295405001987 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 295405001988 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 295405001989 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 295405001990 metal binding site [ion binding]; metal-binding site 295405001991 dimer interface [polypeptide binding]; other site 295405001992 MG2 domain; Region: A2M_N; pfam01835 295405001993 Domain of unknown function (DUF4249); Region: DUF4249; pfam14054 295405001994 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405001995 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 295405001996 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 295405001997 MG2 domain; Region: A2M_N; pfam01835 295405001998 Alpha-2-macroglobulin family; Region: A2M; pfam00207 295405001999 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 295405002000 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 295405002001 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 295405002002 membrane ATPase/protein kinase; Provisional; Region: PRK09435 295405002003 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 295405002004 Walker A; other site 295405002005 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 295405002006 EamA-like transporter family; Region: EamA; pfam00892 295405002007 EamA-like transporter family; Region: EamA; pfam00892 295405002008 Protein of unknown function, DUF258; Region: DUF258; pfam03193 295405002009 AAA domain; Region: AAA_21; pfam13304 295405002010 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405002011 ABC transporter signature motif; other site 295405002012 Walker B; other site 295405002013 D-loop; other site 295405002014 H-loop/switch region; other site 295405002015 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 295405002016 Mechanosensitive ion channel; Region: MS_channel; pfam00924 295405002017 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 295405002018 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405002019 HipA-like N-terminal domain; Region: HipA_N; pfam07805 295405002020 HipA-like C-terminal domain; Region: HipA_C; pfam07804 295405002021 HipA N-terminal domain; Region: couple_hipA; TIGR03071 295405002022 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 295405002023 non-specific DNA binding site [nucleotide binding]; other site 295405002024 salt bridge; other site 295405002025 sequence-specific DNA binding site [nucleotide binding]; other site 295405002026 Domain of unknown function (DUF4373); Region: DUF4373; pfam14297 295405002027 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 295405002028 UpxZ family of transcription anti-terminator antagonists; Region: UpxZ; pfam06603 295405002029 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 295405002030 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 295405002031 substrate binding site; other site 295405002032 tetramer interface; other site 295405002033 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 295405002034 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 295405002035 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 295405002036 NAD binding site [chemical binding]; other site 295405002037 substrate binding site [chemical binding]; other site 295405002038 homodimer interface [polypeptide binding]; other site 295405002039 active site 295405002040 colanic acid exporter; Provisional; Region: PRK10459 295405002041 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 295405002042 NDP-hexose 2,3-dehydratase; Region: Hexose_dehydrat; pfam03559 295405002043 NDP-hexose 2,3-dehydratase; Region: Hexose_dehydrat; pfam03559 295405002044 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 295405002045 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 295405002046 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 295405002047 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 295405002048 inhibitor-cofactor binding pocket; inhibition site 295405002049 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405002050 catalytic residue [active] 295405002051 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405002052 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 295405002053 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 295405002054 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 295405002055 Probable Catalytic site; other site 295405002056 metal-binding site 295405002057 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405002058 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 295405002059 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 295405002060 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405002061 Bacterial sugar transferase; Region: Bac_transf; pfam02397 295405002062 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 295405002063 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 295405002064 putative trimer interface [polypeptide binding]; other site 295405002065 putative CoA binding site [chemical binding]; other site 295405002066 Phosphopantetheine attachment site; Region: PP-binding; cl09936 295405002067 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 295405002068 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 295405002069 dimer interface [polypeptide binding]; other site 295405002070 active site 295405002071 CoA binding pocket [chemical binding]; other site 295405002072 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 295405002073 classical (c) SDRs; Region: SDR_c; cd05233 295405002074 NAD(P) binding site [chemical binding]; other site 295405002075 active site 295405002076 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 295405002077 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 295405002078 dimer interface [polypeptide binding]; other site 295405002079 active site 295405002080 CoA binding pocket [chemical binding]; other site 295405002081 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 295405002082 dimer interface [polypeptide binding]; other site 295405002083 substrate binding site [chemical binding]; other site 295405002084 metal binding site [ion binding]; metal-binding site 295405002085 FkbH-like domain; Region: FkbH; TIGR01686 295405002086 Acid Phosphatase; Region: Acid_PPase; cl17256 295405002087 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 295405002088 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 295405002089 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 295405002090 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 295405002091 inhibitor-cofactor binding pocket; inhibition site 295405002092 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405002093 catalytic residue [active] 295405002094 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 295405002095 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 295405002096 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 295405002097 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 295405002098 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 295405002099 active site 295405002100 catalytic tetrad [active] 295405002101 Probable beta-xylosidase; Provisional; Region: PLN03080 295405002102 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 295405002103 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 295405002104 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405002105 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405002106 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405002107 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405002108 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405002109 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405002110 SusD family; Region: SusD; pfam07980 295405002111 Glycosyl hydrolase family 67 N-terminus; Region: Glyco_hydro_67N; pfam03648 295405002112 Carbohydrate Binding Module 6 (CBM6); many are appended to glycoside hydrolase (GH) family 11 and GH43 xylanase domains; Region: CBM6_xylanase-like; cd04084 295405002113 metal binding site [ion binding]; metal-binding site 295405002114 ligand binding site [chemical binding]; other site 295405002115 Glycosyl hydrolase family 26; Region: Glyco_hydro_26; pfam02156 295405002116 Endo-beta-mannanase [Carbohydrate transport and metabolism]; Region: COG3934 295405002117 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 295405002118 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 295405002119 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 295405002120 The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases; Region: URO-D_CIMS_like; cl00464 295405002121 Predicted cobalamin binding protein [General function prediction only]; Region: COG5012 295405002122 B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or...; Region: corrinoid_protein_B12-BD; cd02070 295405002123 B12 binding site [chemical binding]; other site 295405002124 cobalt ligand [ion binding]; other site 295405002125 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 295405002126 The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four...; Region: URO-D_like; cd03465 295405002127 Glycosyl hydrolase family 26; Region: Glyco_hydro_26; pfam02156 295405002128 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 295405002129 active site 295405002130 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 295405002131 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 295405002132 putative substrate translocation pore; other site 295405002133 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 295405002134 putative active cleft [active] 295405002135 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 295405002136 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 295405002137 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 295405002138 homotrimer interaction site [polypeptide binding]; other site 295405002139 putative active site [active] 295405002140 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405002141 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405002142 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 295405002143 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 295405002144 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 295405002145 GAF domain; Region: GAF; pfam01590 295405002146 PAS fold; Region: PAS_3; pfam08447 295405002147 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405002148 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 295405002149 dimer interface [polypeptide binding]; other site 295405002150 phosphorylation site [posttranslational modification] 295405002151 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 295405002152 ATP binding site [chemical binding]; other site 295405002153 Mg2+ binding site [ion binding]; other site 295405002154 G-X-G motif; other site 295405002155 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 295405002156 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 295405002157 NADH:ubiquinone oxidoreductase subunit 4 (chain M) [Energy production and conversion]; Region: NuoM; COG1008 295405002158 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 295405002159 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 295405002160 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 295405002161 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 295405002162 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 295405002163 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 295405002164 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 295405002165 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 295405002166 4Fe-4S binding domain; Region: Fer4; cl02805 295405002167 4Fe-4S binding domain; Region: Fer4; pfam00037 295405002168 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 295405002169 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; pfam00329 295405002170 NADH dehydrogenase subunit D; Validated; Region: PRK06075 295405002171 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 295405002172 NADH dehydrogenase subunit B; Provisional; Region: PRK14816 295405002173 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 295405002174 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 295405002175 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 295405002176 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 295405002177 TrkA-N domain; Region: TrkA_N; pfam02254 295405002178 TrkA-C domain; Region: TrkA_C; pfam02080 295405002179 TrkA-N domain; Region: TrkA_N; pfam02254 295405002180 TrkA-C domain; Region: TrkA_C; pfam02080 295405002181 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 295405002182 1-deoxy-D-xylulose-5-phosphate synthase; Region: DXP_synthase_N; pfam13292 295405002183 TPP-binding site [chemical binding]; other site 295405002184 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 295405002185 PYR/PP interface [polypeptide binding]; other site 295405002186 dimer interface [polypeptide binding]; other site 295405002187 TPP binding site [chemical binding]; other site 295405002188 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 295405002189 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 295405002190 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 295405002191 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 295405002192 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 295405002193 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 295405002194 motif II; other site 295405002195 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405002196 Sulfatase; Region: Sulfatase; pfam00884 295405002197 probable galactinol--sucrose galactosyltransferase 1; Region: PLN02355 295405002198 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 295405002199 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 295405002200 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405002201 Sulfatase; Region: Sulfatase; cl17466 295405002202 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405002203 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405002204 SusD family; Region: SusD; pfam07980 295405002205 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405002206 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405002207 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405002208 Two component regulator propeller; Region: Reg_prop; pfam07494 295405002209 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 295405002210 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 295405002211 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405002212 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 295405002213 dimer interface [polypeptide binding]; other site 295405002214 phosphorylation site [posttranslational modification] 295405002215 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 295405002216 ATP binding site [chemical binding]; other site 295405002217 Mg2+ binding site [ion binding]; other site 295405002218 G-X-G motif; other site 295405002219 Response regulator receiver domain; Region: Response_reg; pfam00072 295405002220 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 295405002221 active site 295405002222 phosphorylation site [posttranslational modification] 295405002223 intermolecular recognition site; other site 295405002224 dimerization interface [polypeptide binding]; other site 295405002225 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405002226 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405002227 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 295405002228 Major Facilitator Superfamily; Region: MFS_1; pfam07690 295405002229 putative substrate translocation pore; other site 295405002230 Alpha-L-fucosidase; Region: Alpha_L_fucos; smart00812 295405002231 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 295405002232 Peptide-N-glycosidase F, N terminal; Region: N-glycanase_N; pfam09112 295405002233 Peptide-N-glycosidase F, C terminal; Region: N-glycanase_C; pfam09113 295405002234 Part of AAA domain; Region: AAA_19; pfam13245 295405002235 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 295405002236 AAA domain; Region: AAA_12; pfam13087 295405002237 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 295405002238 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 295405002239 Sec-independent protein secretion pathway components [Intracellular trafficking and secretion]; Region: TatA; COG1826 295405002240 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional; Region: PRK11930 295405002241 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 295405002242 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 295405002243 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 295405002244 active site 295405002245 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 295405002246 dimer interface [polypeptide binding]; other site 295405002247 substrate binding site [chemical binding]; other site 295405002248 catalytic residues [active] 295405002249 GSCFA family; Region: GSCFA; pfam08885 295405002250 Penicillinase repressor; Region: Pencillinase_R; pfam03965 295405002251 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 295405002252 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405002253 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405002254 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405002255 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 295405002256 Histidine kinase; Region: HisKA_3; pfam07730 295405002257 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 295405002258 ATP binding site [chemical binding]; other site 295405002259 Mg2+ binding site [ion binding]; other site 295405002260 G-X-G motif; other site 295405002261 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 295405002262 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 295405002263 Plasmid pRiA4b ORF-3-like protein; Region: PRiA4_ORF3; pfam07929 295405002264 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 295405002265 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 295405002266 active site 295405002267 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed; Region: PRK13188 295405002268 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 295405002269 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 295405002270 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 295405002271 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 295405002272 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 295405002273 trimer interface [polypeptide binding]; other site 295405002274 active site 295405002275 UDP-GlcNAc binding site [chemical binding]; other site 295405002276 lipid binding site [chemical binding]; lipid-binding site 295405002277 HD superfamily phosphohydrolases [General function prediction only]; Region: COG1078 295405002278 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 295405002279 Zn2+ binding site [ion binding]; other site 295405002280 Mg2+ binding site [ion binding]; other site 295405002281 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 295405002282 active site 295405002283 dimer interface [polypeptide binding]; other site 295405002284 peptide chain release factor 1; Validated; Region: prfA; PRK00591 295405002285 This domain is found in peptide chain release factors; Region: PCRF; smart00937 295405002286 RF-1 domain; Region: RF-1; pfam00472 295405002287 phosphoribosylaminoimidazole synthetase; Region: purM; TIGR00878 295405002288 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 295405002289 dimerization interface [polypeptide binding]; other site 295405002290 ATP binding site [chemical binding]; other site 295405002291 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 295405002292 Repair protein; Region: Repair_PSII; pfam04536 295405002293 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 295405002294 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 295405002295 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 295405002296 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 295405002297 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 295405002298 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 295405002299 shikimate binding site; other site 295405002300 NAD(P) binding site [chemical binding]; other site 295405002301 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 295405002302 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 295405002303 S-adenosylmethionine binding site [chemical binding]; other site 295405002304 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 295405002305 ATP binding site [chemical binding]; other site 295405002306 active site 295405002307 substrate binding site [chemical binding]; other site 295405002308 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 295405002309 PhoH-like protein; Region: PhoH; pfam02562 295405002310 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 295405002311 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 295405002312 Right handed beta helix region; Region: Beta_helix; pfam13229 295405002313 Uncharacterized proteins similar to Bacteroides ovatus 4320; Region: Bacova_04320_like; cd12190 295405002314 Flavin Reductases; Region: FlaRed; cl00801 295405002315 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 295405002316 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 295405002317 dimerization interface 3.5A [polypeptide binding]; other site 295405002318 active site 295405002319 EamA-like transporter family; Region: EamA; cl17759 295405002320 EamA-like transporter family; Region: EamA; pfam00892 295405002321 Protein of unknown function (DUF3256); Region: DUF3256; pfam11644 295405002322 Phosphotransferase enzyme family; Region: APH; pfam01636 295405002323 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 295405002324 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405002325 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405002326 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405002327 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 295405002328 Uncharacterized conserved protein [Function unknown]; Region: COG1284 295405002329 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 295405002330 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 295405002331 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 295405002332 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 295405002333 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 295405002334 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405002335 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405002336 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 295405002337 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 295405002338 TPR motif; other site 295405002339 binding surface 295405002340 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 295405002341 binding surface 295405002342 TPR motif; other site 295405002343 TPR repeat; Region: TPR_11; pfam13414 295405002344 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 295405002345 binding surface 295405002346 TPR motif; other site 295405002347 D-xylose transporter XylE; Provisional; Region: xylE; PRK10077 295405002348 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 295405002349 putative substrate translocation pore; other site 295405002350 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 295405002351 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 295405002352 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 295405002353 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 295405002354 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405002355 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405002356 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 295405002357 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 295405002358 domain in bacterial beta-glucosidases other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins; Region: PA14; smart00758 295405002359 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 295405002360 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 295405002361 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 295405002362 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405002363 SusD family; Region: SusD; pfam07980 295405002364 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405002365 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405002366 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405002367 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405002368 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405002369 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405002370 SusD family; Region: SusD; pfam07980 295405002371 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405002372 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405002373 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405002374 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405002375 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405002376 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405002377 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405002378 SusD family; Region: SusD; pfam07980 295405002379 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405002380 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405002381 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405002382 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405002383 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405002384 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405002385 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 295405002386 DNA binding residues [nucleotide binding] 295405002387 FecR protein; Region: FecR; pfam04773 295405002388 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405002389 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405002390 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405002391 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405002392 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405002393 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405002394 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405002395 SusD family; Region: SusD; pfam07980 295405002396 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 295405002397 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 295405002398 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 295405002399 TPR motif; other site 295405002400 recombination protein F; Reviewed; Region: recF; PRK00064 295405002401 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405002402 Walker A/P-loop; other site 295405002403 ATP binding site [chemical binding]; other site 295405002404 Q-loop/lid; other site 295405002405 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405002406 ABC transporter signature motif; other site 295405002407 Walker B; other site 295405002408 D-loop; other site 295405002409 H-loop/switch region; other site 295405002410 Protein of unknown function (DUF721); Region: DUF721; pfam05258 295405002411 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; Region: PHP_HisPPase_Hisj_like; cd12110 295405002412 histidinol phosphate phosphatase, HisJ family; Region: hisJ_fam; TIGR01856 295405002413 active site 295405002414 dimer interface [polypeptide binding]; other site 295405002415 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 295405002416 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 295405002417 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 295405002418 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 295405002419 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 295405002420 protein binding site [polypeptide binding]; other site 295405002421 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 295405002422 Catalytic dyad [active] 295405002423 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 295405002424 catalytic motif [active] 295405002425 Zn binding site [ion binding]; other site 295405002426 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 295405002427 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 295405002428 active site 295405002429 Zn binding site [ion binding]; other site 295405002430 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 295405002431 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 295405002432 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 295405002433 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 295405002434 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 295405002435 GMP synthase; Reviewed; Region: guaA; PRK00074 295405002436 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 295405002437 AMP/PPi binding site [chemical binding]; other site 295405002438 candidate oxyanion hole; other site 295405002439 catalytic triad [active] 295405002440 potential glutamine specificity residues [chemical binding]; other site 295405002441 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 295405002442 ATP Binding subdomain [chemical binding]; other site 295405002443 Ligand Binding sites [chemical binding]; other site 295405002444 Dimerization subdomain; other site 295405002445 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405002446 SusD family; Region: SusD; pfam07980 295405002447 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405002448 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405002449 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405002450 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405002451 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 295405002452 Enoyl-(Acyl carrier protein) reductase; Region: adh_short_C2; pfam13561 295405002453 NAD binding site [chemical binding]; other site 295405002454 homotetramer interface [polypeptide binding]; other site 295405002455 homodimer interface [polypeptide binding]; other site 295405002456 substrate binding site [chemical binding]; other site 295405002457 active site 295405002458 gliding motility-associated lipoprotein GldB; Region: GldB_lipo; TIGR03514 295405002459 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 295405002460 putative SAM binding site [chemical binding]; other site 295405002461 homodimer interface [polypeptide binding]; other site 295405002462 lipoyl synthase; Provisional; Region: PRK05481 295405002463 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 295405002464 FeS/SAM binding site; other site 295405002465 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 295405002466 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 295405002467 Cell wall-active antibiotics response protein (DUF2154); Region: DUF2154; pfam09922 295405002468 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 295405002469 LytTr DNA-binding domain; Region: LytTR; smart00850 295405002470 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 295405002471 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 295405002472 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 295405002473 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 295405002474 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 295405002475 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 295405002476 active site 295405002477 trimer interface [polypeptide binding]; other site 295405002478 allosteric site; other site 295405002479 active site lid [active] 295405002480 hexamer (dimer of trimers) interface [polypeptide binding]; other site 295405002481 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 295405002482 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 295405002483 Family of unknown function (DUF490); Region: DUF490; pfam04357 295405002484 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 295405002485 PIF1-like helicase; Region: PIF1; pfam05970 295405002486 AAA domain; Region: AAA_30; pfam13604 295405002487 Family description; Region: UvrD_C_2; pfam13538 295405002488 TPR repeat; Region: TPR_11; pfam13414 295405002489 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 295405002490 binding surface 295405002491 TPR motif; other site 295405002492 TPR repeat; Region: TPR_11; pfam13414 295405002493 TPR repeat; Region: TPR_11; pfam13414 295405002494 Predicted hydrolases of the HAD superfamily [General function prediction only]; Region: Cof; COG0561 295405002495 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 295405002496 active site 295405002497 motif I; other site 295405002498 motif II; other site 295405002499 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 295405002500 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 295405002501 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 295405002502 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405002503 homodimer interface [polypeptide binding]; other site 295405002504 catalytic residue [active] 295405002505 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 295405002506 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 295405002507 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 295405002508 catalytic residue [active] 295405002509 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 295405002510 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405002511 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 295405002512 FecR protein; Region: FecR; pfam04773 295405002513 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405002514 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405002515 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 295405002516 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 295405002517 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 295405002518 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 295405002519 Rhomboid family; Region: Rhomboid; cl11446 295405002520 Glycogen debranching enzyme N terminal; Region: GDE_N; pfam12439 295405002521 glycogen debranching enzyme, archaeal type, putative; Region: gde_arch; TIGR01561 295405002522 Amylo-alpha-1,6-glucosidase; Region: GDE_C; pfam06202 295405002523 glycogen synthase, Corynebacterium family; Region: glgA_Coryne; TIGR02149 295405002524 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 295405002525 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 295405002526 Glycosyl hydrolase family 57; Region: Glyco_hydro_57; pfam03065 295405002527 putative active site [active] 295405002528 catalytic site [active] 295405002529 Domain of unknown function (DUF4270); Region: DUF4270; pfam14092 295405002530 Starch synthase catalytic domain; Region: Glyco_transf_5; pfam08323 295405002531 Pantoate-beta-alanine ligase; Region: PanC; cd00560 295405002532 pantoate--beta-alanine ligase; Region: panC; TIGR00018 295405002533 active site 295405002534 ATP-binding site [chemical binding]; other site 295405002535 pantoate-binding site; other site 295405002536 HXXH motif; other site 295405002537 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 295405002538 tetramerization interface [polypeptide binding]; other site 295405002539 active site 295405002540 putative bifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta; Provisional; Region: PRK12778 295405002541 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 295405002542 FAD binding pocket [chemical binding]; other site 295405002543 FAD binding motif [chemical binding]; other site 295405002544 phosphate binding motif [ion binding]; other site 295405002545 beta-alpha-beta structure motif; other site 295405002546 NAD binding pocket [chemical binding]; other site 295405002547 Iron coordination center [ion binding]; other site 295405002548 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 295405002549 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 295405002550 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 295405002551 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 295405002552 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 295405002553 putative substrate translocation pore; other site 295405002554 seryl-tRNA synthetase; Provisional; Region: PRK05431 295405002555 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 295405002556 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 295405002557 dimer interface [polypeptide binding]; other site 295405002558 active site 295405002559 motif 1; other site 295405002560 motif 2; other site 295405002561 motif 3; other site 295405002562 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 295405002563 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 295405002564 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 295405002565 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 295405002566 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 295405002567 motif II; other site 295405002568 NlpC/P60 family; Region: NLPC_P60; pfam00877 295405002569 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 295405002570 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 295405002571 Walker A/P-loop; other site 295405002572 ATP binding site [chemical binding]; other site 295405002573 Q-loop/lid; other site 295405002574 ABC transporter signature motif; other site 295405002575 Walker B; other site 295405002576 D-loop; other site 295405002577 H-loop/switch region; other site 295405002578 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 295405002579 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 295405002580 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 295405002581 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 295405002582 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 295405002583 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 295405002584 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 295405002585 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 295405002586 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 295405002587 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 295405002588 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 295405002589 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 295405002590 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405002591 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 295405002592 Walker A/P-loop; other site 295405002593 ATP binding site [chemical binding]; other site 295405002594 Q-loop/lid; other site 295405002595 ABC transporter signature motif; other site 295405002596 Walker B; other site 295405002597 D-loop; other site 295405002598 H-loop/switch region; other site 295405002599 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 295405002600 RNA methyltransferase, RsmE family; Region: TIGR00046 295405002601 Bifunctional nuclease; Region: DNase-RNase; pfam02577 295405002602 UvrB/uvrC motif; Region: UVR; pfam02151 295405002603 nucleoside transporter; Region: 2A0110; TIGR00889 295405002604 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; cl17904 295405002605 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 295405002606 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; cl17722 295405002607 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 295405002608 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 295405002609 putative RNA binding site [nucleotide binding]; other site 295405002610 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 295405002611 S-adenosylmethionine binding site [chemical binding]; other site 295405002612 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 295405002613 catalytic site [active] 295405002614 putative active site [active] 295405002615 putative substrate binding site [chemical binding]; other site 295405002616 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 295405002617 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 295405002618 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 295405002619 This domain directs oriented DNA translocation and forms a winged helix structure; Region: Ftsk_gamma; smart00843 295405002620 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 295405002621 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 295405002622 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 295405002623 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 295405002624 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 295405002625 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 295405002626 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 295405002627 active site 295405002628 Fn3 associated; Region: Fn3_assoc; pfam13287 295405002629 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 295405002630 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 295405002631 ligand binding site [chemical binding]; other site 295405002632 flexible hinge region; other site 295405002633 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 295405002634 putative switch regulator; other site 295405002635 non-specific DNA interactions [nucleotide binding]; other site 295405002636 DNA binding site [nucleotide binding] 295405002637 sequence specific DNA binding site [nucleotide binding]; other site 295405002638 putative cAMP binding site [chemical binding]; other site 295405002639 Uncharacterized protein related to glutamine synthetase [General function prediction only]; Region: COG3968 295405002640 Glutamine synthetase type III N terminal; Region: GSIII_N; pfam12437 295405002641 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 295405002642 RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_II; cd03487 295405002643 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 295405002644 putative active site [active] 295405002645 putative NTP binding site [chemical binding]; other site 295405002646 putative nucleic acid binding site [nucleotide binding]; other site 295405002647 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 295405002648 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 295405002649 RNA binding site [nucleotide binding]; other site 295405002650 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 295405002651 RNA binding site [nucleotide binding]; other site 295405002652 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 295405002653 RNA binding site [nucleotide binding]; other site 295405002654 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 295405002655 RNA binding site [nucleotide binding]; other site 295405002656 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 295405002657 RNA binding site [nucleotide binding]; other site 295405002658 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 295405002659 RNA binding site [nucleotide binding]; other site 295405002660 ribonuclease Z; Region: RNase_Z; TIGR02651 295405002661 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 295405002662 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405002663 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 295405002664 DNA binding residues [nucleotide binding] 295405002665 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 295405002666 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 295405002667 homodimer interface [polypeptide binding]; other site 295405002668 metal binding site [ion binding]; metal-binding site 295405002669 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 295405002670 homodimer interface [polypeptide binding]; other site 295405002671 active site 295405002672 putative chemical substrate binding site [chemical binding]; other site 295405002673 metal binding site [ion binding]; metal-binding site 295405002674 Protein of unknown function (DUF3810); Region: DUF3810; pfam12725 295405002675 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 295405002676 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 295405002677 HIGH motif; other site 295405002678 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 295405002679 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 295405002680 active site 295405002681 KMSKS motif; other site 295405002682 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 295405002683 tRNA binding surface [nucleotide binding]; other site 295405002684 anticodon binding site; other site 295405002685 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 295405002686 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405002687 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 295405002688 dimer interface [polypeptide binding]; other site 295405002689 phosphorylation site [posttranslational modification] 295405002690 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 295405002691 ATP binding site [chemical binding]; other site 295405002692 Mg2+ binding site [ion binding]; other site 295405002693 G-X-G motif; other site 295405002694 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 295405002695 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405002696 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 295405002697 DNA binding residues [nucleotide binding] 295405002698 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405002699 FecR protein; Region: FecR; pfam04773 295405002700 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405002701 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405002702 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405002703 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405002704 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 295405002705 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 295405002706 Starch-binding associating with outer membrane; Region: SusD-like_2; pfam12771 295405002707 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405002708 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 295405002709 putative catalytic site [active] 295405002710 putative metal binding site [ion binding]; other site 295405002711 putative phosphate binding site [ion binding]; other site 295405002712 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 295405002713 putative catalytic site [active] 295405002714 putative phosphate binding site [ion binding]; other site 295405002715 putative metal binding site [ion binding]; other site 295405002716 Bacillus subtilis YvnB and related proteins, metallophosphatase domain; Region: MPP_YvnB; cd07399 295405002717 putative active site [active] 295405002718 putative metal binding site [ion binding]; other site 295405002719 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 295405002720 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405002721 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405002722 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 295405002723 DNA binding residues [nucleotide binding] 295405002724 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405002725 FecR protein; Region: FecR; pfam04773 295405002726 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405002727 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405002728 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405002729 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405002730 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405002731 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405002732 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405002733 Sulfatase; Region: Sulfatase; cl17466 295405002734 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405002735 Sulfatase; Region: Sulfatase; pfam00884 295405002736 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK12901 295405002737 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 295405002738 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 295405002739 nucleotide binding region [chemical binding]; other site 295405002740 ATP-binding site [chemical binding]; other site 295405002741 SEC-C motif; Region: SEC-C; pfam02810 295405002742 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 295405002743 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 295405002744 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 295405002745 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 295405002746 Domain of unknown function DUF21; Region: DUF21; pfam01595 295405002747 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 295405002748 Transporter associated domain; Region: CorC_HlyC; smart01091 295405002749 SurA N-terminal domain; Region: SurA_N_2; pfam13623 295405002750 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 295405002751 PPIC-type PPIASE domain; Region: Rotamase_3; pfam13616 295405002752 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14466 295405002753 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 295405002754 FeS/SAM binding site; other site 295405002755 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 295405002756 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 295405002757 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 295405002758 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 295405002759 Walker A motif; other site 295405002760 ATP binding site [chemical binding]; other site 295405002761 Walker B motif; other site 295405002762 arginine finger; other site 295405002763 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 295405002764 Lipopolysaccharide-assembly; Region: LptE; pfam04390 295405002765 Preprotein translocase SecG subunit; Region: SecG; pfam03840 295405002766 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 295405002767 Major Facilitator Superfamily; Region: MFS_1; pfam07690 295405002768 putative substrate translocation pore; other site 295405002769 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 295405002770 putative carbohydrate kinase; Provisional; Region: PRK10565 295405002771 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 295405002772 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 295405002773 putative substrate binding site [chemical binding]; other site 295405002774 putative ATP binding site [chemical binding]; other site 295405002775 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 295405002776 S-adenosylmethionine binding site [chemical binding]; other site 295405002777 N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; Region: NGN; cl02766 295405002778 KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); Region: KOW; cl00354 295405002779 UpxZ family of transcription anti-terminator antagonists; Region: UpxZ; pfam06603 295405002780 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 295405002781 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 295405002782 substrate binding site; other site 295405002783 tetramer interface; other site 295405002784 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 295405002785 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 295405002786 O-antigen polysaccharide polymerase Wzy; Region: O-ag_pol_Wzy; pfam14296 295405002787 UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional; Region: wecC; PRK11064 295405002788 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 295405002789 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 295405002790 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 295405002791 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 295405002792 active site 295405002793 homodimer interface [polypeptide binding]; other site 295405002794 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405002795 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 295405002796 WxcM-like, C-terminal; Region: FdtA; pfam05523 295405002797 WxcM-like, C-terminal; Region: FdtA; pfam05523 295405002798 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 295405002799 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 295405002800 inhibitor-cofactor binding pocket; inhibition site 295405002801 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405002802 catalytic residue [active] 295405002803 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 295405002804 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 295405002805 NAD(P) binding site [chemical binding]; other site 295405002806 homodimer interface [polypeptide binding]; other site 295405002807 substrate binding site [chemical binding]; other site 295405002808 active site 295405002809 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 295405002810 capsular polysaccharide assembling protein (CAPF) like, extended (e) SDRs; Region: CAPF_like_SDR_e; cd05261 295405002811 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 295405002812 putative NAD(P) binding site [chemical binding]; other site 295405002813 active site 295405002814 putative substrate binding site [chemical binding]; other site 295405002815 dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfbC; COG1898 295405002816 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 295405002817 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 295405002818 active site 295405002819 homodimer interface [polypeptide binding]; other site 295405002820 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405002821 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 295405002822 Bacterial sugar transferase; Region: Bac_transf; pfam02397 295405002823 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 295405002824 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 295405002825 putative trimer interface [polypeptide binding]; other site 295405002826 putative CoA binding site [chemical binding]; other site 295405002827 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 295405002828 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 295405002829 inhibitor-cofactor binding pocket; inhibition site 295405002830 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405002831 catalytic residue [active] 295405002832 Predicted AAA-ATPase; Region: AAA-ATPase_like; pfam09820 295405002833 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 295405002834 Poxvirus serine/threonine protein kinase; Region: Pox_ser-thr_kin; cl17825 295405002835 Bacterial proteins similar to Porphyromonas gingivalis HmuY; Region: HmuY; cd12105 295405002836 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 295405002837 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 295405002838 N-terminal plug; other site 295405002839 ligand-binding site [chemical binding]; other site 295405002840 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 295405002841 active site 295405002842 adenylate kinase; Reviewed; Region: adk; PRK00279 295405002843 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 295405002844 AMP-binding site [chemical binding]; other site 295405002845 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 295405002846 GTPase CgtA; Reviewed; Region: obgE; PRK12298 295405002847 GTP1/OBG; Region: GTP1_OBG; pfam01018 295405002848 Obg GTPase; Region: Obg; cd01898 295405002849 G1 box; other site 295405002850 GTP/Mg2+ binding site [chemical binding]; other site 295405002851 Switch I region; other site 295405002852 G2 box; other site 295405002853 G3 box; other site 295405002854 Switch II region; other site 295405002855 G4 box; other site 295405002856 G5 box; other site 295405002857 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 295405002858 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 295405002859 B3/4 domain; Region: B3_4; smart00873 295405002860 B3/4 domain; Region: B3_4; pfam03483 295405002861 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 295405002862 Peptidase family M23; Region: Peptidase_M23; pfam01551 295405002863 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 295405002864 Lactonase, 7-bladed beta-propeller; Region: Lactonase; pfam10282 295405002865 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 295405002866 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 295405002867 Response regulator receiver domain; Region: Response_reg; pfam00072 295405002868 active site 295405002869 phosphorylation site [posttranslational modification] 295405002870 intermolecular recognition site; other site 295405002871 dimerization interface [polypeptide binding]; other site 295405002872 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405002873 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405002874 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 295405002875 active site 295405002876 DNA polymerase IV; Validated; Region: PRK02406 295405002877 DNA binding site [nucleotide binding] 295405002878 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 295405002879 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 295405002880 Bacterial Ig-like domain (group 1); Region: Big_1; cl17740 295405002881 Transglutaminase-like superfamily; Region: Transglut_core; cl17362 295405002882 Predicted membrane protein [Function unknown]; Region: COG1288 295405002883 Na+-transporting oxaloacetate decarboxylase beta subunit; Region: OAD_beta; cl00816 295405002884 Peptidase MA superfamily; Region: Peptidase_MA_2; pfam13485 295405002885 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 295405002886 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 295405002887 Coenzyme A binding pocket [chemical binding]; other site 295405002888 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 295405002889 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 295405002890 Coenzyme A binding pocket [chemical binding]; other site 295405002891 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 295405002892 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 295405002893 active site 295405002894 Restriction endonuclease [Defense mechanisms]; Region: COG3587 295405002895 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 295405002896 ATP binding site [chemical binding]; other site 295405002897 putative Mg++ binding site [ion binding]; other site 295405002898 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 295405002899 DNA methylase; Region: N6_N4_Mtase; pfam01555 295405002900 DNA methylase; Region: N6_N4_Mtase; cl17433 295405002901 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 295405002902 Galactose mutarotase-like; Region: Gal_mutarotas_2; pfam13802 295405002903 CPE1046 is an uncharacterized Clostridium perfringens protein with a glycosyl hydrolase family 31 (GH31) domain. The domain architecture of CPE1046 and its orthologs includes a C-terminal fibronectin type 3 (FN3) domain and a coagulation factor 5/8 type...; Region: GH31_CPE1046; cd06596 295405002904 putative active site [active] 295405002905 putative catalytic site [active] 295405002906 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 295405002907 Interdomain contacts; other site 295405002908 Cytokine receptor motif; other site 295405002909 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405002910 Domains similar to the eukaryotic reeler domain and bacterial cohesins; Region: Reeler_cohesin_like; cl14606 295405002911 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405002912 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 295405002913 NAD(P) binding site [chemical binding]; other site 295405002914 active site 295405002915 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 295405002916 non-specific DNA binding site [nucleotide binding]; other site 295405002917 salt bridge; other site 295405002918 sequence-specific DNA binding site [nucleotide binding]; other site 295405002919 HipA N-terminal domain; Region: Couple_hipA; cl11853 295405002920 HipA-like N-terminal domain; Region: HipA_N; pfam07805 295405002921 HipA-like C-terminal domain; Region: HipA_C; pfam07804 295405002922 Competence protein CoiA-like family; Region: CoiA; cl11541 295405002923 AAA ATPase domain; Region: AAA_15; pfam13175 295405002924 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 295405002925 putative active site [active] 295405002926 putative metal-binding site [ion binding]; other site 295405002927 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 295405002928 AAA-like domain; Region: AAA_10; pfam12846 295405002929 DNA sulfur modification protein DndD; Region: DNA_S_dndD; TIGR03185 295405002930 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405002931 Walker A/P-loop; other site 295405002932 ATP binding site [chemical binding]; other site 295405002933 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 295405002934 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 295405002935 Virulence protein [General function prediction only]; Region: COG3943 295405002936 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 295405002937 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 295405002938 DNA methylase; Region: N6_N4_Mtase; pfam01555 295405002939 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 295405002940 non-specific DNA binding site [nucleotide binding]; other site 295405002941 salt bridge; other site 295405002942 sequence-specific DNA binding site [nucleotide binding]; other site 295405002943 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 295405002944 AAA domain; Region: AAA_25; pfam13481 295405002945 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405002946 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 295405002947 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 295405002948 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 295405002949 Int/Topo IB signature motif; other site 295405002950 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405002951 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 295405002952 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 295405002953 trmE is a tRNA modification GTPase; Region: trmE; cd04164 295405002954 G1 box; other site 295405002955 GTP/Mg2+ binding site [chemical binding]; other site 295405002956 Switch I region; other site 295405002957 G2 box; other site 295405002958 Switch II region; other site 295405002959 G3 box; other site 295405002960 G4 box; other site 295405002961 G5 box; other site 295405002962 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 295405002963 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405002964 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 295405002965 dimer interface [polypeptide binding]; other site 295405002966 phosphorylation site [posttranslational modification] 295405002967 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 295405002968 ATP binding site [chemical binding]; other site 295405002969 Mg2+ binding site [ion binding]; other site 295405002970 G-X-G motif; other site 295405002971 Response regulator receiver domain; Region: Response_reg; pfam00072 295405002972 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 295405002973 active site 295405002974 phosphorylation site [posttranslational modification] 295405002975 intermolecular recognition site; other site 295405002976 dimerization interface [polypeptide binding]; other site 295405002977 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 295405002978 NADH(P)-binding; Region: NAD_binding_10; pfam13460 295405002979 NAD binding site [chemical binding]; other site 295405002980 substrate binding site [chemical binding]; other site 295405002981 putative active site [active] 295405002982 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 295405002983 active site 295405002984 catalytic site [active] 295405002985 substrate binding site [chemical binding]; other site 295405002986 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 295405002987 Phosphorylase superfamily; Region: PNP_UDP_1; pfam01048 295405002988 hypothetical protein; Provisional; Region: PRK13665 295405002989 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 295405002990 binding surface 295405002991 Tetratricopeptide repeat; Region: TPR_16; pfam13432 295405002992 TPR motif; other site 295405002993 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 295405002994 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 295405002995 Ligand Binding Site [chemical binding]; other site 295405002996 TIGR00269 family protein; Region: TIGR00269 295405002997 Protein of unknown function, DUF486; Region: DUF486; cl01236 295405002998 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 295405002999 ApbE family; Region: ApbE; pfam02424 295405003000 Predicted membrane protein [Function unknown]; Region: COG1971 295405003001 Domain of unknown function DUF; Region: DUF204; pfam02659 295405003002 Domain of unknown function DUF; Region: DUF204; pfam02659 295405003003 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 295405003004 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 295405003005 Ligand binding site; other site 295405003006 Putative Catalytic site; other site 295405003007 DXD motif; other site 295405003008 Protein of unknown function (DUF4199); Region: DUF4199; pfam13858 295405003009 enolase; Provisional; Region: eno; PRK00077 295405003010 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 295405003011 dimer interface [polypeptide binding]; other site 295405003012 metal binding site [ion binding]; metal-binding site 295405003013 substrate binding pocket [chemical binding]; other site 295405003014 Pentapeptide repeats (9 copies); Region: Pentapeptide_3; pfam13576 295405003015 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 295405003016 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 295405003017 camphor resistance protein CrcB; Provisional; Region: PRK14210 295405003018 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 295405003019 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 295405003020 non-specific DNA binding site [nucleotide binding]; other site 295405003021 salt bridge; other site 295405003022 sequence-specific DNA binding site [nucleotide binding]; other site 295405003023 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 295405003024 RNA binding surface [nucleotide binding]; other site 295405003025 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 295405003026 putative active site [active] 295405003027 catalytic residue [active] 295405003028 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 295405003029 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 295405003030 5S rRNA interface [nucleotide binding]; other site 295405003031 CTC domain interface [polypeptide binding]; other site 295405003032 L16 interface [polypeptide binding]; other site 295405003033 Protein of unknown function (DUF3276); Region: DUF3276; pfam11680 295405003034 transcription antitermination factor NusB; Region: nusB; TIGR01951 295405003035 Preprotein translocase subunit; Region: YajC; pfam02699 295405003036 YbbR-like protein; Region: YbbR; pfam07949 295405003037 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 295405003038 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 295405003039 CoA-binding site [chemical binding]; other site 295405003040 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 295405003041 Clp amino terminal domain; Region: Clp_N; pfam02861 295405003042 Clp amino terminal domain; Region: Clp_N; pfam02861 295405003043 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 295405003044 Walker A motif; other site 295405003045 ATP binding site [chemical binding]; other site 295405003046 Walker B motif; other site 295405003047 arginine finger; other site 295405003048 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 295405003049 Walker A motif; other site 295405003050 ATP binding site [chemical binding]; other site 295405003051 Walker B motif; other site 295405003052 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 295405003053 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 295405003054 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 295405003055 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 295405003056 putative dimerization interface [polypeptide binding]; other site 295405003057 Predicted membrane protein [Function unknown]; Region: COG2855 295405003058 Domain of unknown function (DUF4252); Region: DUF4252; pfam14060 295405003059 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 295405003060 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405003061 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 295405003062 DNA binding residues [nucleotide binding] 295405003063 recombinase A; Provisional; Region: recA; PRK09354 295405003064 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 295405003065 hexamer interface [polypeptide binding]; other site 295405003066 Walker A motif; other site 295405003067 ATP binding site [chemical binding]; other site 295405003068 Walker B motif; other site 295405003069 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 295405003070 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 295405003071 catalytic triad [active] 295405003072 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 295405003073 META domain; Region: META; pfam03724 295405003074 META domain; Region: META; pfam03724 295405003075 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 295405003076 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 295405003077 ABC-ATPase subunit interface; other site 295405003078 dimer interface [polypeptide binding]; other site 295405003079 putative PBP binding regions; other site 295405003080 Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_d; cd01141 295405003081 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 295405003082 putative ligand binding site [chemical binding]; other site 295405003083 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 295405003084 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 295405003085 SLBB domain; Region: SLBB; pfam10531 295405003086 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 295405003087 SLBB domain; Region: SLBB; pfam10531 295405003088 SLBB domain; Region: SLBB; pfam10531 295405003089 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 295405003090 SLBB domain; Region: SLBB; pfam10531 295405003091 N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; Region: NGN; cl02766 295405003092 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 295405003093 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 295405003094 nucleotide binding site [chemical binding]; other site 295405003095 NEF interaction site [polypeptide binding]; other site 295405003096 SBD interface [polypeptide binding]; other site 295405003097 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405003098 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405003099 Superfamily I DNA and RNA helicases [General function prediction only]; Region: COG3972 295405003100 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 295405003101 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 295405003102 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 295405003103 Int/Topo IB signature motif; other site 295405003104 Restriction endonuclease; Region: Mrr_cat; pfam04471 295405003105 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405003106 AAA domain; Region: AAA_25; pfam13481 295405003107 CHC2 zinc finger; Region: zf-CHC2; cl17510 295405003108 Toprim-like; Region: Toprim_2; pfam13155 295405003109 Plasmid recombination enzyme; Region: Mob_Pre; pfam01076 295405003110 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 295405003111 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 295405003112 S-adenosylmethionine binding site [chemical binding]; other site 295405003113 KilA-N domain; Region: KilA-N; pfam04383 295405003114 KilA-N domain; Region: KilA-N; pfam04383 295405003115 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 295405003116 ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-linked...; Region: EriC; cd01031 295405003117 Cl- selectivity filter; other site 295405003118 Cl- binding residues [ion binding]; other site 295405003119 pore gating glutamate residue; other site 295405003120 dimer interface [polypeptide binding]; other site 295405003121 H+/Cl- coupling transport residue; other site 295405003122 TrkA-C domain; Region: TrkA_C; pfam02080 295405003123 endonuclease IV; Provisional; Region: PRK01060 295405003124 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 295405003125 AP (apurinic/apyrimidinic) site pocket; other site 295405003126 DNA interaction; other site 295405003127 Metal-binding active site; metal-binding site 295405003128 tryptophan synthase subunit beta; Reviewed; Region: PRK12391 295405003129 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 295405003130 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 295405003131 catalytic residue [active] 295405003132 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 295405003133 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 295405003134 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 295405003135 TrkA-N domain; Region: TrkA_N; pfam02254 295405003136 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 295405003137 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 295405003138 tetramer interface [polypeptide binding]; other site 295405003139 heme binding pocket [chemical binding]; other site 295405003140 NADPH binding site [chemical binding]; other site 295405003141 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 295405003142 This family represents an uncharacterized glycosyl hydrolase family 31 (GH31) enzyme found in bacteria and eukaryotes that is related to the XylS xylosidase of Sulfolobus solfataricus. Alpha-xylosidases catalyze the release of an alpha-xylose residue...; Region: GH31_xylosidase_XylS-like; cd06595 295405003143 putative active site [active] 295405003144 putative catalytic site [active] 295405003145 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405003146 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405003147 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 295405003148 DNA binding residues [nucleotide binding] 295405003149 Glycosyl hydrolase family 43, includes mostly 1,4-beta-xylanases; Region: GH43_bXyl; cd09004 295405003150 putative substrate binding site [chemical binding]; other site 295405003151 active site 295405003152 beta-lactamase TEM; Provisional; Region: PRK15442 295405003153 Beta-lactamase enzyme family; Region: Beta-lactamase2; pfam13354 295405003154 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405003155 FecR protein; Region: FecR; pfam04773 295405003156 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405003157 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405003158 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405003159 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405003160 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 295405003161 Starch-binding associating with outer membrane; Region: SusD-like_2; pfam12771 295405003162 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405003163 Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain; Region: MPP_Dcr2; cd07383 295405003164 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 295405003165 putative active site [active] 295405003166 putative metal binding site [ion binding]; other site 295405003167 Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain; Region: MPP_Dcr2; cd07383 295405003168 Sulfatase; Region: Sulfatase; cl17466 295405003169 Phosphopentomutase [Carbohydrate transport and metabolism]; Region: DeoB; cl17415 295405003170 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 295405003171 putative catalytic site [active] 295405003172 putative metal binding site [ion binding]; other site 295405003173 putative phosphate binding site [ion binding]; other site 295405003174 alkyl hydroperoxide reductase subunit F; Region: AhpF; TIGR03140 295405003175 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 295405003176 catalytic residue [active] 295405003177 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 295405003178 catalytic residues [active] 295405003179 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 295405003180 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 295405003181 peroxiredoxin; Region: AhpC; TIGR03137 295405003182 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 295405003183 dimer interface [polypeptide binding]; other site 295405003184 decamer (pentamer of dimers) interface [polypeptide binding]; other site 295405003185 catalytic triad [active] 295405003186 peroxidatic and resolving cysteines [active] 295405003187 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405003188 RNA recognition motif (RRM) superfamily; Region: RRM_SF; cl17169 295405003189 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405003190 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405003191 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 295405003192 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 295405003193 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 295405003194 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 295405003195 Thermotoga maritima CorA_like subfamily; Region: TmCorA-like_1; cd12828 295405003196 oligomer interface [polypeptide binding]; other site 295405003197 metal binding site [ion binding]; metal-binding site 295405003198 metal binding site [ion binding]; metal-binding site 295405003199 Cl binding site [ion binding]; other site 295405003200 aspartate ring; other site 295405003201 basic sphincter; other site 295405003202 putative hydrophobic gate; other site 295405003203 periplasmic entrance; other site 295405003204 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 295405003205 MutS domain III; Region: MutS_III; pfam05192 295405003206 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405003207 Walker A/P-loop; other site 295405003208 ATP binding site [chemical binding]; other site 295405003209 Q-loop/lid; other site 295405003210 ABC transporter signature motif; other site 295405003211 Walker B; other site 295405003212 D-loop; other site 295405003213 H-loop/switch region; other site 295405003214 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 295405003215 Smr domain; Region: Smr; pfam01713 295405003216 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 295405003217 peptide modification radical SAM enzyme, YydG family; Region: rSAM_yydG; TIGR04078 295405003218 FeS/SAM binding site; other site 295405003219 Thiol-activated cytolysin; Region: Thiol_cytolysin; pfam01289 295405003220 Thiol-activated cytolysin; Region: Thiol_cytolysin; pfam01289 295405003221 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 295405003222 Plasmid recombination enzyme; Region: Mob_Pre; pfam01076 295405003223 CHC2 zinc finger; Region: zf-CHC2; cl17510 295405003224 Toprim-like; Region: Toprim_2; pfam13155 295405003225 active site 295405003226 metal binding site [ion binding]; metal-binding site 295405003227 AAA domain; Region: AAA_25; pfam13481 295405003228 Protein of unknown function (DUF3853); Region: DUF3853; pfam12964 295405003229 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 295405003230 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 295405003231 active site 295405003232 DNA binding site [nucleotide binding] 295405003233 Int/Topo IB signature motif; other site 295405003234 Predicted permeases [General function prediction only]; Region: RarD; COG2962 295405003235 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 295405003236 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 295405003237 ligand binding site [chemical binding]; other site 295405003238 Formaldehyde dehydrogenases; Region: FDH_like; cd05278 295405003239 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 295405003240 catalytic Zn binding site [ion binding]; other site 295405003241 NAD(P) binding site [chemical binding]; other site 295405003242 structural Zn binding site [ion binding]; other site 295405003243 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 295405003244 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 295405003245 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 295405003246 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405003247 catalytic residues [active] 295405003248 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405003249 Sulfatase; Region: Sulfatase; pfam00884 295405003250 Protein P3 of Potyviral polyprotein; Region: Potyvirid-P3; pfam13608 295405003251 PAS fold; Region: PAS_3; pfam08447 295405003252 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405003253 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 295405003254 dimer interface [polypeptide binding]; other site 295405003255 phosphorylation site [posttranslational modification] 295405003256 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 295405003257 ATP binding site [chemical binding]; other site 295405003258 Mg2+ binding site [ion binding]; other site 295405003259 G-X-G motif; other site 295405003260 Predicted membrane protein [Function unknown]; Region: COG2855 295405003261 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 295405003262 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 295405003263 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 295405003264 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 295405003265 metal binding site 2 [ion binding]; metal-binding site 295405003266 putative DNA binding helix; other site 295405003267 metal binding site 1 [ion binding]; metal-binding site 295405003268 dimer interface [polypeptide binding]; other site 295405003269 structural Zn2+ binding site [ion binding]; other site 295405003270 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 295405003271 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 295405003272 Homeobox associated leucine zipper; Region: HALZ; pfam02183 295405003273 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 295405003274 ligand binding site [chemical binding]; other site 295405003275 Uncharacterized conserved protein [Function unknown]; Region: COG3189 295405003276 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 295405003277 amidophosphoribosyltransferase; Region: purF; TIGR01134 295405003278 active site 295405003279 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 295405003280 active site 295405003281 peptidase T; Region: peptidase-T; TIGR01882 295405003282 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 295405003283 metal binding site [ion binding]; metal-binding site 295405003284 dimer interface [polypeptide binding]; other site 295405003285 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 295405003286 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 295405003287 membrane glycoprotein; Provisional; Region: PHA03332 295405003288 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 295405003289 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 295405003290 TrkA-C domain; Region: TrkA_C; pfam02080 295405003291 TrkA-C domain; Region: TrkA_C; pfam02080 295405003292 LysE type translocator; Region: LysE; cl00565 295405003293 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 295405003294 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 295405003295 NADP binding site [chemical binding]; other site 295405003296 active site 295405003297 putative substrate binding site [chemical binding]; other site 295405003298 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 295405003299 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 295405003300 G1 box; other site 295405003301 putative GEF interaction site [polypeptide binding]; other site 295405003302 GTP/Mg2+ binding site [chemical binding]; other site 295405003303 Switch I region; other site 295405003304 G2 box; other site 295405003305 G3 box; other site 295405003306 Switch II region; other site 295405003307 G4 box; other site 295405003308 G5 box; other site 295405003309 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 295405003310 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 295405003311 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 295405003312 active site 295405003313 motif I; other site 295405003314 motif II; other site 295405003315 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 295405003316 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 295405003317 CoenzymeA binding site [chemical binding]; other site 295405003318 subunit interaction site [polypeptide binding]; other site 295405003319 PHB binding site; other site 295405003320 chorismate binding enzyme; Region: Chorismate_bind; cl10555 295405003321 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylic-acid synthase; Region: menD; TIGR00173 295405003322 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 295405003323 dimer interface [polypeptide binding]; other site 295405003324 tetramer interface [polypeptide binding]; other site 295405003325 PYR/PP interface [polypeptide binding]; other site 295405003326 TPP binding site [chemical binding]; other site 295405003327 Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key...; Region: TPP_SHCHC_synthase; cd02009 295405003328 TPP-binding site; other site 295405003329 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 295405003330 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 295405003331 substrate binding site [chemical binding]; other site 295405003332 oxyanion hole (OAH) forming residues; other site 295405003333 trimer interface [polypeptide binding]; other site 295405003334 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 295405003335 O-succinylbenzoate synthase; Provisional; Region: PRK02714 295405003336 active site 295405003337 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 295405003338 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 295405003339 AMP binding site [chemical binding]; other site 295405003340 active site 295405003341 acyl-activating enzyme (AAE) consensus motif; other site 295405003342 CoA binding site [chemical binding]; other site 295405003343 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 295405003344 putative catalytic site [active] 295405003345 putative metal binding site [ion binding]; other site 295405003346 putative phosphate binding site [ion binding]; other site 295405003347 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 295405003348 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405003349 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405003350 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 295405003351 DNA binding residues [nucleotide binding] 295405003352 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405003353 FecR protein; Region: FecR; pfam04773 295405003354 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405003355 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405003356 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405003357 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405003358 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 295405003359 Starch-binding associating with outer membrane; Region: SusD-like_2; pfam12771 295405003360 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405003361 Endo-beta-N-acetylglucosaminidases are bacterial chitinases that hydrolyze the chitin core of various asparagine (N)-linked glycans and glycoproteins. The endo-beta-N-acetylglucosaminidases have a glycosyl hydrolase family 18 (GH18) catalytic domain; Region: GH18_EndoS-like; cd06542 295405003362 active site 295405003363 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 295405003364 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 295405003365 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 295405003366 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 295405003367 muropeptide transporter; Reviewed; Region: ampG; PRK11902 295405003368 muropeptide transporter; Validated; Region: ampG; cl17669 295405003369 Domain of unknown function (DUF377); Region: DUF377; pfam04041 295405003370 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 295405003371 active site 295405003372 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 295405003373 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 295405003374 dimerization interface [polypeptide binding]; other site 295405003375 DPS ferroxidase diiron center [ion binding]; other site 295405003376 ion pore; other site 295405003377 Transcriptional regulator [Transcription]; Region: LysR; COG0583 295405003378 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 295405003379 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 295405003380 dimerization interface [polypeptide binding]; other site 295405003381 NigD-like protein; Region: NigD; pfam12667 295405003382 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 295405003383 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405003384 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 295405003385 DNA binding residues [nucleotide binding] 295405003386 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 295405003387 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 295405003388 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 295405003389 FeS/SAM binding site; other site 295405003390 Pyruvate formate lyase 1; Region: PFL1; cd01678 295405003391 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 295405003392 coenzyme A binding site [chemical binding]; other site 295405003393 active site 295405003394 catalytic residues [active] 295405003395 glycine loop; other site 295405003396 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 295405003397 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 295405003398 Int/Topo IB signature motif; other site 295405003399 ORF6N domain; Region: ORF6N; pfam10543 295405003400 Antirestriction protein (ArdA); Region: ArdA; pfam07275 295405003401 Domain of unknown function, B. Theta Gene description (DUF3873); Region: DUF3873; pfam12989 295405003402 Domain of unknown function, B. Theta Gene description (DUF3872); Region: DUF3872; pfam12988 295405003403 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 295405003404 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 295405003405 cofactor binding site; other site 295405003406 DNA binding site [nucleotide binding] 295405003407 substrate interaction site [chemical binding]; other site 295405003408 Conjugative transposon protein TraO; Region: TraO; pfam10626 295405003409 Bacteroides conjugative transposon TraN protein; Region: Bac_Flav_CT_N; TIGR03780 295405003410 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 295405003411 Bacteroides conjugative transposon TraM protein; Region: Bac_Flav_CT_M; TIGR03779 295405003412 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 295405003413 Protein of unknown function (DUF3989); Region: DUF3989; pfam13150 295405003414 Bacteroides conjugative transposon TraK protein; Region: Bac_Flav_CT_K; TIGR03781 295405003415 Bacteroides conjugative transposon TraJ protein; Region: Bac_Flav_CT_J; TIGR03782 295405003416 Domain of unknown function (DUF4141); Region: DUF4141; pfam13605 295405003417 Bacteroides conjugation system ATPase, TraG family; Region: Bac_Flav_CT_G; TIGR03783 295405003418 Domain of unknown function, B. Theta Gene description (DUF3875); Region: DUF3875; pfam12991 295405003419 Domain of unknown function (DUF4133); Region: DUF4133; pfam13571 295405003420 Domain of unknown function (DUF4134); Region: DUF4134; pfam13572 295405003421 Protein involved in mRNA turnover and stability [RNA processing and modification]; Region: SSM4; COG5183 295405003422 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 295405003423 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 295405003424 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 295405003425 P-loop; other site 295405003426 Magnesium ion binding site [ion binding]; other site 295405003427 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 295405003428 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 295405003429 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 295405003430 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 295405003431 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 295405003432 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 295405003433 YWFCY protein; Region: YWFCY; pfam14293 295405003434 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 295405003435 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 295405003436 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 295405003437 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 295405003438 Protein of unknown function (DUF4099); Region: DUF4099; pfam13351 295405003439 Protein of unknown function (DUF3945); Region: DUF3945; pfam13101 295405003440 DNA topoisomerase III; Provisional; Region: PRK07726 295405003441 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 295405003442 active site 295405003443 putative interdomain interaction site [polypeptide binding]; other site 295405003444 putative metal-binding site [ion binding]; other site 295405003445 putative nucleotide binding site [chemical binding]; other site 295405003446 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 295405003447 domain I; other site 295405003448 DNA binding groove [nucleotide binding] 295405003449 phosphate binding site [ion binding]; other site 295405003450 domain II; other site 295405003451 domain III; other site 295405003452 nucleotide binding site [chemical binding]; other site 295405003453 catalytic site [active] 295405003454 domain IV; other site 295405003455 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 295405003456 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 295405003457 RibD C-terminal domain; Region: RibD_C; cl17279 295405003458 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 295405003459 active site 295405003460 metal binding site [ion binding]; metal-binding site 295405003461 interdomain interaction site; other site 295405003462 AAA domain; Region: AAA_25; pfam13481 295405003463 Helix-turn-helix domain; Region: HTH_17; cl17695 295405003464 RteC protein; Region: RteC; pfam09357 295405003465 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405003466 GAD-like domain; Region: GAD-like; pfam08887 295405003467 Domain of unknown function (DUF1851); Region: DUF1851; pfam08906 295405003468 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 295405003469 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 295405003470 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 295405003471 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 295405003472 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 295405003473 active site 295405003474 DNA binding site [nucleotide binding] 295405003475 Int/Topo IB signature motif; other site 295405003476 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 295405003477 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 295405003478 MG2 domain; Region: A2M_N; pfam01835 295405003479 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 295405003480 Domain of unknown function (DUF1200); Region: DUF1200; pfam06713 295405003481 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 295405003482 KIAA1161 is an uncharacterized Homo sapiens protein with a glycosyl hydrolase family 31 (GH31) domain that is homologous to the Escherichia coli YihQ glucosidase. Orthologs of KIA1161 are found in eukaryotes and prokaryotes. In bacteria, YihQ (along with...; Region: GH31_glucosidase_KIAA1161; cd06592 295405003483 putative active site [active] 295405003484 putative catalytic site [active] 295405003485 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 295405003486 Domain of unknown function DUF21; Region: DUF21; pfam01595 295405003487 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 295405003488 Transporter associated domain; Region: CorC_HlyC; smart01091 295405003489 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 295405003490 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405003491 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405003492 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 295405003493 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 295405003494 Predicted esterase [General function prediction only]; Region: COG0627 295405003495 S-formylglutathione hydrolase; Region: PLN02442 295405003496 Uncharacterized protein conserved in Bacteroidetes; Region: Bacuni_01323_like; cd12871 295405003497 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 295405003498 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 295405003499 homodimer interface [polypeptide binding]; other site 295405003500 substrate-cofactor binding pocket; other site 295405003501 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405003502 catalytic residue [active] 295405003503 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 295405003504 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 295405003505 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 295405003506 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 295405003507 DNA binding residues [nucleotide binding] 295405003508 dimerization interface [polypeptide binding]; other site 295405003509 Domain of unknown function (DUF4251); Region: DUF4251; pfam14059 295405003510 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 295405003511 Ferritin-CCC1, N-terminal ferritin-like diiron-binding domain; Region: Ferritin_CCC1_N; cd01044 295405003512 diiron binding motif [ion binding]; other site 295405003513 CCC1-related domain of ferritin; Region: Ferritin_CCC1_C; cd02431 295405003514 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 295405003515 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 295405003516 putative substrate translocation pore; other site 295405003517 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 295405003518 Transglycosylase; Region: Transgly; pfam00912 295405003519 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 295405003520 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 295405003521 MG2 domain; Region: A2M_N; pfam01835 295405003522 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 295405003523 Alpha-2-macroglobulin family; Region: A2M; pfam00207 295405003524 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 295405003525 surface patch; other site 295405003526 thioester region; other site 295405003527 specificity defining residues; other site 295405003528 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 295405003529 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 295405003530 Ligand Binding Site [chemical binding]; other site 295405003531 TilS substrate C-terminal domain; Region: TilS_C; smart00977 295405003532 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 295405003533 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 295405003534 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 295405003535 G1 box; other site 295405003536 GTP/Mg2+ binding site [chemical binding]; other site 295405003537 Switch I region; other site 295405003538 G2 box; other site 295405003539 G3 box; other site 295405003540 Switch II region; other site 295405003541 G4 box; other site 295405003542 G5 box; other site 295405003543 Nucleoside recognition; Region: Gate; pfam07670 295405003544 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 295405003545 Nucleoside recognition; Region: Gate; pfam07670 295405003546 Fic family protein [Function unknown]; Region: COG3177 295405003547 Fic/DOC family; Region: Fic; pfam02661 295405003548 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 295405003549 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 295405003550 UpxZ family of transcription anti-terminator antagonists; Region: UpxZ; pfam06603 295405003551 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 295405003552 NAD(P) binding site [chemical binding]; other site 295405003553 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405003554 homodimer interface [polypeptide binding]; other site 295405003555 substrate binding site [chemical binding]; other site 295405003556 active site 295405003557 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 295405003558 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 295405003559 inhibitor-cofactor binding pocket; inhibition site 295405003560 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405003561 catalytic residue [active] 295405003562 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 295405003563 acyl-activating enzyme (AAE) consensus motif; other site 295405003564 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 295405003565 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 295405003566 AMP binding site [chemical binding]; other site 295405003567 active site 295405003568 acyl-activating enzyme (AAE) consensus motif; other site 295405003569 CoA binding site [chemical binding]; other site 295405003570 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 295405003571 classical (c) SDRs; Region: SDR_c; cd05233 295405003572 NAD(P) binding site [chemical binding]; other site 295405003573 active site 295405003574 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 295405003575 putative trimer interface [polypeptide binding]; other site 295405003576 putative CoA binding site [chemical binding]; other site 295405003577 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently...; Region: CBS_pair_NTP_transferase_assoc; cd04607 295405003578 FOG: CBS domain [General function prediction only]; Region: COG0517 295405003579 NTP_trnasferase_like_2 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_2; cd06426 295405003580 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 295405003581 Substrate binding site; other site 295405003582 metal-binding site 295405003583 Glycosyl transferase 4-like domain; Region: Glyco_trans_4_4; cl17183 295405003584 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405003585 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 295405003586 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 295405003587 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 295405003588 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 295405003589 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 295405003590 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 295405003591 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 295405003592 active site 295405003593 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 295405003594 active site 295405003595 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 295405003596 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 295405003597 inhibitor-cofactor binding pocket; inhibition site 295405003598 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405003599 catalytic residue [active] 295405003600 Bacterial sugar transferase; Region: Bac_transf; pfam02397 295405003601 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 295405003602 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405003603 catalytic residues [active] 295405003604 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 295405003605 transmembrane helices; other site 295405003606 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 295405003607 TrkA-C domain; Region: TrkA_C; pfam02080 295405003608 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 295405003609 TrkA-C domain; Region: TrkA_C; pfam02080 295405003610 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 295405003611 Methyltransferase domain; Region: Methyltransf_31; pfam13847 295405003612 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 295405003613 S-adenosylmethionine binding site [chemical binding]; other site 295405003614 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 295405003615 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 295405003616 dimer interface [polypeptide binding]; other site 295405003617 active site 295405003618 metal binding site [ion binding]; metal-binding site 295405003619 glutathione binding site [chemical binding]; other site 295405003620 Uncharacterized proteins similar to Bacteroides ovatus 4320; Region: Bacova_04320_like; cd12190 295405003621 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 295405003622 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 295405003623 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 295405003624 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 295405003625 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 295405003626 Pirin-related protein [General function prediction only]; Region: COG1741 295405003627 Pirin; Region: Pirin; pfam02678 295405003628 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405003629 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405003630 Chagasin family peptidase inhibitor I42; Region: Inhibitor_I42; pfam09394 295405003631 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 295405003632 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; Region: LDH_like_2; cd12183 295405003633 putative ligand binding site [chemical binding]; other site 295405003634 putative NAD binding site [chemical binding]; other site 295405003635 catalytic site [active] 295405003636 Porin subfamily; Region: Porin_2; pfam02530 295405003637 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 295405003638 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405003639 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 295405003640 DNA binding residues [nucleotide binding] 295405003641 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 295405003642 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 295405003643 Ligand Binding Site [chemical binding]; other site 295405003644 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 295405003645 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 295405003646 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 295405003647 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 295405003648 dimerization interface [polypeptide binding]; other site 295405003649 active site 295405003650 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 295405003651 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405003652 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 295405003653 DNA binding residues [nucleotide binding] 295405003654 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 295405003655 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 295405003656 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 295405003657 FMN binding site [chemical binding]; other site 295405003658 substrate binding site [chemical binding]; other site 295405003659 putative catalytic residue [active] 295405003660 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 295405003661 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 295405003662 hexamer interface [polypeptide binding]; other site 295405003663 ligand binding site [chemical binding]; other site 295405003664 putative active site [active] 295405003665 NAD(P) binding site [chemical binding]; other site 295405003666 Peptidase family M23; Region: Peptidase_M23; pfam01551 295405003667 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 295405003668 Peptidase family C69; Region: Peptidase_C69; cl17793 295405003669 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 295405003670 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 295405003671 active site 295405003672 substrate binding site [chemical binding]; other site 295405003673 metal binding site [ion binding]; metal-binding site 295405003674 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405003675 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405003676 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 295405003677 DNA binding residues [nucleotide binding] 295405003678 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405003679 FecR protein; Region: FecR; pfam04773 295405003680 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405003681 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405003682 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405003683 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405003684 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405003685 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405003686 SusD family; Region: SusD; pfam07980 295405003687 He_PIG associated, NEW1 domain of bacterial glycohydrolase; Region: He_PIG_assoc; pfam10632 295405003688 Putative Ig domain; Region: He_PIG; pfam05345 295405003689 alpha-galactosidase; Region: PLN02808; cl17638 295405003690 Histidine carboxylase PI chain; Region: HDC; pfam02329 295405003691 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 295405003692 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 295405003693 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 295405003694 putative NADH binding site [chemical binding]; other site 295405003695 putative active site [active] 295405003696 nudix motif; other site 295405003697 putative metal binding site [ion binding]; other site 295405003698 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 295405003699 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405003700 Walker A/P-loop; other site 295405003701 ATP binding site [chemical binding]; other site 295405003702 Q-loop/lid; other site 295405003703 ABC transporter signature motif; other site 295405003704 Walker B; other site 295405003705 D-loop; other site 295405003706 H-loop/switch region; other site 295405003707 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 295405003708 pyridine nucleotide-disulfide oxidoreductase; Provisional; Region: PRK08010 295405003709 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 295405003710 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 295405003711 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 295405003712 Predicted membrane protein [Function unknown]; Region: COG3059 295405003713 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405003714 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405003715 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 295405003716 active site 295405003717 catalytic motif [active] 295405003718 Zn binding site [ion binding]; other site 295405003719 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 295405003720 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 295405003721 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 295405003722 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405003723 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405003724 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405003725 FtsX-like permease family; Region: FtsX; pfam02687 295405003726 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405003727 FtsX-like permease family; Region: FtsX; pfam02687 295405003728 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405003729 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 295405003730 FtsX-like permease family; Region: FtsX; pfam02687 295405003731 FtsX-like permease family; Region: FtsX; pfam02687 295405003732 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405003733 FtsX-like permease family; Region: FtsX; pfam02687 295405003734 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 295405003735 FtsX-like permease family; Region: FtsX; pfam02687 295405003736 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405003737 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405003738 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 295405003739 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 295405003740 Walker A/P-loop; other site 295405003741 ATP binding site [chemical binding]; other site 295405003742 Q-loop/lid; other site 295405003743 ABC transporter signature motif; other site 295405003744 Walker B; other site 295405003745 D-loop; other site 295405003746 H-loop/switch region; other site 295405003747 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405003748 FtsX-like permease family; Region: FtsX; pfam02687 295405003749 FtsX-like permease family; Region: FtsX; pfam02687 295405003750 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 295405003751 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 295405003752 Walker A/P-loop; other site 295405003753 ATP binding site [chemical binding]; other site 295405003754 Q-loop/lid; other site 295405003755 ABC transporter signature motif; other site 295405003756 Walker B; other site 295405003757 D-loop; other site 295405003758 H-loop/switch region; other site 295405003759 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 295405003760 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405003761 FtsX-like permease family; Region: FtsX; pfam02687 295405003762 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 295405003763 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 295405003764 PAS domain; Region: PAS; smart00091 295405003765 PAS domain; Region: PAS_9; pfam13426 295405003766 PAS fold; Region: PAS_3; pfam08447 295405003767 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405003768 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 295405003769 dimer interface [polypeptide binding]; other site 295405003770 phosphorylation site [posttranslational modification] 295405003771 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 295405003772 ATP binding site [chemical binding]; other site 295405003773 Mg2+ binding site [ion binding]; other site 295405003774 G-X-G motif; other site 295405003775 Outer membrane efflux protein; Region: OEP; pfam02321 295405003776 Outer membrane efflux protein; Region: OEP; pfam02321 295405003777 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 295405003778 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 295405003779 active site 295405003780 phosphorylation site [posttranslational modification] 295405003781 intermolecular recognition site; other site 295405003782 dimerization interface [polypeptide binding]; other site 295405003783 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 295405003784 Walker A motif; other site 295405003785 ATP binding site [chemical binding]; other site 295405003786 Walker B motif; other site 295405003787 arginine finger; other site 295405003788 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 295405003789 HAMP domain; Region: HAMP; pfam00672 295405003790 dimerization interface [polypeptide binding]; other site 295405003791 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 295405003792 PAS domain; Region: PAS; smart00091 295405003793 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 295405003794 ATP binding site [chemical binding]; other site 295405003795 Mg2+ binding site [ion binding]; other site 295405003796 G-X-G motif; other site 295405003797 aspartate 4-decarboxylase; Region: asp_4_decarbox; TIGR03801 295405003798 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 295405003799 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405003800 homodimer interface [polypeptide binding]; other site 295405003801 catalytic residue [active] 295405003802 aspartate-alanine antiporter; Region: Asp_Ala_antiprt; TIGR03802 295405003803 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 295405003804 TrkA-C domain; Region: TrkA_C; pfam02080 295405003805 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 295405003806 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 295405003807 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 295405003808 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 295405003809 Domain of unknown function (DUF4373); Region: DUF4373; pfam14297 295405003810 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 295405003811 UpxZ family of transcription anti-terminator antagonists; Region: UpxZ; pfam06603 295405003812 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 295405003813 4Fe-4S binding domain; Region: Fer4_6; pfam12837 295405003814 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus; Region: FrhB_FdhB_C; pfam04432 295405003815 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 295405003816 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 295405003817 trimer interface [polypeptide binding]; other site 295405003818 active site 295405003819 substrate binding site [chemical binding]; other site 295405003820 CoA binding site [chemical binding]; other site 295405003821 Predicted enzyme involved in methoxymalonyl-ACP biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FkbH; COG3882 295405003822 HAD-superfamily phosphatase, subfamily IIIC; Region: HAD-SF-IIIC; TIGR01681 295405003823 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 295405003824 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 295405003825 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 295405003826 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 295405003827 substrate binding site; other site 295405003828 WxcM-like, C-terminal; Region: FdtA; pfam05523 295405003829 CDP-glucose 4,6-dehydratase; Region: CDP_4_6_dhtase; TIGR02622 295405003830 CDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: CDP_GD_SDR_e; cd05252 295405003831 NAD binding site [chemical binding]; other site 295405003832 homotetramer interface [polypeptide binding]; other site 295405003833 homodimer interface [polypeptide binding]; other site 295405003834 substrate binding site [chemical binding]; other site 295405003835 active site 295405003836 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405003837 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405003838 active site 295405003839 Protein of unknown function (DUF563); Region: DUF563; pfam04577 295405003840 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 295405003841 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 295405003842 active site 295405003843 catalytic tetrad [active] 295405003844 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 295405003845 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 295405003846 active site 295405003847 O-Antigen ligase; Region: Wzy_C; cl04850 295405003848 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 295405003849 metal-binding site 295405003850 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405003851 This family is most closely related to the GT1 family of glycosyltransferases and is named after WbdM in Escherichia coli. In general glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor...; Region: GT1_WbdM_like; cd04951 295405003852 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405003853 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 295405003854 putative ADP-binding pocket [chemical binding]; other site 295405003855 CotH protein; Region: CotH; pfam08757 295405003856 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405003857 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405003858 NAD(P) binding site [chemical binding]; other site 295405003859 active site 295405003860 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 295405003861 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 295405003862 Mg++ binding site [ion binding]; other site 295405003863 putative catalytic motif [active] 295405003864 putative substrate binding site [chemical binding]; other site 295405003865 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 295405003866 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 295405003867 homodimer interface [polypeptide binding]; other site 295405003868 oligonucleotide binding site [chemical binding]; other site 295405003869 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 295405003870 IHF - DNA interface [nucleotide binding]; other site 295405003871 IHF dimer interface [polypeptide binding]; other site 295405003872 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 295405003873 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 295405003874 minor groove reading motif; other site 295405003875 helix-hairpin-helix signature motif; other site 295405003876 substrate binding pocket [chemical binding]; other site 295405003877 active site 295405003878 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 295405003879 DNA binding and oxoG recognition site [nucleotide binding] 295405003880 Sulfatase; Region: Sulfatase; cl17466 295405003881 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405003882 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 295405003883 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 295405003884 dimer interface [polypeptide binding]; other site 295405003885 ssDNA binding site [nucleotide binding]; other site 295405003886 tetramer (dimer of dimers) interface [polypeptide binding]; other site 295405003887 Domain of unknown function DUF21; Region: DUF21; pfam01595 295405003888 magnesium/cobalt efflux protein CorC; Provisional; Region: PRK15094 295405003889 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 295405003890 Transporter associated domain; Region: CorC_HlyC; smart01091 295405003891 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 295405003892 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 295405003893 Alpha-2-macroglobulin family; Region: A2M; pfam00207 295405003894 Protein of unknown function (DUF1271); Region: DUF1271; pfam06902 295405003895 Predicted acetyltransferase [General function prediction only]; Region: COG2388 295405003896 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405003897 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; cl01930 295405003898 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405003899 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405003900 MAC/Perforin domain; Region: MACPF; cl02616 295405003901 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 295405003902 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 295405003903 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 295405003904 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405003905 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 295405003906 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 295405003907 dimer interface [polypeptide binding]; other site 295405003908 phosphorylation site [posttranslational modification] 295405003909 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 295405003910 ATP binding site [chemical binding]; other site 295405003911 Mg2+ binding site [ion binding]; other site 295405003912 G-X-G motif; other site 295405003913 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 295405003914 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 295405003915 active site 295405003916 phosphorylation site [posttranslational modification] 295405003917 intermolecular recognition site; other site 295405003918 dimerization interface [polypeptide binding]; other site 295405003919 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 295405003920 DNA binding site [nucleotide binding] 295405003921 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 295405003922 Domain of unknown function (DUF3805); Region: DUF3805; pfam12712 295405003923 Domain of unknown function (DUF3806); Region: DUF3806; pfam12713 295405003924 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 295405003925 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405003926 Walker A/P-loop; other site 295405003927 ATP binding site [chemical binding]; other site 295405003928 ABC transporter signature motif; other site 295405003929 Walker B; other site 295405003930 D-loop; other site 295405003931 H-loop/switch region; other site 295405003932 ABC transporter; Region: ABC_tran_2; pfam12848 295405003933 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 295405003934 histidinol-phosphatase; Provisional; Region: PRK07328 295405003935 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like; Region: PHP_HisPPase_Hisj_like; cd12110 295405003936 active site 295405003937 dimer interface [polypeptide binding]; other site 295405003938 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 295405003939 active site 295405003940 catalytic residues [active] 295405003941 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; cd01083 295405003942 substrate binding site [chemical binding]; other site 295405003943 catalytic residues [active] 295405003944 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 295405003945 substrate binding site [chemical binding]; other site 295405003946 trimer interface [polypeptide binding]; other site 295405003947 hexamer (dimer of trimers) interface [polypeptide binding]; other site 295405003948 Mn binding site [ion binding]; other site 295405003949 aspartate aminotransferase; Provisional; Region: PRK07568 295405003950 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 295405003951 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405003952 homodimer interface [polypeptide binding]; other site 295405003953 catalytic residue [active] 295405003954 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 295405003955 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405003956 FtsX-like permease family; Region: FtsX; pfam02687 295405003957 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 295405003958 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_e; cd04192 295405003959 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 295405003960 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 295405003961 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 295405003962 dimer interface [polypeptide binding]; other site 295405003963 phosphorylation site [posttranslational modification] 295405003964 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 295405003965 ATP binding site [chemical binding]; other site 295405003966 Mg2+ binding site [ion binding]; other site 295405003967 G-X-G motif; other site 295405003968 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 295405003969 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 295405003970 active site 295405003971 phosphorylation site [posttranslational modification] 295405003972 intermolecular recognition site; other site 295405003973 dimerization interface [polypeptide binding]; other site 295405003974 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 295405003975 Walker A motif; other site 295405003976 ATP binding site [chemical binding]; other site 295405003977 Walker B motif; other site 295405003978 arginine finger; other site 295405003979 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 295405003980 Outer membrane efflux protein; Region: OEP; pfam02321 295405003981 Outer membrane efflux protein; Region: OEP; pfam02321 295405003982 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405003983 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405003984 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405003985 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405003986 Acidobacterial duplicated orphan permease; Region: ADOP; TIGR03434 295405003987 FtsX-like permease family; Region: FtsX; pfam02687 295405003988 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405003989 FtsX-like permease family; Region: FtsX; pfam02687 295405003990 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 295405003991 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 295405003992 Walker A/P-loop; other site 295405003993 ATP binding site [chemical binding]; other site 295405003994 Q-loop/lid; other site 295405003995 ABC transporter signature motif; other site 295405003996 Walker B; other site 295405003997 D-loop; other site 295405003998 H-loop/switch region; other site 295405003999 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405004000 FtsX-like permease family; Region: FtsX; pfam02687 295405004001 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405004002 FtsX-like permease family; Region: FtsX; pfam02687 295405004003 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 295405004004 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 295405004005 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 295405004006 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 295405004007 AAA domain; Region: AAA_26; pfam13500 295405004008 Protein of unknown function (DUF452); Region: DUF452; cl01062 295405004009 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 295405004010 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 295405004011 S-adenosylmethionine binding site [chemical binding]; other site 295405004012 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 295405004013 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 295405004014 substrate-cofactor binding pocket; other site 295405004015 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405004016 catalytic residue [active] 295405004017 biotin synthase; Region: bioB; TIGR00433 295405004018 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 295405004019 FeS/SAM binding site; other site 295405004020 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 295405004021 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 295405004022 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06173 295405004023 inhibitor-cofactor binding pocket; inhibition site 295405004024 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405004025 catalytic residue [active] 295405004026 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405004027 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004028 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405004029 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 295405004030 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405004031 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 295405004032 L-lactate permease; Region: Lactate_perm; cl00701 295405004033 Domain of unknown function, B. Theta Gene description (DUF3868); Region: DUF3868; pfam12984 295405004034 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 295405004035 ligand binding site [chemical binding]; other site 295405004036 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 295405004037 binding surface 295405004038 TPR motif; other site 295405004039 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 295405004040 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 295405004041 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 295405004042 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 295405004043 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 295405004044 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 295405004045 ATP-grasp domain; Region: ATP-grasp_4; cl17255 295405004046 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 295405004047 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 295405004048 carboxyltransferase (CT) interaction site; other site 295405004049 biotinylation site [posttranslational modification]; other site 295405004050 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 295405004051 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 295405004052 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_A; cd01299 295405004053 active site 295405004054 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion]; Region: Lpd; COG1249 295405004055 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 295405004056 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 295405004057 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 295405004058 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 295405004059 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 295405004060 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 295405004061 E3 interaction surface; other site 295405004062 lipoyl attachment site [posttranslational modification]; other site 295405004063 e3 binding domain; Region: E3_binding; pfam02817 295405004064 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 295405004065 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_x; TIGR03181 295405004066 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 295405004067 tetramer interface [polypeptide binding]; other site 295405004068 TPP-binding site [chemical binding]; other site 295405004069 heterodimer interface [polypeptide binding]; other site 295405004070 phosphorylation loop region [posttranslational modification] 295405004071 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 295405004072 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 295405004073 PYR/PP interface [polypeptide binding]; other site 295405004074 dimer interface [polypeptide binding]; other site 295405004075 TPP binding site [chemical binding]; other site 295405004076 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 295405004077 flavodoxin FldA; Validated; Region: PRK09267 295405004078 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 295405004079 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 295405004080 S-adenosylmethionine binding site [chemical binding]; other site 295405004081 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405004082 Peptidase C10 family; Region: Peptidase_C10; pfam01640 295405004083 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 295405004084 MAC/Perforin domain; Region: MACPF; pfam01823 295405004085 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 295405004086 nucleoside/Zn binding site; other site 295405004087 dimer interface [polypeptide binding]; other site 295405004088 catalytic motif [active] 295405004089 Domain of unknown function (DUF4252); Region: DUF4252; pfam14060 295405004090 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405004091 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 295405004092 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 295405004093 DNA binding residues [nucleotide binding] 295405004094 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 295405004095 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 295405004096 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 295405004097 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 295405004098 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 295405004099 substrate binding pocket [chemical binding]; other site 295405004100 membrane-bound complex binding site; other site 295405004101 hinge residues; other site 295405004102 Domain of unknown function (DUF4289); Region: DUF4289; pfam14121 295405004103 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 295405004104 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; pfam01558 295405004105 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit [Energy production and conversion]; Region: PorB; COG1013 295405004106 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 295405004107 TPP-binding site [chemical binding]; other site 295405004108 2-ketoisovalerate ferredoxin reductase; Validated; Region: PRK07119 295405004109 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 295405004110 dimer interface [polypeptide binding]; other site 295405004111 PYR/PP interface [polypeptide binding]; other site 295405004112 TPP binding site [chemical binding]; other site 295405004113 substrate binding site [chemical binding]; other site 295405004114 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 295405004115 Ferredoxin [Energy production and conversion]; Region: COG1146 295405004116 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 295405004117 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 295405004118 TPR motif; other site 295405004119 binding surface 295405004120 Tetratricopeptide repeat; Region: TPR_16; pfam13432 295405004121 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 295405004122 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 295405004123 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 295405004124 TPP-binding site [chemical binding]; other site 295405004125 dimer interface [polypeptide binding]; other site 295405004126 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 295405004127 PYR/PP interface [polypeptide binding]; other site 295405004128 dimer interface [polypeptide binding]; other site 295405004129 TPP binding site [chemical binding]; other site 295405004130 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 295405004131 Galactokinase [Carbohydrate transport and metabolism]; Region: GalK; COG0153 295405004132 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 295405004133 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 295405004134 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 295405004135 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 295405004136 putative substrate translocation pore; other site 295405004137 glucose/galactose transporter; Region: gluP; TIGR01272 295405004138 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 295405004139 active site 295405004140 catalytic residues [active] 295405004141 Phosphomannose isomerase [Carbohydrate transport and metabolism]; Region: ManA; COG1482 295405004142 Alpha-Mannosidase Binding Domain of Atg19/34; Region: ABD; cl15429 295405004143 ligand binding site [chemical binding]; other site 295405004144 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 295405004145 DEAD-like helicases superfamily; Region: DEXDc; smart00487 295405004146 ATP binding site [chemical binding]; other site 295405004147 Mg++ binding site [ion binding]; other site 295405004148 motif III; other site 295405004149 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 295405004150 nucleotide binding region [chemical binding]; other site 295405004151 ATP-binding site [chemical binding]; other site 295405004152 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 295405004153 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 295405004154 putative NAD(P) binding site [chemical binding]; other site 295405004155 homodimer interface [polypeptide binding]; other site 295405004156 homotetramer interface [polypeptide binding]; other site 295405004157 active site 295405004158 Sporulation related domain; Region: SPOR; cl10051 295405004159 Methyltransferase domain; Region: Methyltransf_31; pfam13847 295405004160 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 295405004161 S-adenosylmethionine binding site [chemical binding]; other site 295405004162 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405004163 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405004164 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405004165 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 295405004166 active site 295405004167 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 295405004168 transmembrane helices; other site 295405004169 TrkA-C domain; Region: TrkA_C; pfam02080 295405004170 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 295405004171 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 295405004172 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form...; Region: APSK; cd02027 295405004173 ligand-binding site [chemical binding]; other site 295405004174 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 295405004175 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 295405004176 Active Sites [active] 295405004177 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 295405004178 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 295405004179 CysD dimerization site [polypeptide binding]; other site 295405004180 G1 box; other site 295405004181 putative GEF interaction site [polypeptide binding]; other site 295405004182 GTP/Mg2+ binding site [chemical binding]; other site 295405004183 Switch I region; other site 295405004184 G2 box; other site 295405004185 G3 box; other site 295405004186 Switch II region; other site 295405004187 G4 box; other site 295405004188 G5 box; other site 295405004189 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 295405004190 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 295405004191 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 295405004192 Cupin domain; Region: Cupin_2; cl17218 295405004193 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 295405004194 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 295405004195 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 295405004196 ligand binding site [chemical binding]; other site 295405004197 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 295405004198 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004199 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 295405004200 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 295405004201 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 295405004202 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 295405004203 active site 295405004204 DNA binding site [nucleotide binding] 295405004205 Int/Topo IB signature motif; other site 295405004206 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 295405004207 Domain of unknown function (DUF3869); Region: DUF3869; pfam12985 295405004208 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 295405004209 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 295405004210 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 295405004211 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 295405004212 ligand binding site [chemical binding]; other site 295405004213 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 295405004214 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 295405004215 active site 295405004216 catalytic residues [active] 295405004217 metal binding site [ion binding]; metal-binding site 295405004218 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 295405004219 TPR motif; other site 295405004220 binding surface 295405004221 TPR repeat; Region: TPR_11; pfam13414 295405004222 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 295405004223 binding surface 295405004224 TPR repeat; Region: TPR_11; pfam13414 295405004225 TPR motif; other site 295405004226 TPR repeat; Region: TPR_11; pfam13414 295405004227 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 295405004228 binding surface 295405004229 TPR motif; other site 295405004230 TPR repeat; Region: TPR_11; pfam13414 295405004231 TPR repeat; Region: TPR_11; pfam13414 295405004232 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 295405004233 binding surface 295405004234 TPR motif; other site 295405004235 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 295405004236 TPR motif; other site 295405004237 TPR repeat; Region: TPR_11; pfam13414 295405004238 binding surface 295405004239 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 295405004240 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 295405004241 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 295405004242 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 295405004243 active site 295405004244 dimer interface [polypeptide binding]; other site 295405004245 motif 1; other site 295405004246 motif 2; other site 295405004247 motif 3; other site 295405004248 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 295405004249 anticodon binding site; other site 295405004250 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 295405004251 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 295405004252 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 295405004253 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 295405004254 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 295405004255 23S rRNA binding site [nucleotide binding]; other site 295405004256 L21 binding site [polypeptide binding]; other site 295405004257 L13 binding site [polypeptide binding]; other site 295405004258 Flavodoxin domain; Region: Flavodoxin_5; cl17428 295405004259 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 295405004260 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 295405004261 active site 295405004262 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 295405004263 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 295405004264 acyl-activating enzyme (AAE) consensus motif; other site 295405004265 AMP binding site [chemical binding]; other site 295405004266 active site 295405004267 CoA binding site [chemical binding]; other site 295405004268 indolepyruvate oxidoreductase subunit beta; Reviewed; Region: PRK06853 295405004269 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 295405004270 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 295405004271 dimer interface [polypeptide binding]; other site 295405004272 PYR/PP interface [polypeptide binding]; other site 295405004273 TPP binding site [chemical binding]; other site 295405004274 substrate binding site [chemical binding]; other site 295405004275 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 295405004276 TPP-binding site; other site 295405004277 YceG-like family; Region: YceG; pfam02618 295405004278 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 295405004279 dimerization interface [polypeptide binding]; other site 295405004280 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; cd00091 295405004281 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 295405004282 active site 295405004283 substrate binding site [chemical binding]; other site 295405004284 Mg2+ binding site [ion binding]; other site 295405004285 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 295405004286 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 295405004287 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 295405004288 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 295405004289 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 295405004290 NAD(P) binding site [chemical binding]; other site 295405004291 homodimer interface [polypeptide binding]; other site 295405004292 substrate binding site [chemical binding]; other site 295405004293 active site 295405004294 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 295405004295 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 295405004296 SLBB domain; Region: SLBB; pfam10531 295405004297 SLBB domain; Region: SLBB; pfam10531 295405004298 SLBB domain; Region: SLBB; pfam10531 295405004299 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 295405004300 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 295405004301 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 295405004302 cupin fold metalloprotein, WbuC family; Region: cupin_WbuC; TIGR04366 295405004303 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 295405004304 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 295405004305 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 295405004306 nucleotide binding site [chemical binding]; other site 295405004307 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 295405004308 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 295405004309 Class I aldolases; Region: Aldolase_Class_I; cl17187 295405004310 catalytic residue [active] 295405004311 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 295405004312 dimerization interface [polypeptide binding]; other site 295405004313 putative active cleft [active] 295405004314 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 295405004315 Major Facilitator Superfamily; Region: MFS_1; pfam07690 295405004316 putative substrate translocation pore; other site 295405004317 Domain of unknown function (DUF386); Region: DUF386; cl01047 295405004318 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405004319 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004320 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405004321 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 295405004322 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405004323 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 295405004324 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405004325 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004326 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405004327 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 295405004328 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405004329 Abhydrolase family; Region: Abhydrolase_7; pfam12715 295405004330 AAA ATPase domain; Region: AAA_16; pfam13191 295405004331 Archaeal ATPase; Region: Arch_ATPase; pfam01637 295405004332 Archaea bacterial proteins of unknown function; Region: DUF234; pfam03008 295405004333 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405004334 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004335 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405004336 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 295405004337 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405004338 Alpha-L-fucosidase; Region: Alpha_L_fucos; smart00812 295405004339 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 295405004340 AAA domain; Region: AAA_17; pfam13207 295405004341 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405004342 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004343 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405004344 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 295405004345 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405004346 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405004347 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405004348 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004349 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405004350 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 295405004351 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405004352 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004353 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405004354 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405004355 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405004356 SusD family; Region: SusD; pfam07980 295405004357 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 295405004358 catalytic site [active] 295405004359 BNR repeat-like domain; Region: BNR_2; pfam13088 295405004360 Asp-box motif; other site 295405004361 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 295405004362 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 295405004363 Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides; Region: GH20_hexosaminidase; cl02948 295405004364 active site 295405004365 sialate_O-acetylesterase_like subfamily of the SGNH-hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: sialate_O-acetylesterase_like2; cd01828 295405004366 active site 295405004367 catalytic triad [active] 295405004368 oxyanion hole [active] 295405004369 sialate O-acetylesterase_like family of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: sialate_O-acetylesterase_like1; cd01827 295405004370 active site 295405004371 catalytic triad [active] 295405004372 oxyanion hole [active] 295405004373 Domain of unknown function (DUF303); Region: DUF303; pfam03629 295405004374 Beta-galactosidase/beta-glucuronidase [Carbohydrate transport and metabolism]; Region: LacZ; COG3250 295405004375 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405004376 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405004377 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405004378 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 295405004379 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 295405004380 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 295405004381 active site 295405004382 Fn3 associated; Region: Fn3_assoc; pfam13287 295405004383 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405004384 sugar binding site [chemical binding]; other site 295405004385 cyclically-permuted mutarotase family protein; Region: mutarot_permut; TIGR03548 295405004386 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 295405004387 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 295405004388 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 295405004389 active site 295405004390 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405004391 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 295405004392 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 295405004393 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405004394 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405004395 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405004396 Bacterial Ig-like domain (group 1); Region: Big_1; cl17740 295405004397 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405004398 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405004399 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405004400 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405004401 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405004402 SusD family; Region: SusD; pfam07980 295405004403 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405004404 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405004405 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405004406 chaperone protein DnaJ; Provisional; Region: PRK14289 295405004407 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 295405004408 HSP70 interaction site [polypeptide binding]; other site 295405004409 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 295405004410 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 295405004411 dimer interface [polypeptide binding]; other site 295405004412 GrpE; Region: GrpE; pfam01025 295405004413 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 295405004414 dimer interface [polypeptide binding]; other site 295405004415 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 295405004416 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 295405004417 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 295405004418 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 295405004419 ABC transporter; Region: ABC_tran_2; pfam12848 295405004420 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 295405004421 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 295405004422 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405004423 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 295405004424 Catalytic domain of Bacillus cereus phosphatidylinositol-specific phospholipases C and similar proteins; Region: PI-PLCc_BcPLC_like; cd08586 295405004425 active site 295405004426 catalytic site [active] 295405004427 putative metal binding site [ion binding]; other site 295405004428 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 295405004429 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 295405004430 nucleotide binding site [chemical binding]; other site 295405004431 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405004432 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004433 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405004434 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405004435 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405004436 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405004437 SusD family; Region: SusD; pfam07980 295405004438 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 295405004439 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 295405004440 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C; pfam03174 295405004441 domain in bacterial beta-glucosidases other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins; Region: PA14; smart00758 295405004442 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 295405004443 putative catalytic site [active] 295405004444 putative metal binding site [ion binding]; other site 295405004445 putative phosphate binding site [ion binding]; other site 295405004446 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cl15837 295405004447 dimer interface [polypeptide binding]; other site 295405004448 Alkaline phosphatase homologues; Region: alkPPc; smart00098 295405004449 active site 295405004450 Trehalase; Region: Trehalase; cl17346 295405004451 Uncharacterized conserved protein [Function unknown]; Region: COG3538 295405004452 Protein of unknown function (DUF1237); Region: DUF1237; pfam06824 295405004453 Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain; Region: MPP_Dcr2; cd07383 295405004454 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 295405004455 putative active site [active] 295405004456 putative metal binding site [ion binding]; other site 295405004457 Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain; Region: MPP_Dcr2; cd07383 295405004458 domain in bacterial beta-glucosidases other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins; Region: PA14; smart00758 295405004459 Ligand-binding domain of DNA transcription repressor specific for xylose (XylR); Region: PBP1_XylR; cd01543 295405004460 putative dimerization interface [polypeptide binding]; other site 295405004461 Transcriptional regulators [Transcription]; Region: PurR; COG1609 295405004462 putative ligand binding site [chemical binding]; other site 295405004463 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405004464 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405004465 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 295405004466 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004467 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 295405004468 binding surface 295405004469 TPR motif; other site 295405004470 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 295405004471 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 295405004472 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 295405004473 DNA binding residues [nucleotide binding] 295405004474 Uncharacterized conserved protein [Function unknown]; Region: COG4938 295405004475 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405004476 Walker A/P-loop; other site 295405004477 ATP binding site [chemical binding]; other site 295405004478 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405004479 Walker B; other site 295405004480 D-loop; other site 295405004481 H-loop/switch region; other site 295405004482 Protein of unknown function (DUF3696); Region: DUF3696; pfam12476 295405004483 Protein of unknown function DUF262; Region: DUF262; pfam03235 295405004484 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 295405004485 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 295405004486 Transposase; Region: DEDD_Tnp_IS110; pfam01548 295405004487 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 295405004488 AAA ATPase domain; Region: AAA_15; pfam13175 295405004489 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405004490 Walker A/P-loop; other site 295405004491 ATP binding site [chemical binding]; other site 295405004492 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cl00083 295405004493 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405004494 Walker A/P-loop; other site 295405004495 ATP binding site [chemical binding]; other site 295405004496 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 295405004497 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 295405004498 active site 295405004499 DNA binding site [nucleotide binding] 295405004500 Int/Topo IB signature motif; other site 295405004501 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 295405004502 Domain of unknown function, B. Theta Gene description (DUF3868); Region: DUF3868; pfam12984 295405004503 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 295405004504 ligand binding site [chemical binding]; other site 295405004505 Clostripain family; Region: Peptidase_C11; pfam03415 295405004506 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405004507 Major fimbrial subunit protein (FimA); Region: P_gingi_FimA; pfam06321 295405004508 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405004509 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405004510 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405004511 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405004512 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405004513 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405004514 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405004515 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405004516 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405004517 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405004518 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405004519 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405004520 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405004521 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405004522 Tandemly repeated domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like; cd13119 295405004523 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405004524 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405004525 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405004526 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405004527 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405004528 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405004529 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405004530 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405004531 Tandemly repeated domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like; cd13119 295405004532 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405004533 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405004534 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405004535 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405004536 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405004537 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405004538 Tandemly repeated domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like; cl17916 295405004539 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405004540 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405004541 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405004542 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 295405004543 ligand binding site [chemical binding]; other site 295405004544 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 295405004545 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405004546 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 295405004547 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 295405004548 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 295405004549 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 295405004550 RNA binding site [nucleotide binding]; other site 295405004551 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405004552 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 295405004553 dimer interface [polypeptide binding]; other site 295405004554 phosphorylation site [posttranslational modification] 295405004555 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 295405004556 ATP binding site [chemical binding]; other site 295405004557 Mg2+ binding site [ion binding]; other site 295405004558 G-X-G motif; other site 295405004559 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 295405004560 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 295405004561 active site 295405004562 metal binding site [ion binding]; metal-binding site 295405004563 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 295405004564 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 295405004565 GAF domain; Region: GAF_2; pfam13185 295405004566 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004567 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 295405004568 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 295405004569 N-terminal plug; other site 295405004570 ligand-binding site [chemical binding]; other site 295405004571 Creatinine amidohydrolase; Region: Creatininase; pfam02633 295405004572 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 295405004573 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 295405004574 ligand binding site [chemical binding]; other site 295405004575 flexible hinge region; other site 295405004576 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 295405004577 putative efflux protein, MATE family; Region: matE; TIGR00797 295405004578 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 295405004579 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_8; cd13134 295405004580 putative transporter; Validated; Region: PRK03818 295405004581 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 295405004582 TrkA-C domain; Region: TrkA_C; pfam02080 295405004583 TrkA-C domain; Region: TrkA_C; pfam02080 295405004584 AspT/YidE/YbjL antiporter duplication domain; Region: YidE_YbjL_dupl; TIGR01625 295405004585 Firmicute fructose-1,6-bisphosphatase; Region: FBPase_2; pfam06874 295405004586 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 295405004587 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 295405004588 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 295405004589 acyl-activating enzyme (AAE) consensus motif; other site 295405004590 putative AMP binding site [chemical binding]; other site 295405004591 putative active site [active] 295405004592 putative CoA binding site [chemical binding]; other site 295405004593 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 295405004594 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 295405004595 NADP binding site [chemical binding]; other site 295405004596 active site 295405004597 putative substrate binding site [chemical binding]; other site 295405004598 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 295405004599 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 295405004600 NADP-binding site; other site 295405004601 homotetramer interface [polypeptide binding]; other site 295405004602 substrate binding site [chemical binding]; other site 295405004603 homodimer interface [polypeptide binding]; other site 295405004604 active site 295405004605 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 295405004606 AAA domain; Region: AAA_14; pfam13173 295405004607 Domain of unknown function (DUF4373); Region: DUF4373; pfam14297 295405004608 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 295405004609 UpxZ family of transcription anti-terminator antagonists; Region: UpxZ; pfam06603 295405004610 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 295405004611 Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline; Region: PC_cytidylyltransferase; cd02523 295405004612 active site 295405004613 metal-binding site 295405004614 cytidylyltransferase; Region: cytidylyltransferase; cd02170 295405004615 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 295405004616 active site 295405004617 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 295405004618 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 295405004619 tetramer interface [polypeptide binding]; other site 295405004620 active site 295405004621 Mg2+/Mn2+ binding site [ion binding]; other site 295405004622 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 295405004623 phosphonopyruvate decarboxylase; Region: Ppyr-DeCO2ase; TIGR03297 295405004624 PYR/PP interface [polypeptide binding]; other site 295405004625 dimer interface [polypeptide binding]; other site 295405004626 TPP binding site [chemical binding]; other site 295405004627 Thiamine pyrophosphate (TPP) family, PpyrDC subfamily, TPP-binding module; composed of proteins similar to phosphonopyruvate decarboxylase (PpyrDC) proteins. PpyrDC is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as...; Region: TPP_PpyrDC; cd03371 295405004628 TPP-binding site; other site 295405004629 2-aminoethylphosphonate aminotransferase; Region: PhnW-AepZ; TIGR03301 295405004630 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 295405004631 catalytic residue [active] 295405004632 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 295405004633 Sulfatase; Region: Sulfatase; cl17466 295405004634 Sulfatase; Region: Sulfatase; cl17466 295405004635 Alpha-1,2-fucosyltransferase; Region: Fut1_Fut2_like; cd11301 295405004636 GDP-Fucose binding site [chemical binding]; other site 295405004637 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405004638 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 295405004639 putative NAD(P) binding site [chemical binding]; other site 295405004640 active site 295405004641 putative substrate binding site [chemical binding]; other site 295405004642 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 295405004643 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 295405004644 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 295405004645 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 295405004646 active site 295405004647 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 295405004648 active site 295405004649 O-Antigen ligase; Region: Wzy_C; cl04850 295405004650 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405004651 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 295405004652 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 295405004653 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 295405004654 NAD(P) binding site [chemical binding]; other site 295405004655 homodimer interface [polypeptide binding]; other site 295405004656 substrate binding site [chemical binding]; other site 295405004657 active site 295405004658 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 295405004659 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 295405004660 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 295405004661 active site 295405004662 homodimer interface [polypeptide binding]; other site 295405004663 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405004664 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 295405004665 NADP binding site [chemical binding]; other site 295405004666 active site 295405004667 putative substrate binding site [chemical binding]; other site 295405004668 putative glycosyl transferase; Provisional; Region: PRK10307 295405004669 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 295405004670 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405004671 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405004672 NAD(P) binding site [chemical binding]; other site 295405004673 active site 295405004674 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 295405004675 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 295405004676 Mg++ binding site [ion binding]; other site 295405004677 putative catalytic motif [active] 295405004678 putative substrate binding site [chemical binding]; other site 295405004679 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 295405004680 sequence-specific DNA binding site [nucleotide binding]; other site 295405004681 salt bridge; other site 295405004682 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 295405004683 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 295405004684 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 295405004685 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 295405004686 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 295405004687 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 295405004688 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 295405004689 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 295405004690 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 295405004691 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 295405004692 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 295405004693 putative active site [active] 295405004694 DOMON-like type 9 carbohydrate binding module; Region: CBM9_like_3; cd09620 295405004695 putative ligand binding site [chemical binding]; other site 295405004696 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 295405004697 Urea transporter; Region: UT; pfam03253 295405004698 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 295405004699 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 295405004700 active site 295405004701 DNA binding site [nucleotide binding] 295405004702 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 295405004703 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 295405004704 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 295405004705 Catalytic site [active] 295405004706 CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases; Region: CYTH-like_Pase; cl11964 295405004707 putative active site; other site 295405004708 putative metal binding residues [ion binding]; other site 295405004709 two-component response regulator; Provisional; Region: PRK14084 295405004710 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 295405004711 active site 295405004712 phosphorylation site [posttranslational modification] 295405004713 intermolecular recognition site; other site 295405004714 dimerization interface [polypeptide binding]; other site 295405004715 LytTr DNA-binding domain; Region: LytTR; smart00850 295405004716 Histidine kinase; Region: His_kinase; pfam06580 295405004717 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 295405004718 ATP binding site [chemical binding]; other site 295405004719 Mg2+ binding site [ion binding]; other site 295405004720 G-X-G motif; other site 295405004721 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405004722 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 295405004723 FtsX-like permease family; Region: FtsX; pfam02687 295405004724 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 295405004725 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 295405004726 Walker A/P-loop; other site 295405004727 ATP binding site [chemical binding]; other site 295405004728 Q-loop/lid; other site 295405004729 ABC transporter signature motif; other site 295405004730 Walker B; other site 295405004731 D-loop; other site 295405004732 H-loop/switch region; other site 295405004733 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405004734 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 295405004735 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405004736 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 295405004737 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 295405004738 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 295405004739 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 295405004740 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 295405004741 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 295405004742 WGR domain; Region: WGR; cd07994 295405004743 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 295405004744 ATP-grasp domain; Region: ATP-grasp_4; cl17255 295405004745 Sulfatase; Region: Sulfatase; cl17466 295405004746 coproporphyrinogen III oxidase; Validated; Region: PRK08208 295405004747 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 295405004748 FeS/SAM binding site; other site 295405004749 HemN C-terminal domain; Region: HemN_C; pfam06969 295405004750 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 295405004751 FeS/SAM binding site; other site 295405004752 phosphoglycolate phosphatase; Provisional; Region: PRK01158 295405004753 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 295405004754 active site 295405004755 motif I; other site 295405004756 motif II; other site 295405004757 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 295405004758 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 295405004759 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 295405004760 putative ligand binding site [chemical binding]; other site 295405004761 putative NAD binding site [chemical binding]; other site 295405004762 catalytic site [active] 295405004763 recombination factor protein RarA; Reviewed; Region: PRK13342 295405004764 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 295405004765 Walker A motif; other site 295405004766 ATP binding site [chemical binding]; other site 295405004767 Walker B motif; other site 295405004768 arginine finger; other site 295405004769 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 295405004770 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405004771 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405004772 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405004773 Bacterial Ig-like domain (group 1); Region: Big_1; cl17740 295405004774 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405004775 sugar binding site [chemical binding]; other site 295405004776 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004777 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 295405004778 active site 295405004779 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 295405004780 homodimer interface [polypeptide binding]; other site 295405004781 Predicted membrane protein [Function unknown]; Region: COG2860 295405004782 UPF0126 domain; Region: UPF0126; pfam03458 295405004783 UPF0126 domain; Region: UPF0126; pfam03458 295405004784 Domain of unknown function (DUF4251); Region: DUF4251; pfam14059 295405004785 Peptidase family M48; Region: Peptidase_M48; cl12018 295405004786 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 295405004787 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 295405004788 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405004789 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 295405004790 DNA binding residues [nucleotide binding] 295405004791 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]; Region: COG5016 295405004792 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 295405004793 active site 295405004794 catalytic residues [active] 295405004795 metal binding site [ion binding]; metal-binding site 295405004796 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405004797 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004798 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405004799 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 295405004800 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405004801 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 295405004802 Transglycosylase; Region: Transgly; cl17702 295405004803 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 295405004804 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 295405004805 ligand binding site [chemical binding]; other site 295405004806 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 295405004807 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_1; cd13140 295405004808 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 295405004809 EamA-like transporter family; Region: EamA; pfam00892 295405004810 EamA-like transporter family; Region: EamA; pfam00892 295405004811 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405004812 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004813 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405004814 FecR protein; Region: FecR; pfam04773 295405004815 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405004816 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405004817 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 295405004818 DNA binding residues [nucleotide binding] 295405004819 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004820 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 295405004821 flavodoxin; Provisional; Region: PRK07116 295405004822 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 295405004823 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 295405004824 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 295405004825 trimer interface [polypeptide binding]; other site 295405004826 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 295405004827 active site 295405004828 substrate binding site [chemical binding]; other site 295405004829 CoA binding site [chemical binding]; other site 295405004830 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 295405004831 PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal)...; Region: PDZ_signaling; cd00992 295405004832 C-terminal processing peptidase-like; serine protease family S41; Region: Peptidase_S41_CPP_like; cd07561 295405004833 Catalytic dyad [active] 295405004834 Protein of unknown function (DUF3795); Region: DUF3795; pfam12675 295405004835 protoporphyrinogen oxidase; Region: PLN02576 295405004836 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 295405004837 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 295405004838 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 295405004839 FeS/SAM binding site; other site 295405004840 HemN C-terminal domain; Region: HemN_C; pfam06969 295405004841 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 295405004842 siderophore transporter, RhtX/FptX family; Region: sider_RhtX_FptX; TIGR02718 295405004843 putative substrate translocation pore; other site 295405004844 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 295405004845 N-terminal plug; other site 295405004846 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 295405004847 ligand-binding site [chemical binding]; other site 295405004848 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 295405004849 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 295405004850 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 295405004851 ligand binding site [chemical binding]; other site 295405004852 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405004853 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405004854 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 295405004855 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 295405004856 N-terminal plug; other site 295405004857 ligand-binding site [chemical binding]; other site 295405004858 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004859 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405004860 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405004861 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 295405004862 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405004863 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405004864 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405004865 Domain of unknown function (DUF4302); Region: DUF4302; pfam14135 295405004866 Carbohydrate binding domain; Region: CBM_4_9; pfam02018 295405004867 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 295405004868 Interdomain contacts; other site 295405004869 Cytokine receptor motif; other site 295405004870 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 295405004871 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 295405004872 SLBB domain; Region: SLBB; pfam10531 295405004873 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 295405004874 SLBB domain; Region: SLBB; pfam10531 295405004875 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 295405004876 SLBB domain; Region: SLBB; pfam10531 295405004877 FOG: PKD repeat [General function prediction only]; Region: COG3291 295405004878 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 295405004879 PKD domain; Region: PKD; pfam00801 295405004880 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 295405004881 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 295405004882 PAAR motif; Region: PAAR_motif; pfam05488 295405004883 Uncharacterized protein conserved in bacteria [Function unknown]; Region: VgrG; COG3501 295405004884 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 295405004885 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 295405004886 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 295405004887 Gene 25-like lysozyme; Region: GPW_gp25; pfam04965 295405004888 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 295405004889 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 295405004890 Walker A motif; other site 295405004891 ATP binding site [chemical binding]; other site 295405004892 Walker B motif; other site 295405004893 arginine finger; other site 295405004894 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 295405004895 Walker A motif; other site 295405004896 ATP binding site [chemical binding]; other site 295405004897 Walker B motif; other site 295405004898 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 295405004899 Protein of unknown function (DUF877); Region: DUF877; pfam05943 295405004900 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 295405004901 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 295405004902 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 295405004903 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 295405004904 catalytic residue [active] 295405004905 Part of AAA domain; Region: AAA_19; pfam13245 295405004906 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 295405004907 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 295405004908 active site 1 [active] 295405004909 dimer interface [polypeptide binding]; other site 295405004910 hexamer interface [polypeptide binding]; other site 295405004911 active site 2 [active] 295405004912 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 295405004913 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 295405004914 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 295405004915 DNA binding site [nucleotide binding] 295405004916 Protein of unknown function (DUF1266); Region: DUF1266; pfam06889 295405004917 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 295405004918 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 295405004919 exonuclease subunit SbcD; Provisional; Region: PRK10966 295405004920 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 295405004921 active site 295405004922 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405004923 ABC transporter signature motif; other site 295405004924 Walker B; other site 295405004925 D-loop; other site 295405004926 H-loop/switch region; other site 295405004927 Predicted helicase [General function prediction only]; Region: COG4889 295405004928 Restriction endonuclease; Region: Mrr_cat_2; pfam13156 295405004929 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 295405004930 ATP binding site [chemical binding]; other site 295405004931 putative Mg++ binding site [ion binding]; other site 295405004932 helicase superfamily c-terminal domain; Region: HELICc; smart00490 295405004933 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 295405004934 non-specific DNA binding site [nucleotide binding]; other site 295405004935 salt bridge; other site 295405004936 sequence-specific DNA binding site [nucleotide binding]; other site 295405004937 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 295405004938 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405004939 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405004940 D-loop; other site 295405004941 H-loop/switch region; other site 295405004942 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405004943 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 295405004944 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 295405004945 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 295405004946 Int/Topo IB signature motif; other site 295405004947 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 295405004948 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 295405004949 Int/Topo IB signature motif; other site 295405004950 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 295405004951 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 295405004952 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 295405004953 ABC transporter; Region: ABC_tran_2; pfam12848 295405004954 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 295405004955 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405004956 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405004957 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 295405004958 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 295405004959 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; Region: EEP-2; cd09084 295405004960 putative catalytic site [active] 295405004961 putative metal binding site [ion binding]; other site 295405004962 putative phosphate binding site [ion binding]; other site 295405004963 PAS domain; Region: PAS_9; pfam13426 295405004964 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 295405004965 putative active site [active] 295405004966 heme pocket [chemical binding]; other site 295405004967 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405004968 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 295405004969 dimer interface [polypeptide binding]; other site 295405004970 phosphorylation site [posttranslational modification] 295405004971 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 295405004972 ATP binding site [chemical binding]; other site 295405004973 Mg2+ binding site [ion binding]; other site 295405004974 G-X-G motif; other site 295405004975 Response regulator receiver domain; Region: Response_reg; pfam00072 295405004976 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 295405004977 active site 295405004978 phosphorylation site [posttranslational modification] 295405004979 intermolecular recognition site; other site 295405004980 dimerization interface [polypeptide binding]; other site 295405004981 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 295405004982 CESA_like_1 is a member of the cellulose synthase (CESA) superfamily; Region: CESA_like_1; cd06439 295405004983 DXD motif; other site 295405004984 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cd10585 295405004985 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 295405004986 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 295405004987 active site 295405004988 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405004989 This family is most closely related to the GT1 family of glycosyltransferases. AmSD in Erwinia amylovora has been shown to be involved in the biosynthesis of amylovoran, the acidic exopolysaccharide acting as a virulence factor. This enzyme may be...; Region: GT1_amsD_like; cd03820 295405004990 putative ADP-binding pocket [chemical binding]; other site 295405004991 glycosyltransferase, SP_1767 family; Region: glyco_access_1; TIGR03728 295405004992 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405004993 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 295405004994 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 295405004995 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 295405004996 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405004997 This family is most closely related to the GT1 family of glycosyltransferases. AmSD in Erwinia amylovora has been shown to be involved in the biosynthesis of amylovoran, the acidic exopolysaccharide acting as a virulence factor. This enzyme may be...; Region: GT1_amsD_like; cd03820 295405004998 putative ADP-binding pocket [chemical binding]; other site 295405004999 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 295405005000 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 295405005001 active site 295405005002 Glycosyl transferase family group 2; Region: Glyco_trans_2_3; pfam13632 295405005003 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 295405005004 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 295405005005 Probable Catalytic site; other site 295405005006 metal-binding site 295405005007 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 295405005008 O-antigen ligase like membrane protein; Region: O-antigen_lig; pfam13425 295405005009 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 295405005010 AAA ATPase domain; Region: AAA_16; pfam13191 295405005011 Outer membrane efflux protein; Region: OEP; pfam02321 295405005012 Surface antigen; Region: Bac_surface_Ag; pfam01103 295405005013 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 295405005014 trimer interface [polypeptide binding]; other site 295405005015 active site 295405005016 G bulge; other site 295405005017 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 295405005018 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 295405005019 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 295405005020 Na(+)-translocating NADH-quinone reductase subunit C; Provisional; Region: PRK05346 295405005021 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 295405005022 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 295405005023 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 295405005024 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 295405005025 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 295405005026 catalytic loop [active] 295405005027 iron binding site [ion binding]; other site 295405005028 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 295405005029 FAD binding pocket [chemical binding]; other site 295405005030 FAD binding motif [chemical binding]; other site 295405005031 phosphate binding motif [ion binding]; other site 295405005032 beta-alpha-beta structure motif; other site 295405005033 NAD binding pocket [chemical binding]; other site 295405005034 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 295405005035 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 295405005036 ATP binding site [chemical binding]; other site 295405005037 putative Mg++ binding site [ion binding]; other site 295405005038 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 295405005039 nucleotide binding region [chemical binding]; other site 295405005040 ATP-binding site [chemical binding]; other site 295405005041 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 295405005042 RNA binding site [nucleotide binding]; other site 295405005043 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 295405005044 homodimer interface [polypeptide binding]; other site 295405005045 substrate-cofactor binding pocket; other site 295405005046 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405005047 catalytic residue [active] 295405005048 Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_like_3; cd12174 295405005049 putative ligand binding site [chemical binding]; other site 295405005050 putative NAD binding site [chemical binding]; other site 295405005051 putative catalytic site [active] 295405005052 Uncharacterized conserved protein [Function unknown]; Region: COG4198 295405005053 Protein of unknown function (DUF1015); Region: DUF1015; pfam06245 295405005054 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 295405005055 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 295405005056 Uncharacterized conserved protein [Function unknown]; Region: COG1739 295405005057 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 295405005058 HpaII restriction endonuclease; Region: RE_HpaII; pfam09561 295405005059 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; cd02062 295405005060 FMN binding site [chemical binding]; other site 295405005061 dimer interface [polypeptide binding]; other site 295405005062 glycine dehydrogenase; Provisional; Region: PRK05367 295405005063 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 295405005064 tetramer interface [polypeptide binding]; other site 295405005065 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405005066 catalytic residue [active] 295405005067 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 295405005068 tetramer interface [polypeptide binding]; other site 295405005069 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405005070 catalytic residue [active] 295405005071 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 295405005072 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 295405005073 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 295405005074 S-adenosylmethionine binding site [chemical binding]; other site 295405005075 Domain of unknown function (DUF4163); Region: DUF4163; pfam13739 295405005076 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 295405005077 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405005078 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 295405005079 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 295405005080 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 295405005081 metal-binding site [ion binding] 295405005082 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 295405005083 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 295405005084 metal-binding site [ion binding] 295405005085 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 295405005086 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 295405005087 motif II; other site 295405005088 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405005089 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405005090 lipoate-protein ligase B; Provisional; Region: PRK14348 295405005091 Protein of unknown function (DUF1460); Region: DUF1460; pfam07313 295405005092 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 295405005093 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 295405005094 OPT oligopeptide transporter protein; Region: OPT; pfam03169 295405005095 putative oligopeptide transporter, OPT family; Region: TIGR00733 295405005096 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 295405005097 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 295405005098 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 295405005099 ATP binding site [chemical binding]; other site 295405005100 Mg2+ binding site [ion binding]; other site 295405005101 G-X-G motif; other site 295405005102 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 295405005103 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 295405005104 active site 295405005105 phosphorylation site [posttranslational modification] 295405005106 intermolecular recognition site; other site 295405005107 dimerization interface [polypeptide binding]; other site 295405005108 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 295405005109 Walker A motif; other site 295405005110 ATP binding site [chemical binding]; other site 295405005111 Walker B motif; other site 295405005112 arginine finger; other site 295405005113 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 295405005114 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005115 FtsX-like permease family; Region: FtsX; pfam02687 295405005116 Acidobacterial duplicated orphan permease; Region: ADOP; TIGR03434 295405005117 FtsX-like permease family; Region: FtsX; pfam02687 295405005118 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 295405005119 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 295405005120 Walker A/P-loop; other site 295405005121 ATP binding site [chemical binding]; other site 295405005122 Q-loop/lid; other site 295405005123 ABC transporter signature motif; other site 295405005124 Walker B; other site 295405005125 D-loop; other site 295405005126 H-loop/switch region; other site 295405005127 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 295405005128 G1 box; other site 295405005129 GTP/Mg2+ binding site [chemical binding]; other site 295405005130 Switch I region; other site 295405005131 G2 box; other site 295405005132 G3 box; other site 295405005133 Switch II region; other site 295405005134 G4 box; other site 295405005135 G5 box; other site 295405005136 Na(+)/iodide (NIS) and Na(+)/multivitamin (SMVT) cotransporters, and related proteins; solute binding domain; Region: SLC5sbd_NIS-like; cd10326 295405005137 Na binding site [ion binding]; other site 295405005138 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1755 295405005139 recombination protein RecR; Reviewed; Region: recR; PRK00076 295405005140 RecR protein; Region: RecR; pfam02132 295405005141 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 295405005142 putative active site [active] 295405005143 putative metal-binding site [ion binding]; other site 295405005144 tetramer interface [polypeptide binding]; other site 295405005145 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 295405005146 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 295405005147 Uncharacterized ACR, COG1678; Region: DUF179; pfam02622 295405005148 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 295405005149 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405005150 homodimer interface [polypeptide binding]; other site 295405005151 catalytic residue [active] 295405005152 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 295405005153 Int/Topo IB signature motif; other site 295405005154 Helix-turn-helix domain; Region: HTH_17; cl17695 295405005155 Domain of unknown function, B. Theta Gene description (DUF3876); Region: DUF3876; pfam12992 295405005156 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405005157 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 295405005158 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405005159 RteC protein; Region: RteC; pfam09357 295405005160 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 295405005161 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 295405005162 active site 295405005163 catalytic tetrad [active] 295405005164 Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; Region: GH38-57_N_LamB_YdjC_SF; cl17191 295405005165 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405005166 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405005167 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 295405005168 Di-sulfide bridge nucleocytoplasmic transport domain; Region: Brr6_like_C_C; cl12377 295405005169 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 295405005170 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 295405005171 active site 295405005172 catalytic tetrad [active] 295405005173 Flavin reductase like domain; Region: Flavin_Reduct; pfam01613 295405005174 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 295405005175 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 295405005176 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 295405005177 active site 295405005178 catalytic tetrad [active] 295405005179 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 295405005180 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 295405005181 catalytic tetrad [active] 295405005182 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; cl00470 295405005183 Protein of unknown function (DUF3737); Region: DUF3737; pfam12541 295405005184 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 295405005185 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 295405005186 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 295405005187 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 295405005188 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405005189 homodimer interface [polypeptide binding]; other site 295405005190 catalytic residue [active] 295405005191 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 295405005192 RibD C-terminal domain; Region: RibD_C; cl17279 295405005193 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 295405005194 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 295405005195 Predicted membrane protein [Function unknown]; Region: COG2311 295405005196 Protein of unknown function (DUF418); Region: DUF418; cl12135 295405005197 Protein of unknown function (DUF418); Region: DUF418; pfam04235 295405005198 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 295405005199 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 295405005200 active site 295405005201 catalytic tetrad [active] 295405005202 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405005203 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 295405005204 putative membrane fusion protein; Region: TIGR02828 295405005205 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 295405005206 Protein export membrane protein; Region: SecD_SecF; cl14618 295405005207 Outer membrane efflux protein; Region: OEP; pfam02321 295405005208 Outer membrane efflux protein; Region: OEP; pfam02321 295405005209 C-terminal processing peptidase family S41; Region: Peptidase_S41; cd06567 295405005210 Active site serine [active] 295405005211 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 295405005212 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 295405005213 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 295405005214 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405005215 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 295405005216 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 295405005217 N-terminal plug; other site 295405005218 ligand-binding site [chemical binding]; other site 295405005219 Bacterial proteins similar to Porphyromonas gingivalis HmuY; Region: HmuY; cd12105 295405005220 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405005221 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 295405005222 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 295405005223 O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3315 295405005224 Leucine carboxyl methyltransferase; Region: LCM; pfam04072 295405005225 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 295405005226 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 295405005227 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405005228 Walker A/P-loop; other site 295405005229 ATP binding site [chemical binding]; other site 295405005230 Q-loop/lid; other site 295405005231 ABC transporter signature motif; other site 295405005232 Walker B; other site 295405005233 D-loop; other site 295405005234 H-loop/switch region; other site 295405005235 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 295405005236 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 295405005237 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405005238 Walker A/P-loop; other site 295405005239 ATP binding site [chemical binding]; other site 295405005240 Q-loop/lid; other site 295405005241 ABC transporter signature motif; other site 295405005242 Walker B; other site 295405005243 D-loop; other site 295405005244 H-loop/switch region; other site 295405005245 PAS fold; Region: PAS_3; pfam08447 295405005246 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405005247 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 295405005248 dimer interface [polypeptide binding]; other site 295405005249 phosphorylation site [posttranslational modification] 295405005250 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 295405005251 ATP binding site [chemical binding]; other site 295405005252 Mg2+ binding site [ion binding]; other site 295405005253 G-X-G motif; other site 295405005254 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405005255 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405005256 Protein of unknown function (DUF2000); Region: DUF2000; pfam09391 295405005257 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 295405005258 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 295405005259 dimerization interface [polypeptide binding]; other site 295405005260 putative DNA binding site [nucleotide binding]; other site 295405005261 putative Zn2+ binding site [ion binding]; other site 295405005262 AsnC family; Region: AsnC_trans_reg; pfam01037 295405005263 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405005264 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405005265 Predicted phosphoadenosine phosphosulfate sulfotransferase [General function prediction only]; Region: COG3969 295405005266 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 295405005267 Active Sites [active] 295405005268 Domain of unknown function (DUF3440); Region: DUF3440; pfam11922 295405005269 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 295405005270 ParB-like nuclease domain; Region: ParB; smart00470 295405005271 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 295405005272 Domain of unknown function, B. Theta Gene description (DUF3868); Region: DUF3868; pfam12984 295405005273 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 295405005274 ligand binding site [chemical binding]; other site 295405005275 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 295405005276 binding surface 295405005277 TPR motif; other site 295405005278 TPR repeat; Region: TPR_11; pfam13414 295405005279 Major fimbrial subunit protein (FimA); Region: P_gingi_FimA; pfam06321 295405005280 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405005281 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405005282 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 295405005283 NAD binding site [chemical binding]; other site 295405005284 putative substrate binding site 2 [chemical binding]; other site 295405005285 putative substrate binding site 1 [chemical binding]; other site 295405005286 active site 295405005287 Response regulator receiver domain; Region: Response_reg; pfam00072 295405005288 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 295405005289 active site 295405005290 phosphorylation site [posttranslational modification] 295405005291 intermolecular recognition site; other site 295405005292 dimerization interface [polypeptide binding]; other site 295405005293 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405005294 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 295405005295 dimer interface [polypeptide binding]; other site 295405005296 phosphorylation site [posttranslational modification] 295405005297 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 295405005298 ATP binding site [chemical binding]; other site 295405005299 Mg2+ binding site [ion binding]; other site 295405005300 G-X-G motif; other site 295405005301 probable DNA repair protein; Region: TIGR03623 295405005302 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 295405005303 Part of AAA domain; Region: AAA_19; pfam13245 295405005304 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 295405005305 Family description; Region: UvrD_C_2; pfam13538 295405005306 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 295405005307 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 295405005308 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 295405005309 active site 295405005310 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 295405005311 active site 295405005312 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405005313 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405005314 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405005315 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405005316 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 295405005317 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405005318 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405005319 hypothetical protein; Provisional; Region: yieM; PRK10997 295405005320 VWA YIEM 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_YIEM_type; cd01462 295405005321 metal ion-dependent adhesion site (MIDAS); other site 295405005322 MoxR-like ATPases [General function prediction only]; Region: COG0714 295405005323 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 295405005324 Walker A motif; other site 295405005325 ATP binding site [chemical binding]; other site 295405005326 Walker B motif; other site 295405005327 arginine finger; other site 295405005328 Protein of unknown function (DUF3037); Region: DUF3037; pfam11236 295405005329 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 295405005330 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 295405005331 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 295405005332 acyl-activating enzyme (AAE) consensus motif; other site 295405005333 acyl-activating enzyme (AAE) consensus motif; other site 295405005334 AMP binding site [chemical binding]; other site 295405005335 active site 295405005336 CoA binding site [chemical binding]; other site 295405005337 potassium/proton antiporter; Reviewed; Region: PRK05326 295405005338 TrkA-C domain; Region: TrkA_C; pfam02080 295405005339 uracil-xanthine permease; Region: ncs2; TIGR00801 295405005340 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 295405005341 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 295405005342 ligand binding site [chemical binding]; other site 295405005343 flexible hinge region; other site 295405005344 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 295405005345 putative switch regulator; other site 295405005346 non-specific DNA interactions [nucleotide binding]; other site 295405005347 DNA binding site [nucleotide binding] 295405005348 sequence specific DNA binding site [nucleotide binding]; other site 295405005349 putative cAMP binding site [chemical binding]; other site 295405005350 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 295405005351 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 295405005352 ATP binding site [chemical binding]; other site 295405005353 Mg2+ binding site [ion binding]; other site 295405005354 G-X-G motif; other site 295405005355 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 295405005356 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 295405005357 active site 295405005358 phosphorylation site [posttranslational modification] 295405005359 intermolecular recognition site; other site 295405005360 dimerization interface [polypeptide binding]; other site 295405005361 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 295405005362 Walker A motif; other site 295405005363 ATP binding site [chemical binding]; other site 295405005364 Walker B motif; other site 295405005365 arginine finger; other site 295405005366 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 295405005367 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 295405005368 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 295405005369 active site 295405005370 metal binding site [ion binding]; metal-binding site 295405005371 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005372 FtsX-like permease family; Region: FtsX; pfam02687 295405005373 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005374 FtsX-like permease family; Region: FtsX; pfam02687 295405005375 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 295405005376 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 295405005377 Walker A/P-loop; other site 295405005378 ATP binding site [chemical binding]; other site 295405005379 Q-loop/lid; other site 295405005380 ABC transporter signature motif; other site 295405005381 Walker B; other site 295405005382 D-loop; other site 295405005383 H-loop/switch region; other site 295405005384 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005385 FtsX-like permease family; Region: FtsX; pfam02687 295405005386 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005387 FtsX-like permease family; Region: FtsX; pfam02687 295405005388 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 295405005389 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 295405005390 Walker A/P-loop; other site 295405005391 ATP binding site [chemical binding]; other site 295405005392 Q-loop/lid; other site 295405005393 ABC transporter signature motif; other site 295405005394 Walker B; other site 295405005395 D-loop; other site 295405005396 H-loop/switch region; other site 295405005397 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005398 FtsX-like permease family; Region: FtsX; pfam02687 295405005399 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005400 FtsX-like permease family; Region: FtsX; pfam02687 295405005401 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005402 FtsX-like permease family; Region: FtsX; pfam02687 295405005403 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005404 FtsX-like permease family; Region: FtsX; pfam02687 295405005405 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 295405005406 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 295405005407 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 295405005408 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 295405005409 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 295405005410 motif II; other site 295405005411 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 295405005412 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 295405005413 quinone interaction residues [chemical binding]; other site 295405005414 active site 295405005415 catalytic residues [active] 295405005416 FMN binding site [chemical binding]; other site 295405005417 substrate binding site [chemical binding]; other site 295405005418 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 295405005419 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 295405005420 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 295405005421 oligomerization interface [polypeptide binding]; other site 295405005422 active site 295405005423 metal binding site [ion binding]; metal-binding site 295405005424 Major Facilitator Superfamily; Region: MFS_1; pfam07690 295405005425 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 295405005426 putative substrate translocation pore; other site 295405005427 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; pfam01219 295405005428 HD domain; Region: HD_4; pfam13328 295405005429 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 295405005430 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 295405005431 synthetase active site [active] 295405005432 NTP binding site [chemical binding]; other site 295405005433 metal binding site [ion binding]; metal-binding site 295405005434 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 295405005435 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 295405005436 Domain of unknown function (DUF4301); Region: DUF4301; pfam14134 295405005437 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 295405005438 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 295405005439 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 295405005440 ATP-grasp domain; Region: ATP-grasp; pfam02222 295405005441 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 295405005442 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 295405005443 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 295405005444 alpha subunit interaction interface [polypeptide binding]; other site 295405005445 Walker A motif; other site 295405005446 ATP binding site [chemical binding]; other site 295405005447 Walker B motif; other site 295405005448 inhibitor binding site; inhibition site 295405005449 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 295405005450 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 295405005451 gamma subunit interface [polypeptide binding]; other site 295405005452 LBP interface [polypeptide binding]; other site 295405005453 ATP synthase A chain; Region: ATP-synt_A; cl00413 295405005454 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 295405005455 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 295405005456 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13429 295405005457 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; COG0712 295405005458 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 295405005459 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 295405005460 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 295405005461 beta subunit interaction interface [polypeptide binding]; other site 295405005462 Walker A motif; other site 295405005463 ATP binding site [chemical binding]; other site 295405005464 Walker B motif; other site 295405005465 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 295405005466 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 295405005467 core domain interface [polypeptide binding]; other site 295405005468 delta subunit interface [polypeptide binding]; other site 295405005469 epsilon subunit interface [polypeptide binding]; other site 295405005470 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 295405005471 PIF1-like helicase; Region: PIF1; pfam05970 295405005472 Walker A motif; other site 295405005473 ATP binding site [chemical binding]; other site 295405005474 Walker B motif; other site 295405005475 Family description; Region: UvrD_C_2; pfam13538 295405005476 HRDC domain; Region: HRDC; pfam00570 295405005477 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 295405005478 catalytic residues [active] 295405005479 Outer membrane efflux protein; Region: OEP; pfam02321 295405005480 Outer membrane efflux protein; Region: OEP; pfam02321 295405005481 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405005482 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 295405005483 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405005484 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 295405005485 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 295405005486 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 295405005487 active site 295405005488 phosphorylation site [posttranslational modification] 295405005489 intermolecular recognition site; other site 295405005490 dimerization interface [polypeptide binding]; other site 295405005491 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 295405005492 DNA binding site [nucleotide binding] 295405005493 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 295405005494 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 295405005495 dimerization interface [polypeptide binding]; other site 295405005496 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 295405005497 dimer interface [polypeptide binding]; other site 295405005498 phosphorylation site [posttranslational modification] 295405005499 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 295405005500 ATP binding site [chemical binding]; other site 295405005501 Mg2+ binding site [ion binding]; other site 295405005502 G-X-G motif; other site 295405005503 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 295405005504 SGNH_hydrolase subfamily. SGNH hydrolases are 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...; Region: SGNH_hydrolase_like_6; cd01844 295405005505 active site 295405005506 catalytic triad [active] 295405005507 oxyanion hole [active] 295405005508 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 295405005509 active site 295405005510 catalytic triad [active] 295405005511 oxyanion hole [active] 295405005512 Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Region: Precorrin_2_C20_MT; cd11645 295405005513 active site 295405005514 SAM binding site [chemical binding]; other site 295405005515 homodimer interface [polypeptide binding]; other site 295405005516 Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_d; cd01141 295405005517 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 295405005518 putative ligand binding site [chemical binding]; other site 295405005519 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 295405005520 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 295405005521 ABC-ATPase subunit interface; other site 295405005522 dimer interface [polypeptide binding]; other site 295405005523 putative PBP binding regions; other site 295405005524 iron-dicitrate transporter ATP-binding subunit; Provisional; Region: fecE; PRK11231 295405005525 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 295405005526 Walker A/P-loop; other site 295405005527 ATP binding site [chemical binding]; other site 295405005528 Q-loop/lid; other site 295405005529 ABC transporter signature motif; other site 295405005530 Walker B; other site 295405005531 D-loop; other site 295405005532 H-loop/switch region; other site 295405005533 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 295405005534 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 295405005535 NADP binding site [chemical binding]; other site 295405005536 active site 295405005537 putative substrate binding site [chemical binding]; other site 295405005538 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 295405005539 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 295405005540 active site 295405005541 phosphorylation site [posttranslational modification] 295405005542 intermolecular recognition site; other site 295405005543 dimerization interface [polypeptide binding]; other site 295405005544 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 295405005545 DNA binding site [nucleotide binding] 295405005546 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405005547 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 295405005548 dimer interface [polypeptide binding]; other site 295405005549 phosphorylation site [posttranslational modification] 295405005550 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 295405005551 ATP binding site [chemical binding]; other site 295405005552 Mg2+ binding site [ion binding]; other site 295405005553 G-X-G motif; other site 295405005554 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 295405005555 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405005556 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405005557 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405005558 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 295405005559 dimer interface [polypeptide binding]; other site 295405005560 phosphorylation site [posttranslational modification] 295405005561 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 295405005562 ATP binding site [chemical binding]; other site 295405005563 Mg2+ binding site [ion binding]; other site 295405005564 G-X-G motif; other site 295405005565 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 295405005566 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 295405005567 Potassium binding sites [ion binding]; other site 295405005568 Cesium cation binding sites [ion binding]; other site 295405005569 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 295405005570 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 295405005571 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 295405005572 dimer interface [polypeptide binding]; other site 295405005573 active site 295405005574 glycine-pyridoxal phosphate binding site [chemical binding]; other site 295405005575 folate binding site [chemical binding]; other site 295405005576 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 295405005577 Flavin reductase like domain; Region: Flavin_Reduct; pfam01613 295405005578 aspartate carbamoyltransferase regulatory subunit; Reviewed; Region: PRK00893 295405005579 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 295405005580 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 295405005581 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 295405005582 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 295405005583 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 295405005584 Membrane protein of unknown function (DUF340); Region: DUF340; pfam03956 295405005585 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405005586 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 295405005587 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405005588 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405005589 SusD family; Region: SusD; pfam07980 295405005590 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405005591 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405005592 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405005593 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405005594 BNR repeat-like domain; Region: BNR_2; pfam13088 295405005595 AAA domain; Region: AAA_17; pfam13207 295405005596 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 295405005597 catalytic core [active] 295405005598 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 295405005599 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 295405005600 Ligand binding site; other site 295405005601 oligomer interface; other site 295405005602 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 295405005603 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 295405005604 Transglycosylase; Region: Transgly; pfam00912 295405005605 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 295405005606 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 295405005607 catalytic center binding site [active] 295405005608 ATP binding site [chemical binding]; other site 295405005609 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 295405005610 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 295405005611 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 295405005612 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4642 295405005613 MORN repeat; Region: MORN; cl14787 295405005614 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4642 295405005615 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4642 295405005616 MORN repeat; Region: MORN; cl14787 295405005617 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 295405005618 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 295405005619 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 295405005620 active site 295405005621 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405005622 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 295405005623 ATP binding site [chemical binding]; other site 295405005624 Mg2+ binding site [ion binding]; other site 295405005625 G-X-G motif; other site 295405005626 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405005627 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 295405005628 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 295405005629 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 295405005630 active site 295405005631 phosphorylation site [posttranslational modification] 295405005632 intermolecular recognition site; other site 295405005633 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 295405005634 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 295405005635 Uncharacterized ACR, COG2135; Region: DUF159; cl03646 295405005636 TPR repeat; Region: TPR_11; pfam13414 295405005637 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 295405005638 binding surface 295405005639 TPR motif; other site 295405005640 para-aminobenzoate synthase component I; Validated; Region: PRK07093 295405005641 hypothetical protein; Provisional; Region: PRK07101 295405005642 substrate-cofactor binding pocket; other site 295405005643 TIGR02453 family protein; Region: TIGR02453 295405005644 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]; Region: GlgB; COG0296 295405005645 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 295405005646 Alpha amylase catalytic domain found in bacterial and eukaryotic branching enzymes; Region: AmyAc_bac_euk_BE; cd11321 295405005647 active site 295405005648 catalytic site [active] 295405005649 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 295405005650 Alpha amylase catalytic domain found in an uncharacterized protein family; Region: AmyAc_3; cd11349 295405005651 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 295405005652 active site 295405005653 catalytic site [active] 295405005654 putative oxidoreductase; Provisional; Region: PRK11579 295405005655 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 295405005656 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 295405005657 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 295405005658 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 295405005659 active site 295405005660 nucleophile elbow; other site 295405005661 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 295405005662 Major Facilitator Superfamily; Region: MFS_1; pfam07690 295405005663 putative substrate translocation pore; other site 295405005664 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 295405005665 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 295405005666 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 295405005667 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 295405005668 Cyclic nucleotide-binding domain; Region: cNMP_binding; pfam00027 295405005669 ligand binding site [chemical binding]; other site 295405005670 flexible hinge region; other site 295405005671 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 295405005672 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405005673 NAD(P) binding site [chemical binding]; other site 295405005674 active site 295405005675 PAP2_like_5 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_5; cd03394 295405005676 active site 295405005677 Protein of unknown function (DUF2582); Region: DUF2582; pfam10771 295405005678 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 295405005679 CoA binding domain; Region: CoA_binding; smart00881 295405005680 CoA-ligase; Region: Ligase_CoA; pfam00549 295405005681 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 295405005682 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 295405005683 CoA-ligase; Region: Ligase_CoA; pfam00549 295405005684 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 295405005685 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 295405005686 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 295405005687 dimer interface [polypeptide binding]; other site 295405005688 substrate binding site [chemical binding]; other site 295405005689 ATP binding site [chemical binding]; other site 295405005690 NUDIX domain; Region: NUDIX; pfam00293 295405005691 nudix motif; other site 295405005692 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 295405005693 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 295405005694 D-xylulose kinases, subgroup 2; members of the FGGY family of carbohydrate kinases; Region: FGGY_D-XK_2; cd07810 295405005695 putative N- and C-terminal domain interface [polypeptide binding]; other site 295405005696 putative active site [active] 295405005697 putative MgATP binding site [chemical binding]; other site 295405005698 catalytic site [active] 295405005699 metal binding site [ion binding]; metal-binding site 295405005700 putative xylulose binding site [chemical binding]; other site 295405005701 putative homodimer interface [polypeptide binding]; other site 295405005702 xylose isomerase; Provisional; Region: PRK05474 295405005703 xylose isomerase; Region: xylose_isom_A; TIGR02630 295405005704 D-xylose transporter XylE; Provisional; Region: xylE; PRK10077 295405005705 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 295405005706 putative substrate translocation pore; other site 295405005707 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 295405005708 phosphonoacetate hydrolase; Region: hydr_PhnA; TIGR02335 295405005709 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 295405005710 Coenzyme A binding pocket [chemical binding]; other site 295405005711 Predicted amidohydrolase [General function prediction only]; Region: COG0388 295405005712 Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases); Region: nitrilase_Rim1_like; cd07574 295405005713 putative active site [active] 295405005714 catalytic triad [active] 295405005715 putative dimer interface [polypeptide binding]; other site 295405005716 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 295405005717 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 295405005718 dimer interface [polypeptide binding]; other site 295405005719 decamer (pentamer of dimers) interface [polypeptide binding]; other site 295405005720 catalytic triad [active] 295405005721 peroxidatic and resolving cysteines [active] 295405005722 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 295405005723 Haem-binding domain; Region: Haem_bd; pfam14376 295405005724 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 295405005725 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 295405005726 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 295405005727 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 295405005728 Active site serine [active] 295405005729 Protein of unknown function (DUF2776); Region: DUF2776; pfam10951 295405005730 isoleucyl-tRNA synthetase; Region: ileS; TIGR00392 295405005731 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 295405005732 active site 295405005733 HIGH motif; other site 295405005734 nucleotide binding site [chemical binding]; other site 295405005735 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 295405005736 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 295405005737 active site 295405005738 KMSKS motif; other site 295405005739 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 295405005740 tRNA binding surface [nucleotide binding]; other site 295405005741 anticodon binding site; other site 295405005742 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 295405005743 lipoprotein signal peptidase; Provisional; Region: PRK14788 295405005744 lipoprotein signal peptidase; Provisional; Region: PRK14787 295405005745 Domain of unknown function (DUF4296); Region: DUF4296; pfam14129 295405005746 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 295405005747 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 295405005748 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 295405005749 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 295405005750 Surface antigen; Region: Bac_surface_Ag; pfam01103 295405005751 Domain of unknown function (DUF3332); Region: DUF3332; pfam11810 295405005752 DoxX; Region: DoxX; pfam07681 295405005753 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 295405005754 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 295405005755 H+ Antiporter protein; Region: 2A0121; TIGR00900 295405005756 putative substrate translocation pore; other site 295405005757 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 295405005758 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 295405005759 putative substrate translocation pore; other site 295405005760 glucuronate isomerase; Reviewed; Region: PRK02925 295405005761 Glucuronate isomerase [Carbohydrate transport and metabolism]; Region: UxaC; COG1904 295405005762 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cl00062 295405005763 Sporulation related domain; Region: SPOR; pfam05036 295405005764 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 295405005765 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 295405005766 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 295405005767 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 295405005768 helicase 45; Provisional; Region: PTZ00424 295405005769 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 295405005770 ATP binding site [chemical binding]; other site 295405005771 Mg++ binding site [ion binding]; other site 295405005772 motif III; other site 295405005773 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 295405005774 nucleotide binding region [chemical binding]; other site 295405005775 ATP-binding site [chemical binding]; other site 295405005776 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_1; cd04870 295405005777 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_2; cd04871 295405005778 phosphoserine phosphatase SerB; Region: serB; TIGR00338 295405005779 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 295405005780 motif II; other site 295405005781 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 295405005782 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405005783 catalytic residues [active] 295405005784 Predicted permeases [General function prediction only]; Region: COG0795 295405005785 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 295405005786 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 295405005787 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 295405005788 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 295405005789 Found in ATP-dependent protease La (LON); Region: LON; smart00464 295405005790 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 295405005791 Walker A motif; other site 295405005792 ATP binding site [chemical binding]; other site 295405005793 Walker B motif; other site 295405005794 arginine finger; other site 295405005795 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 295405005796 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 295405005797 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 295405005798 S-adenosylmethionine binding site [chemical binding]; other site 295405005799 The HIRAN protein (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p; Region: HIRAN; smart00910 295405005800 ORF6N domain; Region: ORF6N; pfam10543 295405005801 ORF6N domain; Region: ORF6N; pfam10543 295405005802 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 295405005803 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405005804 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 295405005805 active site 295405005806 motif I; other site 295405005807 motif II; other site 295405005808 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 295405005809 active site 295405005810 Int/Topo IB signature motif; other site 295405005811 DNA binding site [nucleotide binding] 295405005812 Helix-turn-helix domain; Region: HTH_36; pfam13730 295405005813 Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_36K_type; cd07022 295405005814 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 295405005815 tandem repeat interface [polypeptide binding]; other site 295405005816 oligomer interface [polypeptide binding]; other site 295405005817 active site residues [active] 295405005818 TATA element modulatory factor 1 TATA binding; Region: TMF_TATA_bd; pfam12325 295405005819 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 295405005820 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 295405005821 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 295405005822 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 295405005823 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 295405005824 Peptidase M15; Region: Peptidase_M15_3; pfam08291 295405005825 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 295405005826 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 295405005827 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 295405005828 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405005829 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 295405005830 active site 295405005831 DNA binding site [nucleotide binding] 295405005832 Int/Topo IB signature motif; other site 295405005833 Protein of unknown function (DUF1622); Region: DUF1622; pfam07784 295405005834 PAS domain; Region: PAS; smart00091 295405005835 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 295405005836 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 295405005837 ATP binding site [chemical binding]; other site 295405005838 Mg2+ binding site [ion binding]; other site 295405005839 G-X-G motif; other site 295405005840 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 295405005841 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 295405005842 active site 295405005843 phosphorylation site [posttranslational modification] 295405005844 intermolecular recognition site; other site 295405005845 dimerization interface [polypeptide binding]; other site 295405005846 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 295405005847 Walker A motif; other site 295405005848 ATP binding site [chemical binding]; other site 295405005849 Walker B motif; other site 295405005850 arginine finger; other site 295405005851 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 295405005852 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 295405005853 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405005854 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405005855 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005856 FtsX-like permease family; Region: FtsX; pfam02687 295405005857 FtsX-like permease family; Region: FtsX; pfam02687 295405005858 Acidobacterial duplicated orphan permease; Region: ADOP; TIGR03434 295405005859 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005860 FtsX-like permease family; Region: FtsX; pfam02687 295405005861 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005862 FtsX-like permease family; Region: FtsX; pfam02687 295405005863 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005864 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005865 FtsX-like permease family; Region: FtsX; pfam02687 295405005866 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005867 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005868 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 295405005869 FtsX-like permease family; Region: FtsX; pfam02687 295405005870 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005871 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 295405005872 FtsX-like permease family; Region: FtsX; pfam02687 295405005873 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005874 FtsX-like permease family; Region: FtsX; pfam02687 295405005875 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405005876 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 295405005877 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 295405005878 Walker A/P-loop; other site 295405005879 ATP binding site [chemical binding]; other site 295405005880 Q-loop/lid; other site 295405005881 ABC transporter signature motif; other site 295405005882 Walker B; other site 295405005883 D-loop; other site 295405005884 H-loop/switch region; other site 295405005885 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 295405005886 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 295405005887 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 295405005888 substrate-cofactor binding pocket; other site 295405005889 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405005890 catalytic residue [active] 295405005891 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 295405005892 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 295405005893 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 295405005894 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 295405005895 dimer interface [polypeptide binding]; other site 295405005896 anticodon binding site; other site 295405005897 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 295405005898 homodimer interface [polypeptide binding]; other site 295405005899 motif 1; other site 295405005900 active site 295405005901 motif 2; other site 295405005902 GAD domain; Region: GAD; pfam02938 295405005903 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 295405005904 motif 3; other site 295405005905 Predicted membrane protein [Function unknown]; Region: COG2246 295405005906 GtrA-like protein; Region: GtrA; pfam04138 295405005907 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 295405005908 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 295405005909 putative active site; other site 295405005910 catalytic triad [active] 295405005911 putative dimer interface [polypeptide binding]; other site 295405005912 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 295405005913 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 295405005914 Uncharacterized protein containing a ferredoxin domain [Function unknown]; Region: COG4739 295405005915 Uncharacterized protein containing a ferredoxin domain (DUF2148); Region: DUF2148; pfam09918 295405005916 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 295405005917 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405005918 Walker A/P-loop; other site 295405005919 ATP binding site [chemical binding]; other site 295405005920 Q-loop/lid; other site 295405005921 ABC transporter signature motif; other site 295405005922 Walker B; other site 295405005923 D-loop; other site 295405005924 H-loop/switch region; other site 295405005925 Uncharacterized protein family (UPF0014); Region: UPF0014; cl00424 295405005926 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_3; cd07241 295405005927 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 295405005928 putative metal binding site [ion binding]; other site 295405005929 Uncharacterized conserved protein [Function unknown]; Region: COG0327 295405005930 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 295405005931 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3323 295405005932 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 295405005933 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 295405005934 Putative zinc ribbon domain; Region: DUF164; pfam02591 295405005935 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 295405005936 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405005937 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405005938 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405005939 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 295405005940 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N_2; pfam13588 295405005941 AMP nucleosidase; Provisional; Region: PRK07115 295405005942 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 295405005943 DNA polymerase III, delta subunit; Region: holA; TIGR01128 295405005944 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 295405005945 non-specific DNA binding site [nucleotide binding]; other site 295405005946 salt bridge; other site 295405005947 sequence-specific DNA binding site [nucleotide binding]; other site 295405005948 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiB; COG0543 295405005949 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 295405005950 FAD binding pocket [chemical binding]; other site 295405005951 FAD binding motif [chemical binding]; other site 295405005952 phosphate binding motif [ion binding]; other site 295405005953 beta-alpha-beta structure motif; other site 295405005954 NAD binding pocket [chemical binding]; other site 295405005955 Iron coordination center [ion binding]; other site 295405005956 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 295405005957 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 295405005958 heterodimer interface [polypeptide binding]; other site 295405005959 active site 295405005960 FMN binding site [chemical binding]; other site 295405005961 homodimer interface [polypeptide binding]; other site 295405005962 substrate binding site [chemical binding]; other site 295405005963 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 295405005964 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 295405005965 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cd00114 295405005966 nucleotide binding pocket [chemical binding]; other site 295405005967 K-X-D-G motif; other site 295405005968 catalytic site [active] 295405005969 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 295405005970 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 295405005971 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 295405005972 Dimer interface [polypeptide binding]; other site 295405005973 BRCT sequence motif; other site 295405005974 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 295405005975 dihydrodipicolinate synthase; Region: dapA; TIGR00674 295405005976 dimer interface [polypeptide binding]; other site 295405005977 active site 295405005978 catalytic residue [active] 295405005979 Chloramphenicol O-acetyltransferase [Defense mechanisms]; Region: COG4845 295405005980 Chloramphenicol acetyltransferase; Region: CAT; smart01059 295405005981 Protein of unknown function (DUF419); Region: DUF419; pfam04237 295405005982 Uncharacterized conserved protein [Function unknown]; Region: COG1262 295405005983 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 295405005984 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 295405005985 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 295405005986 active site 295405005987 nucleophile elbow; other site 295405005988 heat shock protein 90; Provisional; Region: PRK05218 295405005989 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 295405005990 ATP binding site [chemical binding]; other site 295405005991 Mg2+ binding site [ion binding]; other site 295405005992 G-X-G motif; other site 295405005993 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 295405005994 Clp amino terminal domain; Region: Clp_N; pfam02861 295405005995 Clp amino terminal domain; Region: Clp_N; pfam02861 295405005996 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 295405005997 Walker A motif; other site 295405005998 ATP binding site [chemical binding]; other site 295405005999 Walker B motif; other site 295405006000 arginine finger; other site 295405006001 UvrB/uvrC motif; Region: UVR; pfam02151 295405006002 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 295405006003 Walker A motif; other site 295405006004 ATP binding site [chemical binding]; other site 295405006005 Walker B motif; other site 295405006006 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 295405006007 DNA gyrase subunit A; Validated; Region: PRK05560 295405006008 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 295405006009 CAP-like domain; other site 295405006010 active site 295405006011 primary dimer interface [polypeptide binding]; other site 295405006012 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 295405006013 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 295405006014 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 295405006015 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 295405006016 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 295405006017 TPR repeat; Region: TPR_11; pfam13414 295405006018 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 295405006019 binding surface 295405006020 TPR motif; other site 295405006021 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 295405006022 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 295405006023 Ligand Binding Site [chemical binding]; other site 295405006024 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 295405006025 binding surface 295405006026 Tetratricopeptide repeat; Region: TPR_16; pfam13432 295405006027 TPR motif; other site 295405006028 Bacterial SH3 domain homologues; Region: SH3b; smart00287 295405006029 Oxygen tolerance; Region: BatD; pfam13584 295405006030 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 295405006031 binding surface 295405006032 TPR motif; other site 295405006033 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405006034 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 295405006035 metal ion-dependent adhesion site (MIDAS); other site 295405006036 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 295405006037 metal ion-dependent adhesion site (MIDAS); other site 295405006038 Oxygen tolerance; Region: BatD; pfam13584 295405006039 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 295405006040 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; cd00198 295405006041 metal ion-dependent adhesion site (MIDAS); other site 295405006042 MoxR-like ATPases [General function prediction only]; Region: COG0714 295405006043 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 295405006044 Walker A motif; other site 295405006045 ATP binding site [chemical binding]; other site 295405006046 Walker B motif; other site 295405006047 arginine finger; other site 295405006048 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 295405006049 IHF - DNA interface [nucleotide binding]; other site 295405006050 IHF dimer interface [polypeptide binding]; other site 295405006051 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 295405006052 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 295405006053 IHF dimer interface [polypeptide binding]; other site 295405006054 IHF - DNA interface [nucleotide binding]; other site 295405006055 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 295405006056 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 295405006057 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 295405006058 FeS/SAM binding site; other site 295405006059 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 295405006060 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 295405006061 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 295405006062 ribosomal protein L33; Region: rpl33; CHL00104 295405006063 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 295405006064 competence damage-inducible protein A; Provisional; Region: PRK00549 295405006065 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 295405006066 putative MPT binding site; other site 295405006067 Competence-damaged protein; Region: CinA; pfam02464 295405006068 UGMP family protein; Validated; Region: PRK09604 295405006069 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 295405006070 Family of unknown function (DUF490); Region: DUF490; pfam04357 295405006071 hypothetical protein; Provisional; Region: PRK11770 295405006072 Domain of unknown function (DUF307); Region: DUF307; pfam03733 295405006073 Domain of unknown function (DUF307); Region: DUF307; pfam03733 295405006074 prolyl-tRNA synthetase; Provisional; Region: PRK08661 295405006075 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 295405006076 dimer interface [polypeptide binding]; other site 295405006077 motif 1; other site 295405006078 active site 295405006079 motif 2; other site 295405006080 motif 3; other site 295405006081 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 295405006082 anticodon binding site; other site 295405006083 zinc-binding site [ion binding]; other site 295405006084 TIGR02757 family protein; Region: TIGR02757 295405006085 Uncharacterized protein related to the periplasmic component of the Tol biopolymer transport system [Function unknown]; Region: COG4946 295405006086 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 295405006087 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 295405006088 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 295405006089 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 295405006090 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 295405006091 protein binding site [polypeptide binding]; other site 295405006092 Tricorn protease; serine protease family S41; Region: Peptidase_S41_TRI; cd07562 295405006093 Domain interface; other site 295405006094 Peptide binding site; other site 295405006095 Active site tetrad [active] 295405006096 Peptidase M15; Region: Peptidase_M15_3; pfam08291 295405006097 Phage major tail protein 2; Region: Phage_tail_2; pfam06199 295405006098 Protein of unknown function (DUF3168); Region: DUF3168; pfam11367 295405006099 Phage head-tail joining protein; Region: Phage_H_T_join; pfam05521 295405006100 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 295405006101 oligomerization interface [polypeptide binding]; other site 295405006102 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 295405006103 Phage capsid family; Region: Phage_capsid; pfam05065 295405006104 Caudovirus prohead protease; Region: Peptidase_U35; pfam04586 295405006105 Phage portal protein; Region: Phage_portal; pfam04860 295405006106 Phage-related protein [Function unknown]; Region: COG4695; cl01923 295405006107 Phage terminase-like protein, large subunit [General function prediction only]; Region: COG4626 295405006108 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 295405006109 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 295405006110 active site 295405006111 hypothetical protein; Provisional; Region: PRK05968 295405006112 Domain of unknown function (DUF3127); Region: DUF3127; pfam11325 295405006113 PcfJ-like protein; Region: PcfJ; pfam14284 295405006114 PcfK-like protein; Region: PcfK; pfam14058 295405006115 DNA methylase; Region: N6_N4_Mtase; pfam01555 295405006116 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 295405006117 Bacteriophage Lambda NinG protein; Region: NinG; pfam05766 295405006118 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 295405006119 non-specific DNA binding site [nucleotide binding]; other site 295405006120 salt bridge; other site 295405006121 sequence-specific DNA binding site [nucleotide binding]; other site 295405006122 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 295405006123 YcfA-like protein; Region: YcfA; pfam07927 295405006124 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 295405006125 sequence-specific DNA binding site [nucleotide binding]; other site 295405006126 salt bridge; other site 295405006127 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 295405006128 active site 295405006129 DNA binding site [nucleotide binding] 295405006130 Int/Topo IB signature motif; other site 295405006131 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 295405006132 AAA domain; Region: AAA_18; pfam13238 295405006133 homotrimer interface [polypeptide binding]; other site 295405006134 Walker A motif; other site 295405006135 GTP binding site [chemical binding]; other site 295405006136 Walker B motif; other site 295405006137 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 295405006138 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 295405006139 active site pocket [active] 295405006140 putative dimer interface [polypeptide binding]; other site 295405006141 putative cataytic base [active] 295405006142 cobalamin synthase; Reviewed; Region: cobS; PRK00235 295405006143 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 295405006144 catalytic core [active] 295405006145 CobD/Cbib protein; Region: CobD_Cbib; pfam03186 295405006146 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 295405006147 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 295405006148 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405006149 homodimer interface [polypeptide binding]; other site 295405006150 catalytic residue [active] 295405006151 cobyric acid synthase; Provisional; Region: PRK00784 295405006152 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 295405006153 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 295405006154 catalytic triad [active] 295405006155 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 295405006156 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 295405006157 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405006158 ABC exporter membrane fusion protein, DevB family; Region: heterocyst_DevB; TIGR02971 295405006159 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405006160 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 295405006161 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 295405006162 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 295405006163 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 295405006164 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 295405006165 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 295405006166 GAF domain; Region: GAF; pfam01590 295405006167 GAF domain; Region: GAF_2; pfam13185 295405006168 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 295405006169 PAS fold; Region: PAS_3; pfam08447 295405006170 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 295405006171 dimer interface [polypeptide binding]; other site 295405006172 phosphorylation site [posttranslational modification] 295405006173 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 295405006174 ATP binding site [chemical binding]; other site 295405006175 Mg2+ binding site [ion binding]; other site 295405006176 G-X-G motif; other site 295405006177 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 295405006178 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 295405006179 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 295405006180 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 295405006181 catalytic triad [active] 295405006182 Protein of unknown function (DUF3815); Region: DUF3815; pfam12821 295405006183 Uncharacterized conserved protein [Function unknown]; Region: COG2966 295405006184 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 295405006185 Protein of unknown function (DUF3815); Region: DUF3815; cl01118 295405006186 putative transporter; Validated; Region: PRK03818 295405006187 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 295405006188 TrkA-C domain; Region: TrkA_C; pfam02080 295405006189 TrkA-C domain; Region: TrkA_C; pfam02080 295405006190 AspT/YidE/YbjL antiporter duplication domain; Region: YidE_YbjL_dupl; TIGR01625 295405006191 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 295405006192 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 295405006193 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 295405006194 N-terminal plug; other site 295405006195 ligand-binding site [chemical binding]; other site 295405006196 Cobalt chelatase (CbiK); Region: CbiK; pfam06180 295405006197 Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the...; Region: CbiK_N; cd03412 295405006198 active site 295405006199 C-terminal domain interface [polypeptide binding]; other site 295405006200 Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), C-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the...; Region: CbiK_C; cd03413 295405006201 active site 295405006202 N-terminal domain interface [polypeptide binding]; other site 295405006203 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 295405006204 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 295405006205 N-terminal plug; other site 295405006206 ligand-binding site [chemical binding]; other site 295405006207 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 295405006208 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 295405006209 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 295405006210 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 295405006211 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 295405006212 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 295405006213 Uncharacterized conserved protein (DUF2149); Region: DUF2149; pfam09919 295405006214 Precorrin-3B C(17)-methyltransferase (CobJ/CbiH); Region: Precorrin_3B_C17_MT; cd11646 295405006215 active site 295405006216 SAM binding site [chemical binding]; other site 295405006217 homodimer interface [polypeptide binding]; other site 295405006218 Precorrin-8X methylmutase; Region: CbiC; pfam02570 295405006219 cobalt-precorrin-8X methylmutase; Validated; Region: cbiC; cl00913 295405006220 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 295405006221 active site 295405006222 putative homodimer interface [polypeptide binding]; other site 295405006223 SAM binding site [chemical binding]; other site 295405006224 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 295405006225 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 295405006226 S-adenosylmethionine binding site [chemical binding]; other site 295405006227 cobalamin biosynthesis protein CbiG; Validated; Region: PRK05788 295405006228 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 295405006229 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 295405006230 Cobalamin synthesis G C-terminus; Region: CbiG_C; pfam01890 295405006231 Precorrin-4 C11-methyltransferase (CbiF/CobM); Region: Precorrin-4_C11-MT; cd11641 295405006232 active site 295405006233 SAM binding site [chemical binding]; other site 295405006234 homodimer interface [polypeptide binding]; other site 295405006235 Precorrin-6x reductase [Coenzyme metabolism]; Region: CobK; COG2099 295405006236 Precorrin-6x reductase CbiJ/CobK; Region: CbiJ; cl00922 295405006237 cobalt-precorrin-6A synthase; Reviewed; Region: cbiD; PRK00075 295405006238 Hexokinase [Carbohydrate transport and metabolism]; Region: COG5026 295405006239 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 295405006240 nucleotide binding site [chemical binding]; other site 295405006241 Hexokinase; Region: Hexokinase_2; pfam03727 295405006242 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 295405006243 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 295405006244 dimer interface [polypeptide binding]; other site 295405006245 active site 295405006246 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 295405006247 catalytic residues [active] 295405006248 substrate binding site [chemical binding]; other site 295405006249 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 295405006250 Part of AAA domain; Region: AAA_19; pfam13245 295405006251 Family description; Region: UvrD_C_2; pfam13538 295405006252 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 295405006253 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 295405006254 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 295405006255 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 295405006256 thiS-thiF/thiG interaction site; other site 295405006257 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 295405006258 thiamine phosphate binding site [chemical binding]; other site 295405006259 active site 295405006260 pyrophosphate binding site [ion binding]; other site 295405006261 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 295405006262 ThiS interaction site; other site 295405006263 putative active site [active] 295405006264 tetramer interface [polypeptide binding]; other site 295405006265 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 295405006266 ThiC-associated domain; Region: ThiC-associated; pfam13667 295405006267 ThiC family; Region: ThiC; pfam01964 295405006268 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 295405006269 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 295405006270 FeS/SAM binding site; other site 295405006271 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 295405006272 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 295405006273 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 295405006274 ATP binding site [chemical binding]; other site 295405006275 substrate interface [chemical binding]; other site 295405006276 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 295405006277 thiamine phosphate binding site [chemical binding]; other site 295405006278 active site 295405006279 pyrophosphate binding site [ion binding]; other site 295405006280 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 295405006281 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 295405006282 pyruvate phosphate dikinase; Provisional; Region: PRK09279 295405006283 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 295405006284 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 295405006285 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 295405006286 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 295405006287 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 295405006288 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 295405006289 S-adenosylmethionine binding site [chemical binding]; other site 295405006290 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 295405006291 RNA binding surface [nucleotide binding]; other site 295405006292 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 295405006293 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 295405006294 active site 295405006295 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 295405006296 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-B; cd09722 295405006297 Domain of unknown function DUF83; Region: Cas_Cas4; pfam01930 295405006298 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I; cl00803 295405006299 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 295405006300 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 295405006301 CRISPR-associated helicase Cas3; Region: cas3_core; TIGR01587 295405006302 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09652 295405006303 methionine aminopeptidase; Provisional; Region: PRK12318 295405006304 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 295405006305 active site 295405006306 RmuC family; Region: RmuC; pfam02646 295405006307 Uncharacterized ArCR, COG2043; Region: DUF169; cl00894 295405006308 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 295405006309 GTP-binding protein LepA; Provisional; Region: PRK05433 295405006310 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 295405006311 G1 box; other site 295405006312 putative GEF interaction site [polypeptide binding]; other site 295405006313 GTP/Mg2+ binding site [chemical binding]; other site 295405006314 Switch I region; other site 295405006315 G2 box; other site 295405006316 G3 box; other site 295405006317 Switch II region; other site 295405006318 G4 box; other site 295405006319 G5 box; other site 295405006320 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 295405006321 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 295405006322 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 295405006323 Protein of unknown function (DUF2582); Region: DUF2582; pfam10771 295405006324 Putative redox-active protein (C_GCAxxG_C_C); Region: C_GCAxxG_C_C; pfam09719 295405006325 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 295405006326 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 295405006327 putative active site [active] 295405006328 putative catalytic site [active] 295405006329 putative DNA binding site [nucleotide binding]; other site 295405006330 putative phosphate binding site [ion binding]; other site 295405006331 metal binding site A [ion binding]; metal-binding site 295405006332 putative AP binding site [nucleotide binding]; other site 295405006333 putative metal binding site B [ion binding]; other site 295405006334 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; cl15845 295405006335 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 295405006336 TSCPD domain; Region: TSCPD; cl14834 295405006337 hypothetical protein; Provisional; Region: PRK12378 295405006338 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 295405006339 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 295405006340 putative tRNA-binding site [nucleotide binding]; other site 295405006341 B3/4 domain; Region: B3_4; pfam03483 295405006342 tRNA synthetase B5 domain; Region: B5; smart00874 295405006343 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 295405006344 dimer interface [polypeptide binding]; other site 295405006345 motif 1; other site 295405006346 motif 3; other site 295405006347 motif 2; other site 295405006348 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 295405006349 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 295405006350 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 295405006351 Mg++ binding site [ion binding]; other site 295405006352 putative catalytic motif [active] 295405006353 putative substrate binding site [chemical binding]; other site 295405006354 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405006355 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405006356 NAD(P) binding site [chemical binding]; other site 295405006357 active site 295405006358 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 295405006359 putative glycosyl transferase; Provisional; Region: PRK10307 295405006360 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 295405006361 NADP binding site [chemical binding]; other site 295405006362 active site 295405006363 putative substrate binding site [chemical binding]; other site 295405006364 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 295405006365 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 295405006366 active site 295405006367 homodimer interface [polypeptide binding]; other site 295405006368 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 295405006369 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 295405006370 NAD(P) binding site [chemical binding]; other site 295405006371 homodimer interface [polypeptide binding]; other site 295405006372 substrate binding site [chemical binding]; other site 295405006373 active site 295405006374 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 295405006375 putative glycosyl transferase; Provisional; Region: PRK10073 295405006376 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 295405006377 active site 295405006378 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 295405006379 active site 295405006380 Alpha-1,2-fucosyltransferase; Region: Fut1_Fut2_like; cd11301 295405006381 Glycosyl transferase family 11; Region: Glyco_transf_11; pfam01531 295405006382 GDP-Fucose binding site [chemical binding]; other site 295405006383 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 295405006384 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 295405006385 active site 295405006386 Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP); Region: HEPD; cd08182 295405006387 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 295405006388 putative active site [active] 295405006389 metal binding site [ion binding]; metal-binding site 295405006390 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 295405006391 phosphonopyruvate decarboxylase; Region: Ppyr-DeCO2ase; TIGR03297 295405006392 PYR/PP interface [polypeptide binding]; other site 295405006393 dimer interface [polypeptide binding]; other site 295405006394 TPP binding site [chemical binding]; other site 295405006395 Thiamine pyrophosphate (TPP) family, PpyrDC subfamily, TPP-binding module; composed of proteins similar to phosphonopyruvate decarboxylase (PpyrDC) proteins. PpyrDC is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as...; Region: TPP_PpyrDC; cd03371 295405006396 TPP-binding site; other site 295405006397 cytidylyltransferase; Region: cytidylyltransferase; cd02170 295405006398 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 295405006399 active site 295405006400 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 295405006401 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 295405006402 tetramer interface [polypeptide binding]; other site 295405006403 active site 295405006404 Mg2+/Mn2+ binding site [ion binding]; other site 295405006405 LicD family; Region: LicD; pfam04991 295405006406 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 295405006407 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 295405006408 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 295405006409 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 295405006410 inhibitor-cofactor binding pocket; inhibition site 295405006411 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405006412 catalytic residue [active] 295405006413 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 295405006414 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 295405006415 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 295405006416 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 295405006417 substrate binding site; other site 295405006418 tetramer interface; other site 295405006419 UpxZ family of transcription anti-terminator antagonists; Region: UpxZ; pfam06603 295405006420 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 295405006421 Transcription antiterminator [Transcription]; Region: NusG; COG0250 295405006422 bifunctional fucokinase/L-fucose-1-P-guanylyltransferase; Provisional; Region: fkp; PRK13412 295405006423 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 295405006424 Domain of unknown function (DUF718); Region: DUF718; pfam05336 295405006425 replicative DNA helicase; Region: DnaB; TIGR00665 295405006426 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 295405006427 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 295405006428 Walker A motif; other site 295405006429 ATP binding site [chemical binding]; other site 295405006430 Walker B motif; other site 295405006431 DNA binding loops [nucleotide binding] 295405006432 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14609 295405006433 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 295405006434 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 295405006435 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 295405006436 NAD binding site [chemical binding]; other site 295405006437 homodimer interface [polypeptide binding]; other site 295405006438 active site 295405006439 substrate binding site [chemical binding]; other site 295405006440 electron transport complex, RnfABCDGE type, A subunit; Region: rnfA; TIGR01943 295405006441 electron transport complex RsxE subunit; Provisional; Region: PRK12405 295405006442 FMN-binding domain; Region: FMN_bind; cl01081 295405006443 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 295405006444 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 295405006445 SLBB domain; Region: SLBB; pfam10531 295405006446 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 295405006447 ferredoxin; Validated; Region: PRK07118 295405006448 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 295405006449 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 295405006450 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 295405006451 Protein of unknown function (DUF3078); Region: DUF3078; pfam11276 295405006452 CTP synthetase; Validated; Region: pyrG; PRK05380 295405006453 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 295405006454 Catalytic site [active] 295405006455 active site 295405006456 UTP binding site [chemical binding]; other site 295405006457 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 295405006458 active site 295405006459 putative oxyanion hole; other site 295405006460 catalytic triad [active] 295405006461 membrane protein insertase; Provisional; Region: PRK01318 295405006462 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 295405006463 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_7; cd13133 295405006464 putative efflux protein, MATE family; Region: matE; TIGR00797 295405006465 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 295405006466 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 295405006467 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 295405006468 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 295405006469 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 295405006470 PspC domain; Region: PspC; pfam04024 295405006471 Predicted transcriptional regulators [Transcription]; Region: COG1695 295405006472 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 295405006473 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 295405006474 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 295405006475 Coenzyme A binding pocket [chemical binding]; other site 295405006476 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 295405006477 putative substrate translocation pore; other site 295405006478 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 295405006479 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 295405006480 putative deacylase active site [active] 295405006481 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 295405006482 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 295405006483 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 295405006484 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 295405006485 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 295405006486 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 295405006487 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 295405006488 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 295405006489 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 295405006490 Domain of unknown function (DUF4293); Region: DUF4293; pfam14126 295405006491 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 295405006492 ACT domain-containing protein [General function prediction only]; Region: COG4747 295405006493 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains; Region: ACT_Bt0572_1; cd04908 295405006494 C-terminal ACT domain of a novel protein composed of just two ACT domains; Region: ACT_Bt0572_2; cd04882 295405006495 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 295405006496 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 295405006497 acyl-activating enzyme (AAE) consensus motif; other site 295405006498 AMP binding site [chemical binding]; other site 295405006499 active site 295405006500 CoA binding site [chemical binding]; other site 295405006501 excinuclease ABC subunit B; Provisional; Region: PRK05298 295405006502 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 295405006503 ATP binding site [chemical binding]; other site 295405006504 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 295405006505 nucleotide binding region [chemical binding]; other site 295405006506 ATP-binding site [chemical binding]; other site 295405006507 Ultra-violet resistance protein B; Region: UvrB; pfam12344 295405006508 UvrB/uvrC motif; Region: UVR; pfam02151 295405006509 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 295405006510 putative active site [active] 295405006511 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 295405006512 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 295405006513 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 295405006514 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 295405006515 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 295405006516 putative dimer interface [polypeptide binding]; other site 295405006517 PAS domain; Region: PAS_9; pfam13426 295405006518 PAS fold; Region: PAS_4; pfam08448 295405006519 PAS fold; Region: PAS_3; pfam08447 295405006520 PAS fold; Region: PAS_4; pfam08448 295405006521 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405006522 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 295405006523 dimer interface [polypeptide binding]; other site 295405006524 phosphorylation site [posttranslational modification] 295405006525 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 295405006526 ATP binding site [chemical binding]; other site 295405006527 Mg2+ binding site [ion binding]; other site 295405006528 G-X-G motif; other site 295405006529 Response regulator receiver domain; Region: Response_reg; pfam00072 295405006530 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 295405006531 active site 295405006532 phosphorylation site [posttranslational modification] 295405006533 intermolecular recognition site; other site 295405006534 dimerization interface [polypeptide binding]; other site 295405006535 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 295405006536 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 295405006537 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 295405006538 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 295405006539 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 295405006540 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 295405006541 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 295405006542 Walker A/P-loop; other site 295405006543 ATP binding site [chemical binding]; other site 295405006544 Q-loop/lid; other site 295405006545 ABC transporter signature motif; other site 295405006546 Walker B; other site 295405006547 D-loop; other site 295405006548 H-loop/switch region; other site 295405006549 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 295405006550 Walker A/P-loop; other site 295405006551 ATP binding site [chemical binding]; other site 295405006552 Q-loop/lid; other site 295405006553 ABC transporter signature motif; other site 295405006554 Walker B; other site 295405006555 D-loop; other site 295405006556 H-loop/switch region; other site 295405006557 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405006558 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405006559 Outer membrane efflux protein; Region: OEP; pfam02321 295405006560 Outer membrane efflux protein; Region: OEP; pfam02321 295405006561 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405006562 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405006563 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 295405006564 catalytic residues [active] 295405006565 carbamoyl-phosphate synthase, large subunit; Region: CPSaseII_lrg; TIGR01369 295405006566 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 295405006567 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 295405006568 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 295405006569 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 295405006570 ATP-grasp domain; Region: ATP-grasp_4; cl17255 295405006571 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 295405006572 probable substrate binding site [chemical binding]; other site 295405006573 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 295405006574 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 295405006575 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 295405006576 catalytic site [active] 295405006577 subunit interface [polypeptide binding]; other site 295405006578 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 295405006579 Glutamine amidotransferase domain; Region: GATase_6; pfam13522 295405006580 active site 295405006581 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 295405006582 active site 295405006583 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 295405006584 asparagine synthetase B; Provisional; Region: asnB; PRK09431 295405006585 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 295405006586 active site 295405006587 dimer interface [polypeptide binding]; other site 295405006588 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 295405006589 Ligand Binding Site [chemical binding]; other site 295405006590 Molecular Tunnel; other site 295405006591 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 295405006592 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 295405006593 active site 295405006594 catalytic site [active] 295405006595 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 295405006596 catalytic motif [active] 295405006597 Catalytic residue [active] 295405006598 Aspartyl protease; Region: Asp_protease_2; pfam13650 295405006599 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 295405006600 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 295405006601 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 295405006602 L,L-diaminopimelate aminotransferase; Validated; Region: PRK07590 295405006603 Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a...; Region: Mth938-like; cl00182 295405006604 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 295405006605 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405006606 homodimer interface [polypeptide binding]; other site 295405006607 catalytic residue [active] 295405006608 Uncharacterized conserved protein [Function unknown]; Region: HdeD; COG3247 295405006609 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 295405006610 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 295405006611 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 295405006612 Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C1_like; cd09164 295405006613 domain interface [polypeptide binding]; other site 295405006614 active site 295405006615 catalytic site [active] 295405006616 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 295405006617 domain interface [polypeptide binding]; other site 295405006618 active site 295405006619 catalytic site [active] 295405006620 exopolyphosphatase; Region: exo_poly_only; TIGR03706 295405006621 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 295405006622 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 295405006623 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 295405006624 dimer interface [polypeptide binding]; other site 295405006625 active site 295405006626 metal binding site [ion binding]; metal-binding site 295405006627 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 295405006628 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 295405006629 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405006630 catalytic residue [active] 295405006631 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 295405006632 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 295405006633 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 295405006634 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 295405006635 Glutamine amidotransferase class-I; Region: GATase; pfam00117 295405006636 glutamine binding [chemical binding]; other site 295405006637 catalytic triad [active] 295405006638 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 295405006639 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 295405006640 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 295405006641 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 295405006642 active site 295405006643 ribulose/triose binding site [chemical binding]; other site 295405006644 phosphate binding site [ion binding]; other site 295405006645 substrate (anthranilate) binding pocket [chemical binding]; other site 295405006646 product (indole) binding pocket [chemical binding]; other site 295405006647 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 295405006648 active site 295405006649 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 295405006650 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 295405006651 substrate binding site [chemical binding]; other site 295405006652 active site 295405006653 catalytic residues [active] 295405006654 heterodimer interface [polypeptide binding]; other site 295405006655 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 295405006656 active site 295405006657 homodimer interface [polypeptide binding]; other site 295405006658 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 295405006659 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 295405006660 active site 295405006661 phosphorylation site [posttranslational modification] 295405006662 intermolecular recognition site; other site 295405006663 dimerization interface [polypeptide binding]; other site 295405006664 Bacterial sugar transferase; Region: Bac_transf; pfam02397 295405006665 Glycosyl transferase family group 2; Region: Glyco_trans_2_3; pfam13632 295405006666 putative lipopolysaccharide biosynthesis O-acetyl transferase WbbJ; Provisional; Region: PRK09677 295405006667 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 295405006668 trimer interface [polypeptide binding]; other site 295405006669 active site 295405006670 substrate binding site [chemical binding]; other site 295405006671 CoA binding site [chemical binding]; other site 295405006672 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 295405006673 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 295405006674 DNA binding residues [nucleotide binding] 295405006675 dimerization interface [polypeptide binding]; other site 295405006676 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 295405006677 AICAR transformylase/IMP cyclohydrolase PurH (only IMP cyclohydrolase domain in Aful) [Nucleotide transport and metabolism]; Region: PurH; COG0138 295405006678 5-aminoimidazole-4-carboxamide ribonucleotide transformylase; Provisional; Region: PRK07106 295405006679 flavodoxin FldA; Validated; Region: PRK09267 295405006680 Protein of unknown function (DUF2023); Region: DUF2023; pfam09633 295405006681 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 295405006682 TQO small subunit DoxD; Region: DoxD; pfam04173 295405006683 TQO small subunit DoxA; Region: DoxA; pfam07680 295405006684 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 295405006685 catalytic residues [active] 295405006686 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 295405006687 The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases; Region: URO-D_CIMS_like; cl00464 295405006688 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405006689 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405006690 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 295405006691 N-terminal plug; other site 295405006692 ligand-binding site [chemical binding]; other site 295405006693 Predicted membrane protein [Function unknown]; Region: COG2311 295405006694 Protein of unknown function (DUF418); Region: DUF418; pfam04235 295405006695 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 295405006696 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 295405006697 putative substrate translocation pore; other site 295405006698 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 295405006699 carboxyltransferase (CT) interaction site; other site 295405006700 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405006701 putative transporter; Validated; Region: PRK03818 295405006702 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 295405006703 TrkA-C domain; Region: TrkA_C; pfam02080 295405006704 TrkA-C domain; Region: TrkA_C; pfam02080 295405006705 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 295405006706 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 295405006707 MAC/Perforin domain; Region: MACPF; cl02616 295405006708 Lipocalin-like domain; Region: Lipocalin_6; pfam13944 295405006709 Bacterial proteins similar to Porphyromonas gingivalis HmuY; Region: HmuY; cd12105 295405006710 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405006711 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 295405006712 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 295405006713 N-terminal plug; other site 295405006714 ligand-binding site [chemical binding]; other site 295405006715 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 295405006716 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 295405006717 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 295405006718 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 295405006719 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 295405006720 Uncharacterized conserved protein (DUF2149); Region: DUF2149; pfam09919 295405006721 ribonucleotide-diphosphate reductase subunit alpha; Provisional; Region: PRK12364 295405006722 ATP cone domain; Region: ATP-cone; pfam03477 295405006723 Class I ribonucleotide reductase; Region: RNR_I; cd01679 295405006724 active site 295405006725 dimer interface [polypeptide binding]; other site 295405006726 catalytic residues [active] 295405006727 effector binding site; other site 295405006728 R2 peptide binding site; other site 295405006729 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 295405006730 dimer interface [polypeptide binding]; other site 295405006731 putative radical transfer pathway; other site 295405006732 diiron center [ion binding]; other site 295405006733 tyrosyl radical; other site 295405006734 Uncharacterized conserved protein [Function unknown]; Region: COG2966 295405006735 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 295405006736 Protein of unknown function (DUF3815); Region: DUF3815; pfam12821 295405006737 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]; Region: Eda; COG0800 295405006738 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 295405006739 active site 295405006740 intersubunit interface [polypeptide binding]; other site 295405006741 catalytic residue [active] 295405006742 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 295405006743 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 295405006744 substrate binding site [chemical binding]; other site 295405006745 ATP binding site [chemical binding]; other site 295405006746 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 295405006747 DNA binding site [nucleotide binding] 295405006748 domain linker motif; other site 295405006749 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 295405006750 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 295405006751 ligand binding site [chemical binding]; other site 295405006752 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 295405006753 Coenzyme A binding pocket [chemical binding]; other site 295405006754 Predicted transcriptional regulators [Transcription]; Region: COG1733 295405006755 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 295405006756 PAS domain S-box; Region: sensory_box; TIGR00229 295405006757 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405006758 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 295405006759 dimer interface [polypeptide binding]; other site 295405006760 phosphorylation site [posttranslational modification] 295405006761 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 295405006762 ATP binding site [chemical binding]; other site 295405006763 Mg2+ binding site [ion binding]; other site 295405006764 G-X-G motif; other site 295405006765 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 295405006766 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 295405006767 active site 295405006768 phosphorylation site [posttranslational modification] 295405006769 intermolecular recognition site; other site 295405006770 dimerization interface [polypeptide binding]; other site 295405006771 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 295405006772 Zn2+ binding site [ion binding]; other site 295405006773 Mg2+ binding site [ion binding]; other site 295405006774 AAA domain; Region: AAA_33; pfam13671 295405006775 RNA ligase; Region: RNA_ligase; pfam09414 295405006776 putative peptide chain release factor H; Region: release_prfH; TIGR03072 295405006777 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 295405006778 hypothetical protein; Reviewed; Region: PRK09588 295405006779 Uncharacterized protein family UPF0027; Region: UPF0027; pfam01139 295405006780 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 295405006781 DNA-binding HTH domain-containing proteins [Transcription]; Region: CsgD; COG2771 295405006782 The C-terminal domain of uncharacterized bacterial proteins; Region: Bvu_2165_C_like; cd12843 295405006783 30S ribosomal protein S16; Provisional; Region: rpsP; PRK14521 295405006784 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 295405006785 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 295405006786 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 295405006787 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 295405006788 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 295405006789 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 295405006790 dimer interface [polypeptide binding]; other site 295405006791 conserved gate region; other site 295405006792 putative PBP binding loops; other site 295405006793 ABC-ATPase subunit interface; other site 295405006794 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 295405006795 dimer interface [polypeptide binding]; other site 295405006796 conserved gate region; other site 295405006797 putative PBP binding loops; other site 295405006798 ABC-ATPase subunit interface; other site 295405006799 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 295405006800 ATP-binding cassette domain of the polyamine transporter; Region: ABC_PotA_N; cd03300 295405006801 Walker A/P-loop; other site 295405006802 ATP binding site [chemical binding]; other site 295405006803 Q-loop/lid; other site 295405006804 ABC transporter signature motif; other site 295405006805 Walker B; other site 295405006806 D-loop; other site 295405006807 H-loop/switch region; other site 295405006808 TOBE domain; Region: TOBE_2; pfam08402 295405006809 TOBE domain; Region: TOBE_2; pfam08402 295405006810 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 295405006811 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 295405006812 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405006813 catalytic residues [active] 295405006814 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 295405006815 putative homodimer interface [polypeptide binding]; other site 295405006816 putative active site pocket [active] 295405006817 alpha-glucan phosphorylases; Region: more_P_ylases; TIGR02094 295405006818 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 295405006819 Glycogen synthase; Region: Glycogen_syn; pfam05693 295405006820 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 295405006821 V-type ATP synthase subunit K; Validated; Region: PRK08344 295405006822 ATP synthase subunit C; Region: ATP-synt_C; pfam00137 295405006823 V-type ATP synthase subunit I; Validated; Region: PRK05771 295405006824 V-type ATP synthase subunit D; Provisional; Region: PRK02195 295405006825 V-type ATP synthase subunit B; Provisional; Region: PRK02118 295405006826 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 295405006827 V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_B; cd01135 295405006828 Walker A motif homologous position; other site 295405006829 Walker B motif; other site 295405006830 V-type ATP synthase subunit A; Provisional; Region: PRK04192 295405006831 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 295405006832 V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_A; cd01134 295405006833 Walker A motif/ATP binding site; other site 295405006834 Walker B motif; other site 295405006835 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 295405006836 Protein of unknown function (DUF2764); Region: DUF2764; pfam10962 295405006837 V-type ATP synthase subunit E; Provisional; Region: PRK01558 295405006838 Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion]; Region: NtpE; COG1390 295405006839 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 295405006840 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 295405006841 active site 295405006842 dimer interface [polypeptide binding]; other site 295405006843 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 295405006844 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 295405006845 active site 295405006846 phosphorylation site [posttranslational modification] 295405006847 intermolecular recognition site; other site 295405006848 dimerization interface [polypeptide binding]; other site 295405006849 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 295405006850 DNA binding site [nucleotide binding] 295405006851 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405006852 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 295405006853 dimer interface [polypeptide binding]; other site 295405006854 phosphorylation site [posttranslational modification] 295405006855 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 295405006856 ATP binding site [chemical binding]; other site 295405006857 Mg2+ binding site [ion binding]; other site 295405006858 G-X-G motif; other site 295405006859 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405006860 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405006861 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405006862 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405006863 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405006864 Clostripain family; Region: Peptidase_C11; pfam03415 295405006865 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 295405006866 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 295405006867 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405006868 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 295405006869 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 295405006870 DNA binding residues [nucleotide binding] 295405006871 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 295405006872 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 295405006873 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 295405006874 protein binding site [polypeptide binding]; other site 295405006875 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 295405006876 protein binding site [polypeptide binding]; other site 295405006877 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 295405006878 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 295405006879 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 295405006880 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of...; Region: L-Ala-DL-Glu_epimerase; cd03319 295405006881 active site 295405006882 Bacterial SH3 domain; Region: SH3_4; pfam06347 295405006883 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 295405006884 NlpC/P60 family; Region: NLPC_P60; pfam00877 295405006885 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 295405006886 Nitroreductase-like family 3. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_3; cd02139 295405006887 putative FMN binding site [chemical binding]; other site 295405006888 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 295405006889 Lumazine binding domain; Region: Lum_binding; pfam00677 295405006890 Lumazine binding domain; Region: Lum_binding; pfam00677 295405006891 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 295405006892 PhoU domain; Region: PhoU; pfam01895 295405006893 PhoU domain; Region: PhoU; pfam01895 295405006894 phosphate ABC transporter ATP-binding protein; Provisional; Region: PRK14245 295405006895 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 295405006896 Walker A/P-loop; other site 295405006897 ATP binding site [chemical binding]; other site 295405006898 Q-loop/lid; other site 295405006899 ABC transporter signature motif; other site 295405006900 Walker B; other site 295405006901 D-loop; other site 295405006902 H-loop/switch region; other site 295405006903 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 295405006904 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 295405006905 dimer interface [polypeptide binding]; other site 295405006906 conserved gate region; other site 295405006907 putative PBP binding loops; other site 295405006908 ABC-ATPase subunit interface; other site 295405006909 PBP superfamily domain; Region: PBP_like_2; cl17296 295405006910 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 295405006911 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 295405006912 dimer interface [polypeptide binding]; other site 295405006913 conserved gate region; other site 295405006914 putative PBP binding loops; other site 295405006915 ABC-ATPase subunit interface; other site 295405006916 PBP superfamily domain; Region: PBP_like_2; cl17296 295405006917 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 295405006918 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 295405006919 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 295405006920 active site 295405006921 HIGH motif; other site 295405006922 nucleotide binding site [chemical binding]; other site 295405006923 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 295405006924 active site 295405006925 KMSKS motif; other site 295405006926 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 295405006927 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 295405006928 binding surface 295405006929 TPR motif; other site 295405006930 TPR repeat; Region: TPR_11; pfam13414 295405006931 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 295405006932 binding surface 295405006933 TPR motif; other site 295405006934 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405006935 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 295405006936 binding surface 295405006937 TPR motif; other site 295405006938 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 295405006939 binding surface 295405006940 TPR motif; other site 295405006941 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 295405006942 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 295405006943 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 295405006944 dimer interface [polypeptide binding]; other site 295405006945 catalytic triad [active] 295405006946 peroxidatic and resolving cysteines [active] 295405006947 Short repeat of unknown function (DUF308); Region: DUF308; cl15828 295405006948 multiple promoter invertase; Provisional; Region: mpi; PRK13413 295405006949 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 295405006950 catalytic residues [active] 295405006951 catalytic nucleophile [active] 295405006952 Presynaptic Site I dimer interface [polypeptide binding]; other site 295405006953 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 295405006954 Synaptic Flat tetramer interface [polypeptide binding]; other site 295405006955 Synaptic Site I dimer interface [polypeptide binding]; other site 295405006956 DNA binding site [nucleotide binding] 295405006957 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl17393 295405006958 DNA-binding interface [nucleotide binding]; DNA binding site 295405006959 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 295405006960 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 295405006961 active site 295405006962 DNA binding site [nucleotide binding] 295405006963 Int/Topo IB signature motif; other site 295405006964 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 295405006965 Bacterial sugar transferase; Region: Bac_transf; pfam02397 295405006966 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 295405006967 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 295405006968 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 295405006969 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 295405006970 capsular exopolysaccharide family; Region: eps_fam; TIGR01007 295405006971 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 295405006972 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 295405006973 amidase catalytic site [active] 295405006974 Zn binding residues [ion binding]; other site 295405006975 substrate binding site [chemical binding]; other site 295405006976 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 295405006977 Domain of unknown function (DUF4248); Region: DUF4248; pfam14053 295405006978 VirE N-terminal domain; Region: VirE_N; pfam08800 295405006979 Primase C terminal 1 (PriCT-1); Region: PriCT_1; smart00942 295405006980 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 295405006981 transcriptional activator RfaH; Region: RfaH; TIGR01955 295405006982 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 295405006983 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 295405006984 heterodimer interface [polypeptide binding]; other site 295405006985 homodimer interface [polypeptide binding]; other site 295405006986 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 295405006987 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 295405006988 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 295405006989 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 295405006990 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 295405006991 active site 295405006992 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 295405006993 Acyltransferase family; Region: Acyl_transf_3; pfam01757 295405006994 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405006995 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 295405006996 putative acyl transferase; Provisional; Region: PRK10191 295405006997 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 295405006998 trimer interface [polypeptide binding]; other site 295405006999 active site 295405007000 substrate binding site [chemical binding]; other site 295405007001 CoA binding site [chemical binding]; other site 295405007002 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 295405007003 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 295405007004 active site 295405007005 GDP-fucose protein O-fucosyltransferase and related proteins; Region: O-FucT_like; cl16914 295405007006 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 295405007007 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 295405007008 active site 295405007009 DNA binding site [nucleotide binding] 295405007010 Int/Topo IB signature motif; other site 295405007011 Helix-turn-helix domain; Region: HTH_17; pfam12728 295405007012 AAA domain; Region: AAA_25; pfam13481 295405007013 CHC2 zinc finger; Region: zf-CHC2; cl17510 295405007014 Toprim-like; Region: Toprim_2; pfam13155 295405007015 Domain of unknown function (DUF4134); Region: DUF4134; pfam13572 295405007016 Domain of unknown function (DUF4134); Region: DUF4134; pfam13572 295405007017 Bacteroides conjugation system ATPase, TraG family; Region: Bac_Flav_CT_G; TIGR03783 295405007018 AAA-like domain; Region: AAA_10; pfam12846 295405007019 Autophagy protein 16 (ATG16); Region: ATG16; pfam08614 295405007020 TATA element modulatory factor 1 DNA binding; Region: TMF_DNA_bd; pfam12329 295405007021 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 295405007022 DNA methylase; Region: N6_N4_Mtase; pfam01555 295405007023 Bacteroides conjugative transposon TraK protein; Region: Bac_Flav_CT_K; TIGR03781 295405007024 DNA N-6-adenine-methyltransferase (Dam); Region: Dam; cl05442 295405007025 Bacteroides conjugative transposon TraM protein; Region: Bac_Flav_CT_M; TIGR03779 295405007026 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 295405007027 Bacteroides conjugative transposon TraN protein; Region: Bac_Flav_CT_N; TIGR03780 295405007028 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 295405007029 hypothetical protein; Provisional; Region: PRK07758 295405007030 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 295405007031 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 295405007032 Walker B motif; other site 295405007033 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3666 295405007034 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 295405007035 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 295405007036 ParB-like nuclease domain; Region: ParBc; pfam02195 295405007037 Archaeal ATPase; Region: Arch_ATPase; pfam01637 295405007038 AAA domain; Region: AAA_14; pfam13173 295405007039 Archaea bacterial proteins of unknown function; Region: DUF234; pfam03008 295405007040 hypothetical protein; Region: PHA01623 295405007041 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 295405007042 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 295405007043 P-loop; other site 295405007044 Magnesium ion binding site [ion binding]; other site 295405007045 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 295405007046 Magnesium ion binding site [ion binding]; other site 295405007047 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 295405007048 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 295405007049 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 295405007050 dimer interface [polypeptide binding]; other site 295405007051 ssDNA binding site [nucleotide binding]; other site 295405007052 tetramer (dimer of dimers) interface [polypeptide binding]; other site 295405007053 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 295405007054 Protein of unknown function (DUF877); Region: DUF877; pfam05943 295405007055 Gene 25-like lysozyme; Region: GPW_gp25; pfam04965 295405007056 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 295405007057 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 295405007058 Walker A motif; other site 295405007059 ATP binding site [chemical binding]; other site 295405007060 Walker B motif; other site 295405007061 arginine finger; other site 295405007062 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 295405007063 Walker A motif; other site 295405007064 ATP binding site [chemical binding]; other site 295405007065 Walker B motif; other site 295405007066 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 295405007067 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cl17457 295405007068 PKD domain; Region: PKD; pfam00801 295405007069 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 295405007070 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 295405007071 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 295405007072 RHS Repeat; Region: RHS_repeat; pfam05593 295405007073 YD repeat (two copies); Region: YD_repeat_2x; TIGR01643 295405007074 RHS Repeat; Region: RHS_repeat; pfam05593 295405007075 RHS Repeat; Region: RHS_repeat; cl11982 295405007076 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 295405007077 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 295405007078 RHS Repeat; Region: RHS_repeat; pfam05593 295405007079 YD repeat (two copies); Region: YD_repeat_2x; TIGR01643 295405007080 RHS Repeat; Region: RHS_repeat; pfam05593 295405007081 RHS Repeat; Region: RHS_repeat; pfam05593 295405007082 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 295405007083 Domain of unknown function (DUF4284); Region: DUF4284; pfam14112 295405007084 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 295405007085 RHS Repeat; Region: RHS_repeat; pfam05593 295405007086 YD repeat (two copies); Region: YD_repeat_2x; TIGR01643 295405007087 RHS Repeat; Region: RHS_repeat; pfam05593 295405007088 RHS Repeat; Region: RHS_repeat; pfam05593 295405007089 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 295405007090 A nuclease family of the HNH/ENDO VII superfamily with conserved AHH; Region: AHH; pfam14412 295405007091 This domain contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterised; Region: FRG; smart00901 295405007092 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 295405007093 Methyltransferase domain; Region: Methyltransf_26; pfam13659 295405007094 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 295405007095 DEAD-like helicases superfamily; Region: DEXDc; smart00487 295405007096 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 295405007097 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 295405007098 helicase superfamily c-terminal domain; Region: HELICc; smart00490 295405007099 nucleotide binding region [chemical binding]; other site 295405007100 ATP-binding site [chemical binding]; other site 295405007101 Protein of unknown function (DUF4065); Region: DUF4065; pfam13274 295405007102 RibD C-terminal domain; Region: RibD_C; cl17279 295405007103 Protein of unknown function (DUF1273); Region: DUF1273; cl01859 295405007104 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cl00309 295405007105 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cl00309 295405007106 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 295405007107 Peptidase family M23; Region: Peptidase_M23; pfam01551 295405007108 Protein of unknown function (DUF4099); Region: DUF4099; pfam13351 295405007109 Protein of unknown function (DUF3945); Region: DUF3945; pfam13101 295405007110 Protein of unknown function (DUF3991); Region: DUF3991; pfam13154 295405007111 Toprim-like; Region: Toprim_2; pfam13155 295405007112 Bacterial PH domain; Region: DUF304; pfam03703 295405007113 Herpesvirus Glycoprotein B; Region: Glycoprotein_B; pfam00606 295405007114 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 295405007115 Peptidase family M23; Region: Peptidase_M23; pfam01551 295405007116 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 295405007117 MutS domain I; Region: MutS_I; pfam01624 295405007118 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 295405007119 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 295405007120 Peptidase family M23; Region: Peptidase_M23; pfam01551 295405007121 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 295405007122 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 295405007123 OmpA family; Region: OmpA; pfam00691 295405007124 ligand binding site [chemical binding]; other site 295405007125 Plasmid recombination enzyme; Region: Mob_Pre; pfam01076 295405007126 Resolvase, N terminal domain; Region: Resolvase; smart00857 295405007127 catalytic residues [active] 295405007128 catalytic nucleophile [active] 295405007129 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 295405007130 Domain of unknown function (DUF4313); Region: DUF4313; pfam14190 295405007131 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 295405007132 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 295405007133 dimer interface [polypeptide binding]; other site 295405007134 ssDNA binding site [nucleotide binding]; other site 295405007135 tetramer (dimer of dimers) interface [polypeptide binding]; other site 295405007136 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 295405007137 GDP-fucose protein O-fucosyltransferase and related proteins; Region: O-FucT_like; cl16914 295405007138 GDP-Fucose binding site [chemical binding]; other site 295405007139 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 295405007140 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405007141 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405007142 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 295405007143 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405007144 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 295405007145 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 295405007146 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 295405007147 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 295405007148 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 295405007149 gliding motility-associated protein GldL; Region: GldL_gliding; TIGR03513 295405007150 gliding motility-associated protein GldM; Region: GldM_gliding; TIGR03517 295405007151 GldM N-terminal domain; Region: GldM_N; pfam12081 295405007152 GldM C-terminal domain; Region: GldM_C; pfam12080 295405007153 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 295405007154 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 295405007155 ligand binding site [chemical binding]; other site 295405007156 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 295405007157 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 295405007158 Substrate binding site; other site 295405007159 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit [Energy production and conversion]; Region: OadB; COG1883 295405007160 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]; Region: COG5016 295405007161 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 295405007162 active site 295405007163 catalytic residues [active] 295405007164 metal binding site [ion binding]; metal-binding site 295405007165 Biotin carboxyl carrier protein [Lipid metabolism]; Region: AccB; COG0511 295405007166 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 295405007167 carboxyltransferase (CT) interaction site; other site 295405007168 biotinylation site [posttranslational modification]; other site 295405007169 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; pfam04277 295405007170 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 295405007171 Escherichia coli UshA-like family, N-terminal metallophosphatase domain; Region: MPP_UshA_N_like; cd00845 295405007172 active site 295405007173 metal binding site [ion binding]; metal-binding site 295405007174 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 295405007175 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cl01287 295405007176 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 295405007177 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 295405007178 ATP binding site [chemical binding]; other site 295405007179 putative Mg++ binding site [ion binding]; other site 295405007180 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; cl17351 295405007181 nucleotide binding region [chemical binding]; other site 295405007182 ATP-binding site [chemical binding]; other site 295405007183 C-terminal putative phospholipase D-like domain of uncharacterized prokaryotic HKD family nucleases fused to DEAD/DEAH box helicases; Region: PLDc_C_DEXD_like; cd09126 295405007184 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 295405007185 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 295405007186 non-specific DNA binding site [nucleotide binding]; other site 295405007187 salt bridge; other site 295405007188 sequence-specific DNA binding site [nucleotide binding]; other site 295405007189 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 295405007190 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 295405007191 catalytic residue [active] 295405007192 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK07565 295405007193 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 295405007194 phosphate binding site [ion binding]; other site 295405007195 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 295405007196 Protein of unknown function (DUF3380); Region: DUF3380; pfam11860 295405007197 Protein of unknown function (DUF2589); Region: DUF2589; pfam11655 295405007198 Protein of unknown function (DUF2589); Region: DUF2589; pfam11655 295405007199 LytTr DNA-binding domain; Region: LytTR; smart00850 295405007200 Domain of unknown function, B. Theta Gene description (DUF3876); Region: DUF3876; pfam12992 295405007201 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 295405007202 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 295405007203 acyl-activating enzyme (AAE) consensus motif; other site 295405007204 AMP binding site [chemical binding]; other site 295405007205 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 295405007206 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405007207 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 295405007208 N-terminal plug; other site 295405007209 ligand-binding site [chemical binding]; other site 295405007210 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405007211 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 295405007212 dimer interface [polypeptide binding]; other site 295405007213 phosphorylation site [posttranslational modification] 295405007214 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 295405007215 ATP binding site [chemical binding]; other site 295405007216 Mg2+ binding site [ion binding]; other site 295405007217 G-X-G motif; other site 295405007218 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 295405007219 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405007220 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 295405007221 ATP binding site [chemical binding]; other site 295405007222 G-X-G motif; other site 295405007223 FOG: WD40 repeat [General function prediction only]; Region: COG2319 295405007224 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 295405007225 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 295405007226 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 295405007227 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 295405007228 anti sigma factor interaction site; other site 295405007229 regulatory phosphorylation site [posttranslational modification]; other site 295405007230 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 295405007231 active site 295405007232 phosphorylation site [posttranslational modification] 295405007233 intermolecular recognition site; other site 295405007234 dimerization interface [polypeptide binding]; other site 295405007235 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 295405007236 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 295405007237 [FeFe] hydrogenase, group B1/B3; Region: FeFe_hydrog_B1; TIGR04105 295405007238 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 295405007239 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 295405007240 NAD(P) binding site [chemical binding]; other site 295405007241 homodimer interface [polypeptide binding]; other site 295405007242 substrate binding site [chemical binding]; other site 295405007243 active site 295405007244 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 295405007245 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 295405007246 putative active site [active] 295405007247 PhoH-like protein; Region: PhoH; pfam02562 295405007248 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 295405007249 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 295405007250 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 295405007251 homotrimer interaction site [polypeptide binding]; other site 295405007252 putative active site [active] 295405007253 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 295405007254 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 295405007255 TPR motif; other site 295405007256 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405007257 binding surface 295405007258 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 295405007259 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 295405007260 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 295405007261 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 295405007262 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 295405007263 Walker A/P-loop; other site 295405007264 ATP binding site [chemical binding]; other site 295405007265 Q-loop/lid; other site 295405007266 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 295405007267 ABC transporter signature motif; other site 295405007268 Walker B; other site 295405007269 D-loop; other site 295405007270 H-loop/switch region; other site 295405007271 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 295405007272 Flavoprotein; Region: Flavoprotein; pfam02441 295405007273 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 295405007274 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 295405007275 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 295405007276 active site 295405007277 catalytic site [active] 295405007278 substrate binding site [chemical binding]; other site 295405007279 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 295405007280 DNA polymerase III subunit beta; Validated; Region: PRK05643 295405007281 putative DNA binding surface [nucleotide binding]; other site 295405007282 dimer interface [polypeptide binding]; other site 295405007283 beta-clamp/translesion DNA polymerase binding surface; other site 295405007284 beta-clamp/clamp loader binding surface; other site 295405007285 Domain of unknown function (DUF3127); Region: DUF3127; pfam11325 295405007286 putative hydrolase; Provisional; Region: PRK02113 295405007287 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 295405007288 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 295405007289 FAD binding domain; Region: FAD_binding_4; pfam01565 295405007290 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 295405007291 Domain of unknown function (DUF4348); Region: DUF4348; pfam14254 295405007292 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405007293 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405007294 NAD(P) binding site [chemical binding]; other site 295405007295 active site 295405007296 2-amino-3-ketobutyrate coenzyme A ligase; Provisional; Region: PRK06939 295405007297 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 295405007298 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 295405007299 catalytic residue [active] 295405007300 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 295405007301 Tandemly repeated domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like; cd13119 295405007302 Tandemly repeated domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like; cd13119 295405007303 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405007304 Major fimbrial subunit protein (FimA); Region: P_gingi_FimA; pfam06321 295405007305 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405007306 Domain of unknown function, B. Theta Gene description (DUF3868); Region: DUF3868; pfam12984 295405007307 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 295405007308 ligand binding site [chemical binding]; other site 295405007309 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 295405007310 Transcriptional regulator; Region: Rrf2; cl17282 295405007311 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 295405007312 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 295405007313 Int/Topo IB signature motif; other site 295405007314 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 295405007315 Int/Topo IB signature motif; other site 295405007316 Type II restriction enzyme, methylase subunits [Defense mechanisms]; Region: COG1002 295405007317 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 295405007318 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 295405007319 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 295405007320 multiple promoter invertase; Provisional; Region: mpi; PRK13413 295405007321 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 295405007322 catalytic residues [active] 295405007323 catalytic nucleophile [active] 295405007324 Presynaptic Site I dimer interface [polypeptide binding]; other site 295405007325 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 295405007326 Synaptic Flat tetramer interface [polypeptide binding]; other site 295405007327 Synaptic Site I dimer interface [polypeptide binding]; other site 295405007328 DNA binding site [nucleotide binding] 295405007329 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl17393 295405007330 Transposase; Region: DEDD_Tnp_IS110; pfam01548 295405007331 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 295405007332 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 295405007333 Transposase; Region: DEDD_Tnp_IS110; pfam01548 295405007334 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 295405007335 Putative amidoligase enzyme; Region: Amidoligase_2; pfam12224 295405007336 AAA domain; Region: AAA_31; pfam13614 295405007337 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 295405007338 P-loop; other site 295405007339 Magnesium ion binding site [ion binding]; other site 295405007340 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 295405007341 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 295405007342 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 295405007343 Predicted metal-binding protein (DUF2284); Region: DUF2284; pfam10050 295405007344 ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CeuD; COG4604 295405007345 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 295405007346 Walker A/P-loop; other site 295405007347 ATP binding site [chemical binding]; other site 295405007348 Q-loop/lid; other site 295405007349 ABC transporter signature motif; other site 295405007350 Walker B; other site 295405007351 D-loop; other site 295405007352 H-loop/switch region; other site 295405007353 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 295405007354 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 295405007355 ABC-ATPase subunit interface; other site 295405007356 dimer interface [polypeptide binding]; other site 295405007357 putative PBP binding regions; other site 295405007358 Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_d; cd01141 295405007359 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 295405007360 putative ligand binding site [chemical binding]; other site 295405007361 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 295405007362 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 295405007363 Uncharacterized conserved protein [Function unknown]; Region: COG3391 295405007364 Putative glycoside hydrolase xylanase; Region: Xylanase; pfam13201 295405007365 Receptor L domain; Region: Recep_L_domain; pfam01030 295405007366 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 295405007367 active site 295405007368 Int/Topo IB signature motif; other site 295405007369 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 295405007370 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 295405007371 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 295405007372 active site 295405007373 catalytic residues [active] 295405007374 Int/Topo IB signature motif; other site 295405007375 DNA binding site [nucleotide binding] 295405007376 Protein of unknown function (DUF3990); Region: DUF3990; pfam13151 295405007377 Protein of unknown function (DUF3791); Region: DUF3791; pfam12668 295405007378 HicB family; Region: HicB; pfam05534 295405007379 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 295405007380 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 295405007381 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 295405007382 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 295405007383 Ferritin-like domain; Region: Ferritin; pfam00210 295405007384 ferroxidase diiron center [ion binding]; other site 295405007385 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 295405007386 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 295405007387 active site 295405007388 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 295405007389 substrate binding site [chemical binding]; other site 295405007390 catalytic residues [active] 295405007391 dimer interface [polypeptide binding]; other site 295405007392 aspartate kinase III; Validated; Region: PRK09084 295405007393 AAK_AK-HSDH-like: Amino Acid Kinase Superfamily (AAK), AK-HSDH-like; this family includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK- homoserine dehydrogenase (HSDH). These aspartokinases are found in such...; Region: AAK_AK-HSDH-like; cd04243 295405007394 putative catalytic residues [active] 295405007395 nucleotide binding site [chemical binding]; other site 295405007396 aspartate binding site [chemical binding]; other site 295405007397 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC-like_1; cd04912 295405007398 dimer interface [polypeptide binding]; other site 295405007399 allosteric regulatory binding pocket; other site 295405007400 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 295405007401 dimer interface [polypeptide binding]; other site 295405007402 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 295405007403 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405007404 Walker A/P-loop; other site 295405007405 ATP binding site [chemical binding]; other site 295405007406 Q-loop/lid; other site 295405007407 ABC transporter signature motif; other site 295405007408 Walker B; other site 295405007409 D-loop; other site 295405007410 H-loop/switch region; other site 295405007411 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 295405007412 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]; Region: HisI; COG0139 295405007413 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 295405007414 metal binding site [ion binding]; metal-binding site 295405007415 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 295405007416 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 295405007417 substrate binding site [chemical binding]; other site 295405007418 glutamase interaction surface [polypeptide binding]; other site 295405007419 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 295405007420 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 295405007421 catalytic residues [active] 295405007422 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13181 295405007423 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 295405007424 putative active site [active] 295405007425 oxyanion strand; other site 295405007426 catalytic triad [active] 295405007427 Uncharacterized conserved protein [Function unknown]; Region: COG1479 295405007428 Protein of unknown function DUF262; Region: DUF262; pfam03235 295405007429 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 295405007430 Uncharacterized conserved protein [Function unknown]; Region: COG3586 295405007431 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 295405007432 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405007433 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 295405007434 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 295405007435 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405007436 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405007437 Glycoside hydrolase family 44; Region: Glyco_hydro_44; pfam12891 295405007438 Right handed beta helix region; Region: Beta_helix; pfam13229 295405007439 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 295405007440 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 295405007441 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 295405007442 The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four...; Region: URO-D_like; cd03465 295405007443 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 295405007444 B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or...; Region: corrinoid_protein_B12-BD; cd02070 295405007445 methyltransferase cognate corrinoid proteins, Methanosarcina family; Region: pyl_corrinoid; TIGR02370 295405007446 B12 binding site [chemical binding]; other site 295405007447 cobalt ligand [ion binding]; other site 295405007448 The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases; Region: URO-D_CIMS_like; cl00464 295405007449 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 295405007450 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 295405007451 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 295405007452 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405007453 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405007454 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405007455 SusD family; Region: SusD; pfam07980 295405007456 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405007457 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405007458 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405007459 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 295405007460 FecR protein; Region: FecR; pfam04773 295405007461 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405007462 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405007463 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 295405007464 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_3; cd03140 295405007465 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 295405007466 conserved cys residue [active] 295405007467 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 295405007468 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 295405007469 active site 295405007470 8-oxo-dGMP binding site [chemical binding]; other site 295405007471 nudix motif; other site 295405007472 metal binding site [ion binding]; metal-binding site 295405007473 Protein of unknown function (DUF3276); Region: DUF3276; pfam11680 295405007474 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 295405007475 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 295405007476 S-adenosylmethionine binding site [chemical binding]; other site 295405007477 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 295405007478 active site 295405007479 Low molecular weight phosphatase family; Region: LMWPc; cl00105 295405007480 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 295405007481 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 295405007482 EamA-like transporter family; Region: EamA; pfam00892 295405007483 hypothetical protein; Provisional; Region: PRK10410 295405007484 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 295405007485 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 295405007486 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405007487 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405007488 putative transporter; Provisional; Region: PRK11043 295405007489 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 295405007490 putative substrate translocation pore; other site 295405007491 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 295405007492 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405007493 NAD(P) binding site [chemical binding]; other site 295405007494 active site 295405007495 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405007496 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405007497 GyrI-like small molecule binding domain; Region: GyrI-like; pfam06445 295405007498 Putative zinc ribbon domain; Region: Zn_ribbon_2; pfam12674 295405007499 Predicted acetyltransferase [General function prediction only]; Region: COG2388 295405007500 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405007501 TIGR01777 family protein; Region: yfcH 295405007502 NAD(P) binding site [chemical binding]; other site 295405007503 active site 295405007504 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 295405007505 YegX is an uncharacterized bacterial protein with a glycosyl hydrolase family 25 (GH25) catalytic domain that is similar in sequence to the CH-type (Chalaropsis-type) lysozymes of the GH25 family of endolysins; Region: GH25_YegX-like; cd06524 295405007506 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 295405007507 active site 295405007508 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 295405007509 Asp-box motif; other site 295405007510 diphosphate--fructose-6-phosphate 1-phosphotransferase; Provisional; Region: PRK07085 295405007511 pyrophosphate-dependent phosphofructokinase; Region: PLN02251 295405007512 active site 295405007513 ADP/pyrophosphate binding site [chemical binding]; other site 295405007514 dimerization interface [polypeptide binding]; other site 295405007515 allosteric effector site; other site 295405007516 fructose-1,6-bisphosphate binding site; other site 295405007517 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 295405007518 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 295405007519 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405007520 Peptidase M60-like family; Region: M60-like; pfam13402 295405007521 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405007522 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405007523 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405007524 SusD family; Region: SusD; pfam07980 295405007525 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405007526 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405007527 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405007528 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405007529 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 295405007530 FecR protein; Region: FecR; pfam04773 295405007531 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405007532 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405007533 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 295405007534 DNA binding residues [nucleotide binding] 295405007535 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 295405007536 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 295405007537 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405007538 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405007539 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405007540 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 295405007541 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 295405007542 active site 295405007543 nucleophile elbow; other site 295405007544 Surface antigen; Region: Bac_surface_Ag; pfam01103 295405007545 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 295405007546 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 295405007547 putative acyl-acceptor binding pocket; other site 295405007548 C-N hydrolase family amidase; Provisional; Region: PRK10438 295405007549 Xanthomonas campestris XC1258 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases); Region: Xc-1258_like; cd07575 295405007550 putative active site [active] 295405007551 catalytic triad [active] 295405007552 dimer interface [polypeptide binding]; other site 295405007553 multimer interface [polypeptide binding]; other site 295405007554 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 295405007555 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 295405007556 active site 295405007557 dimer interface [polypeptide binding]; other site 295405007558 glucosamine-6-phosphate deaminase-like protein; Validated; Region: PRK02122 295405007559 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 295405007560 active site 295405007561 trimer interface [polypeptide binding]; other site 295405007562 allosteric site; other site 295405007563 active site lid [active] 295405007564 hexamer (dimer of trimers) interface [polypeptide binding]; other site 295405007565 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 295405007566 Tyrosine phosphatase family; Region: Y_phosphatase3; pfam13350 295405007567 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 295405007568 Tyrosine phosphatase family C-terminal region; Region: Y_phosphatase3C; pfam13348 295405007569 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 295405007570 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; cl02713 295405007571 active site 295405007572 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 295405007573 Interdomain contacts; other site 295405007574 Cytokine receptor motif; other site 295405007575 SirA-like protein; Region: SirA; pfam01206 295405007576 CPxP motif; other site 295405007577 Protein of unknown function (DUF456); Region: DUF456; pfam04306 295405007578 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 295405007579 hypothetical protein; Provisional; Region: PRK00955 295405007580 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 295405007581 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 295405007582 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 295405007583 ATP binding site [chemical binding]; other site 295405007584 putative Mg++ binding site [ion binding]; other site 295405007585 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 295405007586 nucleotide binding region [chemical binding]; other site 295405007587 ATP-binding site [chemical binding]; other site 295405007588 TRCF domain; Region: TRCF; pfam03461 295405007589 DPM1_like represents putative enzymes similar to eukaryotic DPM1; Region: DPM1_like; cd06442 295405007590 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 295405007591 Ligand binding site; other site 295405007592 Putative Catalytic site; other site 295405007593 DXD motif; other site 295405007594 dihydroorotase; Reviewed; Region: PRK09236 295405007595 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 295405007596 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 295405007597 active site 295405007598 S23 ribosomal protein; Region: Ribosomal_S23p; cl05287 295405007599 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 295405007600 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405007601 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 295405007602 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 295405007603 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 295405007604 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 295405007605 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 295405007606 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 295405007607 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 295405007608 Interdomain contacts; other site 295405007609 Domain of unknown function (DUF1905); Region: DUF1905; pfam08922 295405007610 Bacteriocin-protection, YdeI or OmpD-Associated; Region: OmdA; pfam13376 295405007611 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 295405007612 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405007613 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 295405007614 phosphodiesterase YaeI; Provisional; Region: PRK11340 295405007615 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 295405007616 putative active site [active] 295405007617 putative metal binding site [ion binding]; other site 295405007618 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 295405007619 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 295405007620 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405007621 Walker A/P-loop; other site 295405007622 ATP binding site [chemical binding]; other site 295405007623 Q-loop/lid; other site 295405007624 ABC transporter signature motif; other site 295405007625 Walker B; other site 295405007626 D-loop; other site 295405007627 H-loop/switch region; other site 295405007628 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 295405007629 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 295405007630 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 295405007631 Walker A/P-loop; other site 295405007632 ATP binding site [chemical binding]; other site 295405007633 Q-loop/lid; other site 295405007634 ABC transporter signature motif; other site 295405007635 Walker B; other site 295405007636 D-loop; other site 295405007637 H-loop/switch region; other site 295405007638 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 295405007639 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405007640 Walker A/P-loop; other site 295405007641 ATP binding site [chemical binding]; other site 295405007642 Q-loop/lid; other site 295405007643 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405007644 ABC transporter signature motif; other site 295405007645 Walker B; other site 295405007646 D-loop; other site 295405007647 H-loop/switch region; other site 295405007648 exonuclease subunit SbcD; Provisional; Region: PRK10966 295405007649 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 295405007650 active site 295405007651 metal binding site [ion binding]; metal-binding site 295405007652 DNA binding site [nucleotide binding] 295405007653 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 295405007654 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 295405007655 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 295405007656 putative acyl-acceptor binding pocket; other site 295405007657 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 295405007658 Protein export membrane protein; Region: SecD_SecF; cl14618 295405007659 Protein export membrane protein; Region: SecD_SecF; cl14618 295405007660 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 295405007661 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 295405007662 Protein export membrane protein; Region: SecD_SecF; cl14618 295405007663 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405007664 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405007665 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405007666 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 295405007667 O-Antigen ligase; Region: Wzy_C; pfam04932 295405007668 Signal peptidase I [Intracellular trafficking and secretion]; Region: LepB; COG0681 295405007669 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 295405007670 Catalytic site [active] 295405007671 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 295405007672 Transglutaminase/protease-like homologues; Region: TGc; smart00460 295405007673 Transglutaminase-like superfamily; Region: Transglut_core; cl17362 295405007674 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405007675 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 295405007676 NVEALA protein; Region: NVEALA; pfam14055 295405007677 NVEALA protein; Region: NVEALA; pfam14055 295405007678 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 295405007679 DNA binding site [nucleotide binding] 295405007680 Domain of unknown function (DUF3244); Region: DUF3244; pfam11589 295405007681 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 295405007682 binding surface 295405007683 TPR motif; other site 295405007684 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405007685 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 295405007686 binding surface 295405007687 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405007688 TPR motif; other site 295405007689 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 295405007690 anaerobic sulfatase-maturase; Provisional; Region: PRK13745 295405007691 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 295405007692 FeS/SAM binding site; other site 295405007693 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 295405007694 Peptidase S46; Region: Peptidase_S46; pfam10459 295405007695 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 295405007696 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 295405007697 Peptidase S46; Region: Peptidase_S46; pfam10459 295405007698 Peptidase S7, Flavivirus NS3 serine protease; Region: Peptidase_S7; pfam00949 295405007699 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 295405007700 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 295405007701 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 295405007702 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 295405007703 putative active site [active] 295405007704 putative metal binding site [ion binding]; other site 295405007705 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 295405007706 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405007707 catalytic residues [active] 295405007708 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 295405007709 catalytic residues [active] 295405007710 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 295405007711 putative FMN binding site [chemical binding]; other site 295405007712 NADPH bind site [chemical binding]; other site 295405007713 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 295405007714 Rubredoxin; Region: Rubredoxin; pfam00301 295405007715 iron binding site [ion binding]; other site 295405007716 rubrerythrin-like, diiron-binding domain; Region: Rubrerythrin_like; cd01046 295405007717 Rubrerythrin [Energy production and conversion]; Region: COG1592 295405007718 diiron binding motif [ion binding]; other site 295405007719 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 295405007720 metal binding site 2 [ion binding]; metal-binding site 295405007721 putative DNA binding helix; other site 295405007722 metal binding site 1 [ion binding]; metal-binding site 295405007723 dimer interface [polypeptide binding]; other site 295405007724 structural Zn2+ binding site [ion binding]; other site 295405007725 Protein of unknown function (DUF805); Region: DUF805; pfam05656 295405007726 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 295405007727 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 295405007728 active site 295405007729 Zn binding site [ion binding]; other site 295405007730 NAD synthetase; Reviewed; Region: nadE; PRK02628 295405007731 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 295405007732 multimer interface [polypeptide binding]; other site 295405007733 active site 295405007734 catalytic triad [active] 295405007735 protein interface 1 [polypeptide binding]; other site 295405007736 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 295405007737 homodimer interface [polypeptide binding]; other site 295405007738 NAD binding pocket [chemical binding]; other site 295405007739 ATP binding pocket [chemical binding]; other site 295405007740 Mg binding site [ion binding]; other site 295405007741 active-site loop [active] 295405007742 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405007743 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405007744 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405007745 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 295405007746 Starch-binding associating with outer membrane; Region: SusD-like_2; pfam12771 295405007747 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405007748 Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain; Region: MPP_Dcr2; cd07383 295405007749 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 295405007750 putative active site [active] 295405007751 putative metal binding site [ion binding]; other site 295405007752 Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain; Region: MPP_Dcr2; cd07383 295405007753 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 295405007754 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 295405007755 active site 295405007756 motif I; other site 295405007757 motif II; other site 295405007758 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 295405007759 putative active site pocket [active] 295405007760 4-fold oligomerization interface [polypeptide binding]; other site 295405007761 metal binding residues [ion binding]; metal-binding site 295405007762 3-fold/trimer interface [polypeptide binding]; other site 295405007763 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 295405007764 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 295405007765 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405007766 homodimer interface [polypeptide binding]; other site 295405007767 catalytic residue [active] 295405007768 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 295405007769 histidinol dehydrogenase; Region: hisD; TIGR00069 295405007770 NAD binding site [chemical binding]; other site 295405007771 dimerization interface [polypeptide binding]; other site 295405007772 product binding site; other site 295405007773 substrate binding site [chemical binding]; other site 295405007774 zinc binding site [ion binding]; other site 295405007775 catalytic residues [active] 295405007776 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 295405007777 ATP phosphoribosyltransferase; Region: hisG; TIGR00070 295405007778 ATP phosphoribosyltransferase, C-terminal domain; Region: HisG_C-term; TIGR03455 295405007779 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 295405007780 CoenzymeA binding site [chemical binding]; other site 295405007781 subunit interaction site [polypeptide binding]; other site 295405007782 PHB binding site; other site 295405007783 Pirin; Region: Pirin; pfam02678 295405007784 Pirin-related protein [General function prediction only]; Region: COG1741 295405007785 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 295405007786 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 295405007787 Stress responsive A/B Barrel Domain; Region: Dabb; smart00886 295405007788 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 295405007789 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 295405007790 ATP-binding site [chemical binding]; other site 295405007791 Sugar specificity; other site 295405007792 Pyrimidine base specificity; other site 295405007793 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 295405007794 substrate binding pocket [chemical binding]; other site 295405007795 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 295405007796 membrane-bound complex binding site; other site 295405007797 hinge residues; other site 295405007798 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 295405007799 N-acetyl-D-glucosamine binding site [chemical binding]; other site 295405007800 catalytic residue [active] 295405007801 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 295405007802 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 295405007803 Na binding site [ion binding]; other site 295405007804 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 295405007805 putative FMN binding site [chemical binding]; other site 295405007806 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 295405007807 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 295405007808 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Region: MetH; COG1410 295405007809 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 295405007810 substrate binding pocket [chemical binding]; other site 295405007811 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 295405007812 B12 binding site [chemical binding]; other site 295405007813 cobalt ligand [ion binding]; other site 295405007814 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 295405007815 SmpB-tmRNA interface; other site 295405007816 Protein of unknown function (DUF1282); Region: DUF1282; pfam06930 295405007817 NigD-like protein; Region: NigD; pfam12667 295405007818 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 295405007819 TIGR03987 family protein; Region: TIGR03987 295405007820 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 295405007821 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cl00528 295405007822 GGGtGRT protein; Region: GGGtGRT; pfam14057 295405007823 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 295405007824 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 295405007825 dimer interface [polypeptide binding]; other site 295405007826 active site 295405007827 CoA binding pocket [chemical binding]; other site 295405007828 cytoplasmic alpha-amylase; Reviewed; Region: PRK09441 295405007829 Alpha amylase catalytic domain found in bacterial and fungal Alpha amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_bac_fung_AmyA; cd11318 295405007830 active site 295405007831 Na/Ca binding site [ion binding]; other site 295405007832 catalytic site [active] 295405007833 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 295405007834 Domain of unknown function (DUF202); Region: DUF202; pfam02656 295405007835 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 295405007836 4Fe-4S binding domain; Region: Fer4; pfam00037 295405007837 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 295405007838 transcription termination factor Rho; Provisional; Region: PRK12608 295405007839 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 295405007840 RNA binding site [nucleotide binding]; other site 295405007841 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 295405007842 multimer interface [polypeptide binding]; other site 295405007843 Walker A motif; other site 295405007844 ATP binding site [chemical binding]; other site 295405007845 Walker B motif; other site 295405007846 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 295405007847 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405007848 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 295405007849 dimer interface [polypeptide binding]; other site 295405007850 phosphorylation site [posttranslational modification] 295405007851 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 295405007852 ATP binding site [chemical binding]; other site 295405007853 Mg2+ binding site [ion binding]; other site 295405007854 G-X-G motif; other site 295405007855 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405007856 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 295405007857 dimer interface [polypeptide binding]; other site 295405007858 phosphorylation site [posttranslational modification] 295405007859 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_7; cd13133 295405007860 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 295405007861 signal recognition particle protein; Provisional; Region: PRK10867 295405007862 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 295405007863 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 295405007864 P loop; other site 295405007865 GTP binding site [chemical binding]; other site 295405007866 Signal peptide binding domain; Region: SRP_SPB; pfam02978 295405007867 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 295405007868 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 295405007869 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405007870 catalytic residues [active] 295405007871 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14185 295405007872 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 295405007873 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 295405007874 homodimer interface [polypeptide binding]; other site 295405007875 NADP binding site [chemical binding]; other site 295405007876 substrate binding site [chemical binding]; other site 295405007877 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 295405007878 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 295405007879 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405007880 catalytic residues [active] 295405007881 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 295405007882 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 295405007883 putative active site [active] 295405007884 putative metal binding site [ion binding]; other site 295405007885 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 295405007886 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405007887 Walker A/P-loop; other site 295405007888 ATP binding site [chemical binding]; other site 295405007889 Q-loop/lid; other site 295405007890 ABC transporter signature motif; other site 295405007891 Walker B; other site 295405007892 D-loop; other site 295405007893 H-loop/switch region; other site 295405007894 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 295405007895 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 295405007896 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405007897 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405007898 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 295405007899 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14971 295405007900 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 295405007901 Walker A motif; other site 295405007902 ATP binding site [chemical binding]; other site 295405007903 Walker B motif; other site 295405007904 arginine finger; other site 295405007905 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 295405007906 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; pfam09912 295405007907 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 295405007908 LytTr DNA-binding domain; Region: LytTR; smart00850 295405007909 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 295405007910 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 295405007911 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 295405007912 metal binding site [ion binding]; metal-binding site 295405007913 dimer interface [polypeptide binding]; other site 295405007914 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 295405007915 putative catalytic site [active] 295405007916 putative metal binding site [ion binding]; other site 295405007917 putative phosphate binding site [ion binding]; other site 295405007918 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 295405007919 Mechanosensitive ion channel; Region: MS_channel; pfam00924 295405007920 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 295405007921 active site 295405007922 intersubunit interactions; other site 295405007923 catalytic residue [active] 295405007924 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 295405007925 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 295405007926 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405007927 sugar binding site [chemical binding]; other site 295405007928 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 295405007929 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405007930 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405007931 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405007932 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 295405007933 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 295405007934 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 295405007935 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 295405007936 active site 295405007937 Fn3 associated; Region: Fn3_assoc; pfam13287 295405007938 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 295405007939 Sulfatase; Region: Sulfatase; cl17466 295405007940 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405007941 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405007942 Sulfatase; Region: Sulfatase; pfam00884 295405007943 Glycosyl hydrolase family 67 N-terminus; Region: Glyco_hydro_67N; pfam03648 295405007944 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 295405007945 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 295405007946 active site 295405007947 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 295405007948 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 295405007949 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 295405007950 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405007951 fructose-bisphosphate aldolase; Provisional; Region: PRK09250 295405007952 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs); Region: DhnA; cd00958 295405007953 putative active site; other site 295405007954 catalytic residue [active] 295405007955 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 295405007956 catalytic core [active] 295405007957 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 295405007958 Right handed beta helix region; Region: Beta_helix; pfam13229 295405007959 Right handed beta helix region; Region: Beta_helix; pfam13229 295405007960 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 295405007961 protein binding site [polypeptide binding]; other site 295405007962 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405007963 putative molybdenum transport ATP-binding protein ModF; Provisional; Region: PRK10938 295405007964 Walker A/P-loop; other site 295405007965 ATP binding site [chemical binding]; other site 295405007966 Q-loop/lid; other site 295405007967 ABC transporter signature motif; other site 295405007968 Walker B; other site 295405007969 D-loop; other site 295405007970 H-loop/switch region; other site 295405007971 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405007972 Walker A/P-loop; other site 295405007973 ATP binding site [chemical binding]; other site 295405007974 Q-loop/lid; other site 295405007975 ABC transporter signature motif; other site 295405007976 Walker B; other site 295405007977 D-loop; other site 295405007978 H-loop/switch region; other site 295405007979 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405007980 Sulfatase; Region: Sulfatase; pfam00884 295405007981 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 295405007982 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 295405007983 active site 295405007984 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405007985 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405007986 SusD family; Region: SusD; pfam07980 295405007987 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405007988 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405007989 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405007990 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405007991 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405007992 FecR protein; Region: FecR; pfam04773 295405007993 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405007994 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405007995 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 295405007996 pullulanase, type I; Region: pulA_typeI; TIGR02104 295405007997 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 295405007998 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 295405007999 Ca binding site [ion binding]; other site 295405008000 active site 295405008001 catalytic site [active] 295405008002 Domain of unknown function (DUF3372); Region: DUF3372; pfam11852 295405008003 Domain of unknown function (DUF4286); Region: DUF4286; pfam14114 295405008004 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 295405008005 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 295405008006 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 295405008007 dimer interface [polypeptide binding]; other site 295405008008 motif 1; other site 295405008009 active site 295405008010 motif 2; other site 295405008011 motif 3; other site 295405008012 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 295405008013 Major Facilitator Superfamily; Region: MFS_1; pfam07690 295405008014 putative substrate translocation pore; other site 295405008015 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 295405008016 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 295405008017 minor groove reading motif; other site 295405008018 helix-hairpin-helix signature motif; other site 295405008019 substrate binding pocket [chemical binding]; other site 295405008020 active site 295405008021 Phosphoglycerate kinase; Region: PGK; pfam00162 295405008022 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 295405008023 substrate binding site [chemical binding]; other site 295405008024 hinge regions; other site 295405008025 ADP binding site [chemical binding]; other site 295405008026 catalytic site [active] 295405008027 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 295405008028 NMT1/THI5 like; Region: NMT1; pfam09084 295405008029 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 295405008030 Predicted membrane protein [Function unknown]; Region: COG2311 295405008031 Protein of unknown function (DUF418); Region: DUF418; cl12135 295405008032 Protein of unknown function (DUF418); Region: DUF418; pfam04235 295405008033 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 295405008034 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 295405008035 binding surface 295405008036 TPR motif; other site 295405008037 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 295405008038 binding surface 295405008039 TPR motif; other site 295405008040 Family of unknown function (DUF3836); Region: DUF3836; pfam12930 295405008041 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 295405008042 active site 295405008043 catalytic residues [active] 295405008044 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 295405008045 amino acid adenylation domain; Region: AA-adenyl-dom; TIGR01733 295405008046 acyl-activating enzyme (AAE) consensus motif; other site 295405008047 AMP binding site [chemical binding]; other site 295405008048 active site 295405008049 CoA binding site [chemical binding]; other site 295405008050 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 295405008051 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 295405008052 Maf-like protein; Region: Maf; pfam02545 295405008053 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 295405008054 active site 295405008055 dimer interface [polypeptide binding]; other site 295405008056 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 295405008057 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 295405008058 active site 295405008059 motif I; other site 295405008060 motif II; other site 295405008061 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; pfam03807 295405008062 Domain of unknown function (DUF2520); Region: DUF2520; pfam10728 295405008063 NAD(P)H:flavin oxidoreductase-like family 2. 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_2; cd02151 295405008064 putative FMN binding site [chemical binding]; other site 295405008065 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeD; cd03379 295405008066 active site clefts [active] 295405008067 zinc binding site [ion binding]; other site 295405008068 dimer interface [polypeptide binding]; other site 295405008069 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 295405008070 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 295405008071 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 295405008072 dimer interface [polypeptide binding]; other site 295405008073 substrate binding site [chemical binding]; other site 295405008074 metal binding site [ion binding]; metal-binding site 295405008075 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 295405008076 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 295405008077 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 295405008078 Lamin Tail Domain; Region: LTD; pfam00932 295405008079 sodium pump decarboxylases, gamma subunit; Region: oadG_fam; TIGR01195 295405008080 Biotin carboxyl carrier protein [Lipid metabolism]; Region: AccB; COG0511 295405008081 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 295405008082 carboxyltransferase (CT) interaction site; other site 295405008083 biotinylation site [posttranslational modification]; other site 295405008084 Na+-transporting oxaloacetate decarboxylase beta subunit; Region: OAD_beta; cl00816 295405008085 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 295405008086 binding surface 295405008087 Tetratricopeptide repeat; Region: TPR_16; pfam13432 295405008088 TPR motif; other site 295405008089 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 295405008090 binding surface 295405008091 Tetratricopeptide repeat; Region: TPR_16; pfam13432 295405008092 TPR motif; other site 295405008093 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 295405008094 binding surface 295405008095 TPR motif; other site 295405008096 Cyclomaltodextrinase, N-terminal; Region: Cyc-maltodext_N; pfam09087 295405008097 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins; Region: AmyAc_bac_CMD_like_3; cd11340 295405008098 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 295405008099 Ca binding site [ion binding]; other site 295405008100 active site 295405008101 homodimer interface [polypeptide binding]; other site 295405008102 catalytic site [active] 295405008103 Cyclo-malto-dextrinase C-terminal domain; Region: Cyc-maltodext_C; pfam10438 295405008104 Transcriptional regulators [Transcription]; Region: MarR; COG1846 295405008105 MarR family; Region: MarR; pfam01047 295405008106 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 295405008107 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405008108 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405008109 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 295405008110 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 295405008111 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 295405008112 intersubunit interface [polypeptide binding]; other site 295405008113 active site 295405008114 zinc binding site [ion binding]; other site 295405008115 Na+ binding site [ion binding]; other site 295405008116 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 295405008117 putative catalytic site [active] 295405008118 putative metal binding site [ion binding]; other site 295405008119 putative phosphate binding site [ion binding]; other site 295405008120 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 295405008121 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 295405008122 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 295405008123 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 295405008124 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 295405008125 Alpha amylase catalytic domain found in an uncharacterized protein family; Region: AmyAc_4; cd11350 295405008126 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 295405008127 active site 295405008128 catalytic site [active] 295405008129 SusE outer membrane protein; Region: SusE; pfam14292 295405008130 carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins; Region: CBM_SusE-F_like; cl17376 295405008131 carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins; Region: CBM_SusE-F_like; cd12956 295405008132 starch binding site [chemical binding]; other site 295405008133 Uncharacterized subgroup of the CBM-SusE-F_like superfamily; Region: CBM_SusE-F_like_u1; cd12967 295405008134 starch binding site [chemical binding]; other site 295405008135 carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins; Region: CBM_SusE-F_like; cd12956 295405008136 starch binding site [chemical binding]; other site 295405008137 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405008138 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405008139 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405008140 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405008141 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405008142 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405008143 Transcriptional regulators [Transcription]; Region: PurR; COG1609 295405008144 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 295405008145 DNA binding site [nucleotide binding] 295405008146 domain linker motif; other site 295405008147 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 295405008148 dimerization interface [polypeptide binding]; other site 295405008149 ligand binding site [chemical binding]; other site 295405008150 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 295405008151 Major Facilitator Superfamily; Region: MFS_1; pfam07690 295405008152 putative substrate translocation pore; other site 295405008153 maltose phosphorylase; Provisional; Region: PRK13807 295405008154 Glycosyl hydrolase family 65, N-terminal domain; Region: Glyco_hydro_65N; pfam03636 295405008155 Glycosyl hydrolase family 65 central catalytic domain; Region: Glyco_hydro_65m; pfam03632 295405008156 Glycosyl hydrolase family 65, C-terminal domain; Region: Glyco_hydro_65C; pfam03633 295405008157 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405008158 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405008159 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405008160 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 295405008161 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 295405008162 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 295405008163 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 295405008164 dimerization interface [polypeptide binding]; other site 295405008165 ATP binding site [chemical binding]; other site 295405008166 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 295405008167 dimerization interface [polypeptide binding]; other site 295405008168 ATP binding site [chemical binding]; other site 295405008169 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 295405008170 putative active site [active] 295405008171 catalytic triad [active] 295405008172 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 295405008173 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405008174 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 295405008175 dimer interface [polypeptide binding]; other site 295405008176 phosphorylation site [posttranslational modification] 295405008177 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 295405008178 ATP binding site [chemical binding]; other site 295405008179 Mg2+ binding site [ion binding]; other site 295405008180 G-X-G motif; other site 295405008181 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 295405008182 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 295405008183 active site 295405008184 phosphorylation site [posttranslational modification] 295405008185 intermolecular recognition site; other site 295405008186 dimerization interface [polypeptide binding]; other site 295405008187 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405008188 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405008189 Chromate transporter; Region: Chromate_transp; pfam02417 295405008190 Chromate transporter; Region: Chromate_transp; pfam02417 295405008191 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 295405008192 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 295405008193 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 295405008194 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405008195 ATP binding site [chemical binding]; other site 295405008196 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 295405008197 ABC transporter signature motif; other site 295405008198 Walker B; other site 295405008199 D-loop; other site 295405008200 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 295405008201 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 295405008202 Carbon starvation protein CstA; Region: CstA; pfam02554 295405008203 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 295405008204 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 295405008205 ABC transporter substrate binding protein; Region: ABC_sub_bind; cl17301 295405008206 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405008207 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 295405008208 dimer interface [polypeptide binding]; other site 295405008209 phosphorylation site [posttranslational modification] 295405008210 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 295405008211 ATP binding site [chemical binding]; other site 295405008212 Mg2+ binding site [ion binding]; other site 295405008213 G-X-G motif; other site 295405008214 AAA domain; Region: AAA_14; pfam13173 295405008215 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 295405008216 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 295405008217 Short C-terminal domain; Region: SHOCT; pfam09851 295405008218 Tic20-like protein; Region: Tic20; pfam09685 295405008219 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 295405008220 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 295405008221 dimer interface [polypeptide binding]; other site 295405008222 PYR/PP interface [polypeptide binding]; other site 295405008223 TPP binding site [chemical binding]; other site 295405008224 substrate binding site [chemical binding]; other site 295405008225 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 295405008226 Domain of unknown function; Region: EKR; pfam10371 295405008227 4Fe-4S binding domain; Region: Fer4_6; pfam12837 295405008228 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 295405008229 TPP-binding site [chemical binding]; other site 295405008230 dimer interface [polypeptide binding]; other site 295405008231 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 295405008232 membrane-bound complex binding site; other site 295405008233 hinge residues; other site 295405008234 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; COG2113 295405008235 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 295405008236 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 295405008237 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 295405008238 dimer interface [polypeptide binding]; other site 295405008239 conserved gate region; other site 295405008240 putative PBP binding loops; other site 295405008241 ABC-ATPase subunit interface; other site 295405008242 ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]; Region: ProV; COG4175 295405008243 ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system; Region: ABC_Pro_Gly_Betaine; cd03294 295405008244 Walker A/P-loop; other site 295405008245 ATP binding site [chemical binding]; other site 295405008246 Q-loop/lid; other site 295405008247 ABC transporter signature motif; other site 295405008248 Walker B; other site 295405008249 D-loop; other site 295405008250 H-loop/switch region; other site 295405008251 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 295405008252 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 295405008253 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 295405008254 DNA binding site [nucleotide binding] 295405008255 active site 295405008256 Periplasmic binding domain of two-component sensor kinase signaling systems; Region: PBP1_sensor_kinase_like; cd06308 295405008257 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 295405008258 putative ligand binding site [chemical binding]; other site 295405008259 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405008260 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 295405008261 dimer interface [polypeptide binding]; other site 295405008262 phosphorylation site [posttranslational modification] 295405008263 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 295405008264 ATP binding site [chemical binding]; other site 295405008265 Mg2+ binding site [ion binding]; other site 295405008266 G-X-G motif; other site 295405008267 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 295405008268 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 295405008269 active site 295405008270 phosphorylation site [posttranslational modification] 295405008271 intermolecular recognition site; other site 295405008272 dimerization interface [polypeptide binding]; other site 295405008273 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405008274 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405008275 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 295405008276 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 295405008277 putative substrate binding site [chemical binding]; other site 295405008278 putative ATP binding site [chemical binding]; other site 295405008279 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 295405008280 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 295405008281 putative substrate translocation pore; other site 295405008282 Glycosyl hydrolases family 32; Region: Glyco_32; smart00640 295405008283 Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996 295405008284 substrate binding [chemical binding]; other site 295405008285 active site 295405008286 Glycosyl hydrolases family 32 C terminal; Region: Glyco_hydro_32C; pfam08244 295405008287 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405008288 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 295405008289 non-specific DNA binding site [nucleotide binding]; other site 295405008290 salt bridge; other site 295405008291 sequence-specific DNA binding site [nucleotide binding]; other site 295405008292 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 295405008293 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 295405008294 glucose/galactose transporter; Region: gluP; TIGR01272 295405008295 L-fucose transporter; Provisional; Region: PRK10133; cl17665 295405008296 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 295405008297 dimer interface [polypeptide binding]; other site 295405008298 FMN binding site [chemical binding]; other site 295405008299 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 295405008300 dimer interface [polypeptide binding]; other site 295405008301 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 295405008302 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 295405008303 potential catalytic triad [active] 295405008304 conserved cys residue [active] 295405008305 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 295405008306 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 295405008307 active site 295405008308 nucleophile elbow; other site 295405008309 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 295405008310 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 295405008311 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 295405008312 Galactose oxidase, central domain; Region: Kelch_4; pfam13418 295405008313 Galactose oxidase, central domain; Region: Kelch_3; pfam13415 295405008314 Galactose oxidase, central domain; Region: Kelch_3; pfam13415 295405008315 Galactose oxidase, central domain; Region: Kelch_4; pfam13418 295405008316 Kelch motif; Region: Kelch_1; pfam01344 295405008317 Galactose oxidase, central domain; Region: Kelch_3; cl02701 295405008318 Domain of unknown function (DUF4270); Region: DUF4270; pfam14092 295405008319 Uncharacterized lipoprotein NlpE involved in copper resistance [Cell envelope biogenesis, outer membrane / Inorganic ion transport and metabolism]; Region: CutF; COG3015 295405008320 NlpE N-terminal domain; Region: NlpE; pfam04170 295405008321 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 295405008322 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 295405008323 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405008324 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405008325 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405008326 Cupin domain; Region: Cupin_2; cl17218 295405008327 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405008328 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405008329 Peptidase C1-like family; Region: Peptidase_C1_2; cl17447 295405008330 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 295405008331 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 295405008332 active site 295405008333 phosphorylation site [posttranslational modification] 295405008334 intermolecular recognition site; other site 295405008335 dimerization interface [polypeptide binding]; other site 295405008336 LytTr DNA-binding domain; Region: LytTR; smart00850 295405008337 Histidine kinase; Region: His_kinase; pfam06580 295405008338 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405008339 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405008340 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405008341 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405008342 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405008343 SusD family; Region: SusD; pfam07980 295405008344 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 295405008345 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 295405008346 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405008347 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405008348 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 295405008349 Ligand binding site [chemical binding]; other site 295405008350 Electron transfer flavoprotein domain; Region: ETF; pfam01012 295405008351 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 295405008352 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 295405008353 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 295405008354 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 295405008355 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 295405008356 active site 295405008357 Acyl-CoA dehydrogenase C terminal; Region: AcylCoA_dehyd_C; pfam12186 295405008358 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 295405008359 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405008360 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 295405008361 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 295405008362 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 295405008363 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C; pfam03174 295405008364 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405008365 sugar binding site [chemical binding]; other site 295405008366 MerR HTH family regulatory protein; Region: MerR_2; pfam13591 295405008367 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 295405008368 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 295405008369 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 295405008370 HSP70 interaction site [polypeptide binding]; other site 295405008371 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 295405008372 dimer interface [polypeptide binding]; other site 295405008373 PAS domain S-box; Region: sensory_box; TIGR00229 295405008374 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 295405008375 putative active site [active] 295405008376 heme pocket [chemical binding]; other site 295405008377 PAS domain; Region: PAS_9; pfam13426 295405008378 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 295405008379 dimer interface [polypeptide binding]; other site 295405008380 phosphorylation site [posttranslational modification] 295405008381 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 295405008382 ATP binding site [chemical binding]; other site 295405008383 Mg2+ binding site [ion binding]; other site 295405008384 G-X-G motif; other site 295405008385 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 295405008386 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 295405008387 Sulfatase; Region: Sulfatase; pfam00884 295405008388 Surface antigen; Region: Bac_surface_Ag; pfam01103 295405008389 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 295405008390 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405008391 catalytic residues [active] 295405008392 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 295405008393 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 295405008394 tetramer interface [polypeptide binding]; other site 295405008395 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405008396 catalytic residue [active] 295405008397 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 295405008398 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405008399 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 295405008400 DNA binding residues [nucleotide binding] 295405008401 Protein of unknown function (DUF2582); Region: DUF2582; pfam10771 295405008402 pyruvate dehydrogenase; Provisional; Region: PRK06546 295405008403 Pyrimidine (PYR) binding domain of POX; Region: TPP_PYR_POX; cd07039 295405008404 PYR/PP interface [polypeptide binding]; other site 295405008405 dimer interface [polypeptide binding]; other site 295405008406 tetramer interface [polypeptide binding]; other site 295405008407 TPP binding site [chemical binding]; other site 295405008408 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 295405008409 Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX decarboxylates...; Region: TPP_POX; cd02014 295405008410 TPP-binding site [chemical binding]; other site 295405008411 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 295405008412 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 295405008413 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405008414 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 295405008415 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 295405008416 ring oligomerisation interface [polypeptide binding]; other site 295405008417 ATP/Mg binding site [chemical binding]; other site 295405008418 stacking interactions; other site 295405008419 hinge regions; other site 295405008420 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 295405008421 oligomerisation interface [polypeptide binding]; other site 295405008422 mobile loop; other site 295405008423 roof hairpin; other site 295405008424 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405008425 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405008426 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 295405008427 ligand binding site [chemical binding]; other site 295405008428 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 295405008429 polyphosphate:nucleotide phosphotransferase, PPK2 family; Region: PPK2_rel_1; TIGR03709 295405008430 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 295405008431 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405008432 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 295405008433 DNA binding residues [nucleotide binding] 295405008434 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 295405008435 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405008436 This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1; Region: GT1_UGDG_like; cd03817 295405008437 putative ADP-binding pocket [chemical binding]; other site 295405008438 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 295405008439 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 295405008440 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 295405008441 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 295405008442 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 295405008443 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 295405008444 dimer interface [polypeptide binding]; other site 295405008445 motif 1; other site 295405008446 active site 295405008447 motif 2; other site 295405008448 motif 3; other site 295405008449 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 295405008450 anticodon binding site; other site 295405008451 Transglutaminase-like superfamily; Region: Transglut_core; cl17362 295405008452 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; pfam04298 295405008453 Alpha-L-fucosidase; Region: Alpha_L_fucos; pfam01120 295405008454 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 295405008455 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 295405008456 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 295405008457 GDP-binding site [chemical binding]; other site 295405008458 ACT binding site; other site 295405008459 IMP binding site; other site 295405008460 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 295405008461 metal binding site 2 [ion binding]; metal-binding site 295405008462 putative DNA binding helix; other site 295405008463 metal binding site 1 [ion binding]; metal-binding site 295405008464 dimer interface [polypeptide binding]; other site 295405008465 structural Zn2+ binding site [ion binding]; other site 295405008466 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 295405008467 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 295405008468 A new structural DNA glycosylase; Region: AlkD_like; cd06561 295405008469 active site 295405008470 Peptidase family M49; Region: Peptidase_M49; pfam03571 295405008471 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405008472 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405008473 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 295405008474 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 295405008475 ATP binding site [chemical binding]; other site 295405008476 putative Mg++ binding site [ion binding]; other site 295405008477 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 295405008478 nucleotide binding region [chemical binding]; other site 295405008479 ATP-binding site [chemical binding]; other site 295405008480 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 295405008481 HRDC domain; Region: HRDC; pfam00570 295405008482 TPR repeat; Region: TPR_11; pfam13414 295405008483 TPR repeat; Region: TPR_11; pfam13414 295405008484 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 295405008485 binding surface 295405008486 TPR motif; other site 295405008487 TPR repeat; Region: TPR_11; pfam13414 295405008488 Tetratricopeptide repeat; Region: TPR_16; pfam13432 295405008489 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 295405008490 binding surface 295405008491 TPR motif; other site 295405008492 TPR repeat; Region: TPR_11; pfam13414 295405008493 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 295405008494 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 295405008495 dimer interface [polypeptide binding]; other site 295405008496 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405008497 catalytic residue [active] 295405008498 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 295405008499 Sulfatase; Region: Sulfatase; pfam00884 295405008500 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 295405008501 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 295405008502 active site 295405008503 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 295405008504 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 295405008505 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405008506 SusD family; Region: SusD; pfam07980 295405008507 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405008508 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405008509 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405008510 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405008511 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 295405008512 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405008513 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 295405008514 putative NAD(P) binding site [chemical binding]; other site 295405008515 active site 295405008516 putative substrate binding site [chemical binding]; other site 295405008517 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 295405008518 Lipid A Biosynthesis N-terminal domain; Region: LAB_N; cl01627 295405008519 Lipid A Biosynthesis N-terminal domain; Region: LAB_N; cl01627 295405008520 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 295405008521 active site 295405008522 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 295405008523 tartrate dehydrogenase; Region: TTC; TIGR02089 295405008524 (R)-citramalate synthase; Provisional; Region: PRK09389 295405008525 Leptospira interrogans citramalate synthase (CMS) and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_CMS; cd07945 295405008526 active site 295405008527 catalytic residues [active] 295405008528 metal binding site [ion binding]; metal-binding site 295405008529 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; pfam08502 295405008530 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 295405008531 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 295405008532 substrate binding site [chemical binding]; other site 295405008533 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 295405008534 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 295405008535 substrate binding site [chemical binding]; other site 295405008536 ligand binding site [chemical binding]; other site 295405008537 2-isopropylmalate synthase; Validated; Region: PRK00915 295405008538 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 295405008539 active site 295405008540 catalytic residues [active] 295405008541 metal binding site [ion binding]; metal-binding site 295405008542 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; pfam08502 295405008543 DPS-like protein, ferritin-like diiron-binding domain; Region: DPSL; cd01052 295405008544 Ferritin-like domain; Region: Ferritin; pfam00210 295405008545 diiron binding motif [ion binding]; other site 295405008546 signal peptide peptidase SppA, 67K type; Region: SppA_67K; TIGR00705 295405008547 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 295405008548 tandem repeat interface [polypeptide binding]; other site 295405008549 oligomer interface [polypeptide binding]; other site 295405008550 active site residues [active] 295405008551 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 295405008552 tandem repeat interface [polypeptide binding]; other site 295405008553 oligomer interface [polypeptide binding]; other site 295405008554 active site residues [active] 295405008555 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 295405008556 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 295405008557 purine nucleoside phosphorylase; Provisional; Region: PRK08202 295405008558 thiamine monophosphate kinase; Provisional; Region: PRK05731 295405008559 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 295405008560 ATP binding site [chemical binding]; other site 295405008561 dimerization interface [polypeptide binding]; other site 295405008562 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 295405008563 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 295405008564 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 295405008565 active site 295405008566 DNA binding site [nucleotide binding] 295405008567 Int/Topo IB signature motif; other site 295405008568 Domain of unknown function, B. Theta Gene description (DUF3871); Region: DUF3871; pfam12987 295405008569 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 295405008570 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 295405008571 active site 295405008572 DNA binding site [nucleotide binding] 295405008573 Int/Topo IB signature motif; other site 295405008574 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 295405008575 RteC protein; Region: RteC; pfam09357 295405008576 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 295405008577 Putative zinc ribbon domain; Region: Zn_ribbon_2; pfam12674 295405008578 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 295405008579 GyrI-like small molecule binding domain; Region: GyrI-like; pfam06445 295405008580 Protein of unknown function (DUF3788); Region: DUF3788; pfam12663 295405008581 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 295405008582 Divergent AAA domain; Region: AAA_4; pfam04326 295405008583 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 295405008584 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 295405008585 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 295405008586 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 295405008587 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 295405008588 motif II; other site 295405008589 maltose O-acetyltransferase; Provisional; Region: PRK10092 295405008590 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 295405008591 active site 295405008592 substrate binding site [chemical binding]; other site 295405008593 trimer interface [polypeptide binding]; other site 295405008594 CoA binding site [chemical binding]; other site 295405008595 Nitroreductase-like family 3. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_3; cd02139 295405008596 putative FMN binding site [chemical binding]; other site 295405008597 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 295405008598 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405008599 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405008600 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 295405008601 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 295405008602 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405008603 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 295405008604 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 295405008605 ATP binding site [chemical binding]; other site 295405008606 Mg2+ binding site [ion binding]; other site 295405008607 G-X-G motif; other site 295405008608 Response regulator receiver domain; Region: Response_reg; pfam00072 295405008609 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 295405008610 active site 295405008611 phosphorylation site [posttranslational modification] 295405008612 intermolecular recognition site; other site 295405008613 dimerization interface [polypeptide binding]; other site 295405008614 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 295405008615 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405008616 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 295405008617 Domain of unknown function (DUF303); Region: DUF303; pfam03629 295405008618 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 295405008619 Domain of unknown function (DUF303); Region: DUF303; pfam03629 295405008620 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; pfam05592 295405008621 Glycosyl hydrolase families 32 and 68, which for the clan GH-J; Region: GH_J; cd08979 295405008622 active site 295405008623 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405008624 SusD family; Region: SusD; pfam07980 295405008625 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405008626 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405008627 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405008628 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 295405008629 Glycosyl hydrolase family 76; Region: Glyco_hydro_76; pfam03663 295405008630 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 295405008631 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 295405008632 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_7; cd13133 295405008633 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 295405008634 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 295405008635 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 295405008636 ligand binding site [chemical binding]; other site 295405008637 active site 295405008638 UGI interface [polypeptide binding]; other site 295405008639 catalytic site [active] 295405008640 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405008641 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405008642 GyrI-like small molecule binding domain; Region: GyrI-like; pfam06445 295405008643 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405008644 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405008645 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405008646 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; pfam09603 295405008647 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 295405008648 iron-sulfur cluster repair di-iron protein; Region: FeS_repair_RIC; TIGR03652 295405008649 Hemerythrin-like domain; Region: Hr-like; cd12108 295405008650 Fe binding site [ion binding]; other site 295405008651 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 295405008652 putative active site [active] 295405008653 putative catalytic site [active] 295405008654 Protein of unknown function, DUF393; Region: DUF393; pfam04134 295405008655 Protein of unknown function (DUF3829); Region: DUF3829; pfam12889 295405008656 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 295405008657 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405008658 NAD(P) binding site [chemical binding]; other site 295405008659 active site 295405008660 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 295405008661 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405008662 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405008663 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 295405008664 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405008665 Major fimbrial subunit protein (FimA); Region: P_gingi_FimA; pfam06321 295405008666 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405008667 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405008668 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 295405008669 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 295405008670 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 295405008671 active site 295405008672 DNA binding site [nucleotide binding] 295405008673 Int/Topo IB signature motif; other site 295405008674 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405008675 nicotinate phosphoribosyltransferase; Provisional; Region: PRK05321 295405008676 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 295405008677 active site 295405008678 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 295405008679 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405008680 catalytic residues [active] 295405008681 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 295405008682 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 295405008683 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 295405008684 TrkA-C domain; Region: TrkA_C; pfam02080 295405008685 TrkA-C domain; Region: TrkA_C; pfam02080 295405008686 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 295405008687 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 295405008688 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 295405008689 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 295405008690 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 295405008691 carboxyltransferase (CT) interaction site; other site 295405008692 biotinylation site [posttranslational modification]; other site 295405008693 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 295405008694 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 295405008695 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 295405008696 Isochorismatase family; Region: Isochorismatase; pfam00857 295405008697 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; cd00431 295405008698 catalytic triad [active] 295405008699 conserved cis-peptide bond; other site 295405008700 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 295405008701 Beta-lactamase; Region: Beta-lactamase; pfam00144 295405008702 Domain of unknown function DUF302; Region: DUF302; cl01364 295405008703 inosine 5-monophosphate dehydrogenase; Validated; Region: PRK07107 295405008704 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 295405008705 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_2; cd04602 295405008706 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 295405008707 active site 295405008708 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2350 295405008709 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405008710 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405008711 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 295405008712 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405008713 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405008714 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 295405008715 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 295405008716 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 295405008717 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 295405008718 homodimer interface [polypeptide binding]; other site 295405008719 substrate-cofactor binding pocket; other site 295405008720 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405008721 catalytic residue [active] 295405008722 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 295405008723 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 295405008724 active site 295405008725 metal binding site [ion binding]; metal-binding site 295405008726 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 295405008727 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405008728 FtsX-like permease family; Region: FtsX; pfam02687 295405008729 FtsX-like permease family; Region: FtsX; pfam02687 295405008730 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 295405008731 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 295405008732 motif II; other site 295405008733 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405008734 Tandemly repeated domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like; cl17916 295405008735 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405008736 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405008737 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405008738 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 295405008739 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405008740 Heavy-metal-associated domain; Region: HMA; pfam00403 295405008741 Outer membrane efflux protein; Region: OEP; pfam02321 295405008742 Outer membrane efflux protein; Region: OEP; pfam02321 295405008743 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 295405008744 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 295405008745 N-acetyl-D-glucosamine binding site [chemical binding]; other site 295405008746 catalytic residue [active] 295405008747 Ion transport protein; Region: Ion_trans; pfam00520 295405008748 Ion channel; Region: Ion_trans_2; pfam07885 295405008749 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 295405008750 Protein of unknown function (DUF4011); Region: DUF4011; pfam13195 295405008751 Part of AAA domain; Region: AAA_19; pfam13245 295405008752 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 295405008753 AAA domain; Region: AAA_12; pfam13087 295405008754 Protein of unknown function (DUF3320); Region: DUF3320; pfam11784 295405008755 Protein of unknown function (DUF2809); Region: DUF2809; pfam10990 295405008756 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 295405008757 MgtC family; Region: MgtC; pfam02308 295405008758 probable DNA metabolism protein; Region: SAM_7_link_chp; TIGR03915 295405008759 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 295405008760 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 295405008761 FeS/SAM binding site; other site 295405008762 Phage X family; Region: Phage_X; cl11585 295405008763 WYL domain; Region: WYL; pfam13280 295405008764 methionine sulfoxide reductase A; Provisional; Region: PRK14054 295405008765 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 295405008766 SelR domain; Region: SelR; pfam01641 295405008767 Divergent AAA domain; Region: AAA_4; pfam04326 295405008768 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 295405008769 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 295405008770 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cl15377 295405008771 xanthine permease; Region: pbuX; TIGR03173 295405008772 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 295405008773 putative active site [active] 295405008774 Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX)...; Region: ArsC_like; cd03036 295405008775 ArsC family; Region: ArsC; pfam03960 295405008776 putative ArsC-like catalytic residues; other site 295405008777 putative TRX-like catalytic residues [active] 295405008778 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405008779 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 295405008780 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405008781 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 295405008782 DNA binding residues [nucleotide binding] 295405008783 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 295405008784 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 295405008785 putative acyl-acceptor binding pocket; other site 295405008786 Predicted CDP-diglyceride synthetase/phosphatidate cytidylyltransferase [General function prediction only]; Region: COG4589 295405008787 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 295405008788 Phosphatidylglycerophosphate synthase [Lipid metabolism]; Region: PgsA; COG0558 295405008789 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405008790 von Willebrand factor; Region: vWF_A; pfam12450 295405008791 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 295405008792 VWA subgroup: 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_subgroup; cd01465 295405008793 metal ion-dependent adhesion site (MIDAS); other site 295405008794 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 295405008795 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405008796 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 295405008797 dimer interface [polypeptide binding]; other site 295405008798 pyridoxal binding site [chemical binding]; other site 295405008799 ATP binding site [chemical binding]; other site 295405008800 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 295405008801 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 295405008802 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 295405008803 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 295405008804 Cysteine-rich domain; Region: CCG; pfam02754 295405008805 Cysteine-rich domain; Region: CCG; pfam02754 295405008806 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 295405008807 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 295405008808 FeS/SAM binding site; other site 295405008809 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 295405008810 active site 295405008811 Protein of unknown function (DUF454); Region: DUF454; pfam04304 295405008812 nucleosidase; Provisional; Region: PRK05634 295405008813 Phosphorylase superfamily; Region: PNP_UDP_1; pfam01048 295405008814 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 295405008815 Acyltransferase family; Region: Acyl_transf_3; pfam01757 295405008816 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 295405008817 Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism]; Region: CutC; COG3142 295405008818 phosphodiesterase; Provisional; Region: PRK12704 295405008819 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 295405008820 Zn2+ binding site [ion binding]; other site 295405008821 Mg2+ binding site [ion binding]; other site 295405008822 Cell division protein ZapA; Region: ZapA; pfam05164 295405008823 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 295405008824 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 295405008825 Malic enzyme, N-terminal domain; Region: malic; pfam00390 295405008826 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 295405008827 putative NAD(P) binding site [chemical binding]; other site 295405008828 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 295405008829 glutamate dehydrogenase; Provisional; Region: PRK14031 295405008830 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 295405008831 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 295405008832 NAD(P) binding site [chemical binding]; other site 295405008833 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405008834 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405008835 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 295405008836 DNA binding residues [nucleotide binding] 295405008837 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405008838 FecR protein; Region: FecR; pfam04773 295405008839 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405008840 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405008841 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405008842 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 295405008843 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 295405008844 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405008845 Endo-beta-N-acetylglucosaminidases are bacterial chitinases that hydrolyze the chitin core of various asparagine (N)-linked glycans and glycoproteins. The endo-beta-N-acetylglucosaminidases have a glycosyl hydrolase family 18 (GH18) catalytic domain; Region: GH18_EndoS-like; cd06542 295405008846 active site 295405008847 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 295405008848 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 295405008849 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 295405008850 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 295405008851 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 295405008852 non-specific DNA binding site [nucleotide binding]; other site 295405008853 salt bridge; other site 295405008854 sequence-specific DNA binding site [nucleotide binding]; other site 295405008855 AAA domain; Region: AAA_21; pfam13304 295405008856 Putative glycoside hydrolase xylanase; Region: Xylanase; pfam13201 295405008857 Fibronectin type 3 domain; Region: FN3; smart00060 295405008858 Putative glycoside hydrolase xylanase; Region: Xylanase; pfam13201 295405008859 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 295405008860 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 295405008861 intermolecular recognition site; other site 295405008862 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; cl17736 295405008863 active site 295405008864 phosphorylation site [posttranslational modification] 295405008865 intermolecular recognition site; other site 295405008866 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 295405008867 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 295405008868 glutamate dehydrogenase; Provisional; Region: PRK14030 295405008869 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 295405008870 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 295405008871 NAD(P) binding site [chemical binding]; other site 295405008872 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 295405008873 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 295405008874 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cd01066 295405008875 active site 295405008876 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 295405008877 binding surface 295405008878 TPR motif; other site 295405008879 Tetratricopeptide repeat; Region: TPR_16; pfam13432 295405008880 CARDB; Region: CARDB; pfam07705 295405008881 Caspase domain; Region: Peptidase_C14; pfam00656 295405008882 FOG: WD40 repeat [General function prediction only]; Region: COG2319 295405008883 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 295405008884 structural tetrad; other site 295405008885 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 295405008886 tRNA adenylyltransferase; Region: tRNA_CCA_actino; TIGR02692 295405008887 active site 295405008888 NTP binding site [chemical binding]; other site 295405008889 metal binding triad [ion binding]; metal-binding site 295405008890 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 295405008891 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 295405008892 Zn2+ binding site [ion binding]; other site 295405008893 Mg2+ binding site [ion binding]; other site 295405008894 aconitate hydratase, mitochondrial; Region: aconitase_mito; TIGR01340 295405008895 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 295405008896 DNA-binding site [nucleotide binding]; DNA binding site 295405008897 RNA-binding motif; other site 295405008898 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 295405008899 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 295405008900 Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: CapC; COG4464 295405008901 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405008902 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405008903 NAD(P) binding site [chemical binding]; other site 295405008904 active site 295405008905 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 295405008906 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 295405008907 metal-binding site 295405008908 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405008909 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 295405008910 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 295405008911 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 295405008912 active site 295405008913 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 295405008914 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 295405008915 trimer interface [polypeptide binding]; other site 295405008916 active site 295405008917 substrate binding site [chemical binding]; other site 295405008918 CoA binding site [chemical binding]; other site 295405008919 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 295405008920 active site 295405008921 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405008922 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 295405008923 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 295405008924 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 295405008925 active site 295405008926 homodimer interface [polypeptide binding]; other site 295405008927 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 295405008928 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 295405008929 active site 295405008930 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 295405008931 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_10; cd13125 295405008932 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 295405008933 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 295405008934 inhibitor-cofactor binding pocket; inhibition site 295405008935 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405008936 catalytic residue [active] 295405008937 Formyltransferase, catalytic core domain; Region: FMT_core; cd08369 295405008938 active site 295405008939 substrate binding site [chemical binding]; other site 295405008940 cosubstrate binding site; other site 295405008941 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 295405008942 catalytic site [active] 295405008943 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 295405008944 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 295405008945 WxcM-like, C-terminal; Region: FdtA; pfam05523 295405008946 WxcM-like, C-terminal; Region: FdtA; pfam05523 295405008947 WxcM-like, C-terminal; Region: FdtA; pfam05523 295405008948 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 295405008949 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 295405008950 substrate binding site; other site 295405008951 tetramer interface; other site 295405008952 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 295405008953 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 295405008954 Mg++ binding site [ion binding]; other site 295405008955 putative catalytic motif [active] 295405008956 substrate binding site [chemical binding]; other site 295405008957 UpxZ family of transcription anti-terminator antagonists; Region: UpxZ; pfam06603 295405008958 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 295405008959 KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); Region: KOW; cl00354 295405008960 VirE N-terminal domain; Region: VirE_N; pfam08800 295405008961 Virulence-associated protein E; Region: VirE; pfam05272 295405008962 Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]; Region: RelE; COG2026 295405008963 Domain of unknown function (DUF4248); Region: DUF4248; pfam14053 295405008964 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 295405008965 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 295405008966 tetramer (dimer of dimers) interface [polypeptide binding]; other site 295405008967 active site 295405008968 dimer interface [polypeptide binding]; other site 295405008969 Protein of unknown function (DUF3843); Region: DUF3843; pfam12954 295405008970 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 295405008971 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 295405008972 cofactor binding site; other site 295405008973 DNA binding site [nucleotide binding] 295405008974 substrate interaction site [chemical binding]; other site 295405008975 N-terminal domain of type IIE restriction endonuclease EcoRII and similar proteins; Region: EcoRII_N; cd10016 295405008976 DNA binding site [nucleotide binding] 295405008977 EcoRII C terminal; Region: EcoRII-C; pfam09019 295405008978 Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches; Region: Vsr; cd00221 295405008979 additional DNA contacts [nucleotide binding]; other site 295405008980 mismatch recognition site; other site 295405008981 active site 295405008982 zinc binding site [ion binding]; other site 295405008983 DNA intercalation site [nucleotide binding]; other site 295405008984 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 295405008985 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 295405008986 Coenzyme A binding pocket [chemical binding]; other site 295405008987 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 295405008988 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 295405008989 non-specific DNA binding site [nucleotide binding]; other site 295405008990 salt bridge; other site 295405008991 sequence-specific DNA binding site [nucleotide binding]; other site 295405008992 Domain of unknown function (DUF955); Region: DUF955; cl01076 295405008993 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 295405008994 RuvA N terminal domain; Region: RuvA_N; pfam01330 295405008995 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 295405008996 diaminopimelate dehydrogenase; Region: DAP-DH; TIGR01921 295405008997 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 295405008998 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 295405008999 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 295405009000 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK07111 295405009001 ATP cone domain; Region: ATP-cone; pfam03477 295405009002 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 295405009003 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 295405009004 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; cl15804 295405009005 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG; TIGR02491 295405009006 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 295405009007 Major Facilitator Superfamily; Region: MFS_1; pfam07690 295405009008 putative substrate translocation pore; other site 295405009009 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 295405009010 2-aminoethylphosphonate--pyruvate transaminase; Provisional; Region: PRK13479 295405009011 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 295405009012 catalytic residue [active] 295405009013 phosphonoacetaldehyde hydrolase; Provisional; Region: PRK13478 295405009014 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 295405009015 motif II; other site 295405009016 RIP metalloprotease RseP; Region: TIGR00054 295405009017 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 295405009018 active site 295405009019 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 295405009020 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 295405009021 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 295405009022 putative substrate binding region [chemical binding]; other site 295405009023 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 295405009024 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 295405009025 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 295405009026 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 295405009027 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 295405009028 Peptidase family M23; Region: Peptidase_M23; pfam01551 295405009029 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 295405009030 RimM N-terminal domain; Region: RimM; pfam01782 295405009031 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 295405009032 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 295405009033 hinge; other site 295405009034 active site 295405009035 Domain of unknown function (DUF4290); Region: DUF4290; pfam14123 295405009036 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 295405009037 Glycoprotease family; Region: Peptidase_M22; pfam00814 295405009038 hypothetical protein; Provisional; Region: PRK11820 295405009039 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 295405009040 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 295405009041 Guanylate kinase; Region: Guanylate_kin; pfam00625 295405009042 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 295405009043 catalytic site [active] 295405009044 G-X2-G-X-G-K; other site 295405009045 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 295405009046 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 295405009047 active site 295405009048 (T/H)XGH motif; other site 295405009049 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 295405009050 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 295405009051 putative active site [active] 295405009052 putative metal binding site [ion binding]; other site 295405009053 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 295405009054 UbiA prenyltransferase family; Region: UbiA; pfam01040 295405009055 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 295405009056 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 295405009057 NAD binding site [chemical binding]; other site 295405009058 substrate binding site [chemical binding]; other site 295405009059 homodimer interface [polypeptide binding]; other site 295405009060 active site 295405009061 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 295405009062 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 295405009063 substrate binding site; other site 295405009064 tetramer interface; other site 295405009065 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 295405009066 active site 295405009067 metal binding site [ion binding]; metal-binding site 295405009068 homotetramer interface [polypeptide binding]; other site 295405009069 polyphosphate kinase; Provisional; Region: PRK05443 295405009070 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 295405009071 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 295405009072 Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C1_like; cd09164 295405009073 domain interface [polypeptide binding]; other site 295405009074 active site 295405009075 catalytic site [active] 295405009076 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 295405009077 domain interface [polypeptide binding]; other site 295405009078 active site 295405009079 catalytic site [active] 295405009080 Phosphate transporter family; Region: PHO4; cl00396 295405009081 Response regulator receiver domain; Region: Response_reg; pfam00072 295405009082 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 295405009083 active site 295405009084 phosphorylation site [posttranslational modification] 295405009085 intermolecular recognition site; other site 295405009086 dimerization interface [polypeptide binding]; other site 295405009087 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 295405009088 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405009089 Walker A/P-loop; other site 295405009090 ATP binding site [chemical binding]; other site 295405009091 Q-loop/lid; other site 295405009092 ABC transporter signature motif; other site 295405009093 Walker B; other site 295405009094 D-loop; other site 295405009095 H-loop/switch region; other site 295405009096 ABC transporter; Region: ABC_tran_2; pfam12848 295405009097 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 295405009098 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 295405009099 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 295405009100 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 295405009101 Protein export membrane protein; Region: SecD_SecF; cl14618 295405009102 Outer membrane efflux protein; Region: OEP; pfam02321 295405009103 Outer membrane efflux protein; Region: OEP; pfam02321 295405009104 Glycosyl hydrolase family 43; Region: GH43_5; cd08984 295405009105 active site 295405009106 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 295405009107 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 295405009108 S-adenosylmethionine binding site [chemical binding]; other site 295405009109 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; pfam13636 295405009110 ORF6N domain; Region: ORF6N; pfam10543 295405009111 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 295405009112 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405009113 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 295405009114 DNA binding residues [nucleotide binding] 295405009115 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 295405009116 PLD-like domain; Region: PLDc_2; pfam13091 295405009117 putative active site [active] 295405009118 catalytic site [active] 295405009119 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 295405009120 PLD-like domain; Region: PLDc_2; pfam13091 295405009121 putative active site [active] 295405009122 catalytic site [active] 295405009123 thymidylate synthase; Reviewed; Region: thyA; PRK01827 295405009124 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 295405009125 dimerization interface [polypeptide binding]; other site 295405009126 active site 295405009127 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 295405009128 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 295405009129 folate binding site [chemical binding]; other site 295405009130 NADP+ binding site [chemical binding]; other site 295405009131 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 295405009132 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 295405009133 putative DNA binding site [nucleotide binding]; other site 295405009134 putative Zn2+ binding site [ion binding]; other site 295405009135 AsnC family; Region: AsnC_trans_reg; pfam01037 295405009136 IgA Peptidase M64; Region: Peptidase_M64; pfam09471 295405009137 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 295405009138 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 295405009139 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 295405009140 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 295405009141 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 295405009142 active site 295405009143 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 295405009144 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 295405009145 substrate binding pocket [chemical binding]; other site 295405009146 chain length determination region; other site 295405009147 substrate-Mg2+ binding site; other site 295405009148 catalytic residues [active] 295405009149 aspartate-rich region 1; other site 295405009150 active site lid residues [active] 295405009151 aspartate-rich region 2; other site 295405009152 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 295405009153 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 295405009154 cytidylate kinase; Provisional; Region: cmk; PRK00023 295405009155 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 295405009156 CMP-binding site; other site 295405009157 The sites determining sugar specificity; other site 295405009158 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 295405009159 LytB protein; Region: LYTB; cl00507 295405009160 6-phosphofructokinase; Provisional; Region: PRK03202 295405009161 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 295405009162 active site 295405009163 ADP/pyrophosphate binding site [chemical binding]; other site 295405009164 dimerization interface [polypeptide binding]; other site 295405009165 allosteric effector site; other site 295405009166 fructose-1,6-bisphosphate binding site; other site 295405009167 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 295405009168 retinol dehydrogenase (retinol-DH), Light dependent Protochlorophyllide (Pchlide) OxidoReductase (LPOR) and related proteins, classical (c) SDRs; Region: retinol-DH_like_SDR_c_like; cd05327 295405009169 putative NAD(P) binding site [chemical binding]; other site 295405009170 active site 295405009171 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 295405009172 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN_family; cd02803 295405009173 active site 295405009174 FMN binding site [chemical binding]; other site 295405009175 substrate binding site [chemical binding]; other site 295405009176 putative catalytic residue [active] 295405009177 3-oxo-5-alpha-steroid 4-dehydrogenase; Region: Steroid_dh; cl17474 295405009178 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 295405009179 isocitrate dehydrogenase; Validated; Region: PRK06451 295405009180 aconitate hydratase, mitochondrial; Region: aconitase_mito; TIGR01340 295405009181 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 295405009182 substrate binding site [chemical binding]; other site 295405009183 ligand binding site [chemical binding]; other site 295405009184 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 295405009185 substrate binding site [chemical binding]; other site 295405009186 AAA domain; Region: AAA_11; pfam13086 295405009187 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 295405009188 ATP binding site [chemical binding]; other site 295405009189 AAA domain; Region: AAA_30; pfam13604 295405009190 AAA domain; Region: AAA_12; pfam13087 295405009191 Domain of unknown function (DUF4114); Region: DUF4114; pfam13448 295405009192 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 295405009193 ketol-acid reductoisomerase; Region: ilvC; TIGR00465 295405009194 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 295405009195 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 295405009196 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 295405009197 active site 295405009198 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 295405009199 active site 2 [active] 295405009200 Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]; Region: IlvH; COG0440 295405009201 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 295405009202 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 295405009203 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 295405009204 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 295405009205 PYR/PP interface [polypeptide binding]; other site 295405009206 dimer interface [polypeptide binding]; other site 295405009207 TPP binding site [chemical binding]; other site 295405009208 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 295405009209 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 295405009210 TPP-binding site [chemical binding]; other site 295405009211 dimer interface [polypeptide binding]; other site 295405009212 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 295405009213 Domain of unknown function (DUF4221); Region: DUF4221; pfam13970 295405009214 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; pfam09603 295405009215 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; pfam09603 295405009216 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; pfam09603 295405009217 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 295405009218 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 295405009219 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 295405009220 ligand binding site [chemical binding]; other site 295405009221 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 295405009222 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405009223 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 295405009224 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 295405009225 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 295405009226 Glycosyl hydrolase family 43; Region: GH43_6; cd08985 295405009227 active site 295405009228 Putative glycoside hydrolase xylanase; Region: Xylanase; pfam13201 295405009229 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 295405009230 Lipocalin-like domain; Region: Lipocalin_6; pfam13944 295405009231 Putative glycoside hydrolase xylanase; Region: Xylanase; pfam13201 295405009232 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 295405009233 putative catalytic site [active] 295405009234 putative metal binding site [ion binding]; other site 295405009235 putative phosphate binding site [ion binding]; other site 295405009236 Uncharacterized conserved protein [Function unknown]; Region: COG3379 295405009237 Phosphopentomutase [Carbohydrate transport and metabolism]; Region: DeoB; cl17415 295405009238 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 295405009239 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 295405009240 active site 295405009241 metal binding site [ion binding]; metal-binding site 295405009242 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 295405009243 active site 295405009244 PQQ-like domain; Region: PQQ_2; pfam13360 295405009245 Trp docking motif [polypeptide binding]; other site 295405009246 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405009247 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405009248 SusD family; Region: SusD; pfam07980 295405009249 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405009250 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405009251 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405009252 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405009253 FecR protein; Region: FecR; pfam04773 295405009254 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405009255 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405009256 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 295405009257 DNA binding residues [nucleotide binding] 295405009258 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405009259 SusD family; Region: SusD; pfam07980 295405009260 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405009261 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405009262 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405009263 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 295405009264 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 295405009265 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 295405009266 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405009267 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405009268 SusD family; Region: SusD; pfam07980 295405009269 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405009270 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405009271 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405009272 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405009273 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 295405009274 FecR protein; Region: FecR; pfam04773 295405009275 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 295405009276 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405009277 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 295405009278 DNA binding residues [nucleotide binding] 295405009279 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 295405009280 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 295405009281 Tetramer interface [polypeptide binding]; other site 295405009282 active site 295405009283 FMN-binding site [chemical binding]; other site 295405009284 hypothetical protein; Provisional; Region: PRK08201 295405009285 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_3; cd05680 295405009286 metal binding site [ion binding]; metal-binding site 295405009287 putative dimer interface [polypeptide binding]; other site 295405009288 Choloylglycine hydrolase (CGH) is a bile salt-modifying enzyme that hydrolyzes non-peptide carbon-nitrogen bonds in choloylglycine and choloyltaurine, both of which are present in bile. CGH is present in a number of probiotic microbial organisms that...; Region: Ntn_CGH; cd01902 295405009289 Linear amide C-N hydrolases, choloylglycine hydrolase family; Region: CBAH; pfam02275 295405009290 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 295405009291 catalytic residues [active] 295405009292 Domain of unknown function (DUF4396); Region: DUF4396; pfam14342 295405009293 DNA topoisomerase III; Provisional; Region: PRK07726 295405009294 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 295405009295 active site 295405009296 putative interdomain interaction site [polypeptide binding]; other site 295405009297 putative metal-binding site [ion binding]; other site 295405009298 putative nucleotide binding site [chemical binding]; other site 295405009299 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 295405009300 domain I; other site 295405009301 DNA binding groove [nucleotide binding] 295405009302 phosphate binding site [ion binding]; other site 295405009303 domain II; other site 295405009304 domain III; other site 295405009305 nucleotide binding site [chemical binding]; other site 295405009306 catalytic site [active] 295405009307 domain IV; other site 295405009308 Alpha-L-fucosidase; Region: Alpha_L_fucos; pfam01120 295405009309 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 295405009310 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 295405009311 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain...; Region: MM_CoA_mutase_alpha_like; cd03679 295405009312 active site 295405009313 substrate binding site [chemical binding]; other site 295405009314 coenzyme B12 binding site [chemical binding]; other site 295405009315 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 295405009316 B12 binding site [chemical binding]; other site 295405009317 cobalt ligand [ion binding]; other site 295405009318 methylmalonyl-CoA mutase, heterodimeric type, beta chain; Region: mmCoA_mut_beta; TIGR00642 295405009319 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Beta subunit-like subfamily; contains bacterial proteins similar to the beta subunit of MCMs from Propionbacterium shermanni and Streptomyces cinnamonensis, which are alpha/beta...; Region: MM_CoA_mutase_beta; cd03677 295405009320 heterodimer interface [polypeptide binding]; other site 295405009321 substrate interaction site [chemical binding]; other site 295405009322 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 295405009323 putative transporter; Validated; Region: PRK03818 295405009324 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 295405009325 TrkA-C domain; Region: TrkA_C; pfam02080 295405009326 TrkA-C domain; Region: TrkA_C; pfam02080 295405009327 AspT/YidE/YbjL antiporter duplication domain; Region: YidE_YbjL_dupl; TIGR01625 295405009328 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 295405009329 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 295405009330 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 295405009331 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 295405009332 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 295405009333 ligand binding site [chemical binding]; other site 295405009334 flexible hinge region; other site 295405009335 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 295405009336 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 295405009337 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 295405009338 active site 295405009339 nucleophile elbow; other site 295405009340 Surface antigen; Region: Bac_surface_Ag; pfam01103 295405009341 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 295405009342 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 295405009343 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 295405009344 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 295405009345 dimer interface [polypeptide binding]; other site 295405009346 putative anticodon binding site; other site 295405009347 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 295405009348 motif 1; other site 295405009349 active site 295405009350 motif 2; other site 295405009351 motif 3; other site 295405009352 Domain of unknown function (DUF4332); Region: DUF4332; pfam14229 295405009353 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GpsA; COG0240 295405009354 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 295405009355 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 295405009356 glucose-6-phosphate isomerase; Provisional; Region: pgi; PRK14097 295405009357 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 295405009358 active site 295405009359 dimer interface [polypeptide binding]; other site 295405009360 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 295405009361 dimer interface [polypeptide binding]; other site 295405009362 active site 295405009363 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 295405009364 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 295405009365 motif II; other site 295405009366 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 295405009367 dimer interface [polypeptide binding]; other site 295405009368 active site 295405009369 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 295405009370 ligand binding site [chemical binding]; other site 295405009371 active site 295405009372 UGI interface [polypeptide binding]; other site 295405009373 catalytic site [active] 295405009374 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 295405009375 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 295405009376 Zn2+ binding site [ion binding]; other site 295405009377 Mg2+ binding site [ion binding]; other site 295405009378 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 295405009379 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 295405009380 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 295405009381 active site 295405009382 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C; pfam03174 295405009383 PA14 domain; Region: PA14; pfam07691 295405009384 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 295405009385 Coenzyme A binding pocket [chemical binding]; other site 295405009386 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 295405009387 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 295405009388 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 295405009389 active site 295405009390 metal binding site [ion binding]; metal-binding site 295405009391 virulence factor Mce family protein; Region: Mtu_fam_mce; TIGR00996 295405009392 mce related protein; Region: MCE; pfam02470 295405009393 DnaA N-terminal domain; Region: DnaA_N; pfam11638 295405009394 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 295405009395 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 295405009396 Walker A motif; other site 295405009397 ATP binding site [chemical binding]; other site 295405009398 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 295405009399 Walker B motif; other site 295405009400 arginine finger; other site 295405009401 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 295405009402 DnaA box-binding interface [nucleotide binding]; other site 295405009403 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 295405009404 dimer interface [polypeptide binding]; other site 295405009405 FMN binding site [chemical binding]; other site 295405009406 NADPH bind site [chemical binding]; other site 295405009407 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 295405009408 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 295405009409 active site 295405009410 dimer interface [polypeptide binding]; other site 295405009411 effector binding site; other site 295405009412 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 295405009413 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; cd05467 295405009414 4-alpha-glucanotransferase; Region: PLN02950 295405009415 starch-binding site 2 [chemical binding]; other site 295405009416 starch-binding site 1 [chemical binding]; other site 295405009417 Disproportionating enzyme 2 (DPE2), N-terminal CBM20 (carbohydrate-binding module, family 20) domain, repeat 2. DPE2 is a transglucosidase that is essential for the cytosolic metabolism of maltose in plant leaves at night. Maltose is an intermediate on...; Region: CBM20_DPE2_repeat2; cd05816 295405009418 starch binding site 2 [chemical binding]; other site 295405009419 starch binding site 1 [chemical binding]; other site 295405009420 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 295405009421 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 295405009422 Acyltransferase family; Region: Acyl_transf_3; pfam01757 295405009423 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 295405009424 active site 295405009425 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 295405009426 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405009427 catalytic residues [active] 295405009428 Peptidase M15; Region: Peptidase_M15_3; pfam08291 295405009429 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 295405009430 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405009431 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405009432 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405009433 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 295405009434 active site 295405009435 Peptidase M15; Region: Peptidase_M15_3; pfam08291 295405009436 Protein of unknown function (DUF2589); Region: DUF2589; pfam11655 295405009437 Protein of unknown function (DUF2589); Region: DUF2589; pfam11655 295405009438 Protein of unknown function (DUF2589); Region: DUF2589; pfam11655 295405009439 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405009440 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405009441 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405009442 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405009443 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405009444 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405009445 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405009446 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 295405009447 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405009448 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405009449 Fic family protein [Function unknown]; Region: COG3177 295405009450 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 295405009451 Fic/DOC family; Region: Fic; pfam02661 295405009452 Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to...; Region: MGS; cd01422 295405009453 active site 295405009454 dimer interfaces [polypeptide binding]; other site 295405009455 catalytic residues [active] 295405009456 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 295405009457 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 295405009458 Probable Catalytic site; other site 295405009459 metal-binding site 295405009460 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 295405009461 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 295405009462 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 295405009463 putative acyl-acceptor binding pocket; other site 295405009464 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 295405009465 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 295405009466 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 295405009467 FeS/SAM binding site; other site 295405009468 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 295405009469 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 295405009470 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 295405009471 putative AMP binding site [chemical binding]; other site 295405009472 putative active site [active] 295405009473 acyl-activating enzyme (AAE) consensus motif; other site 295405009474 putative CoA binding site [chemical binding]; other site 295405009475 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 295405009476 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 295405009477 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 295405009478 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 295405009479 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 295405009480 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 295405009481 MarR family; Region: MarR_2; pfam12802 295405009482 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 295405009483 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 295405009484 active site 295405009485 phosphorylation site [posttranslational modification] 295405009486 intermolecular recognition site; other site 295405009487 dimerization interface [polypeptide binding]; other site 295405009488 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 295405009489 DNA binding site [nucleotide binding] 295405009490 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405009491 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 295405009492 dimer interface [polypeptide binding]; other site 295405009493 phosphorylation site [posttranslational modification] 295405009494 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 295405009495 ATP binding site [chemical binding]; other site 295405009496 Mg2+ binding site [ion binding]; other site 295405009497 G-X-G motif; other site 295405009498 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 295405009499 elongation factor G; Reviewed; Region: PRK12740 295405009500 G1 box; other site 295405009501 putative GEF interaction site [polypeptide binding]; other site 295405009502 GTP/Mg2+ binding site [chemical binding]; other site 295405009503 Switch I region; other site 295405009504 G2 box; other site 295405009505 G3 box; other site 295405009506 Switch II region; other site 295405009507 G4 box; other site 295405009508 G5 box; other site 295405009509 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 295405009510 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 295405009511 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 295405009512 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 295405009513 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 295405009514 FeS/SAM binding site; other site 295405009515 HemN C-terminal domain; Region: HemN_C; pfam06969 295405009516 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405009517 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405009518 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 295405009519 DNA binding residues [nucleotide binding] 295405009520 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405009521 FecR protein; Region: FecR; pfam04773 295405009522 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405009523 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405009524 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405009525 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 295405009526 Domain of unknown function (DUF4249); Region: DUF4249; pfam14054 295405009527 Domain of unknown function (DUF2357); Region: DUF2357; pfam09823 295405009528 Membrane protein of unknown function (DUF340); Region: DUF340; pfam03956 295405009529 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 295405009530 non-specific DNA binding site [nucleotide binding]; other site 295405009531 salt bridge; other site 295405009532 sequence-specific DNA binding site [nucleotide binding]; other site 295405009533 Domain of unknown function (DUF955); Region: DUF955; pfam06114 295405009534 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 295405009535 Archaeal ATPase; Region: Arch_ATPase; pfam01637 295405009536 Domain of unknown function (DUF2027); Region: DUF2027; pfam09640 295405009537 Smr domain; Region: Smr; pfam01713 295405009538 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 295405009539 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 295405009540 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_34; cd04693 295405009541 nudix motif; other site 295405009542 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 295405009543 catalytic residues [active] 295405009544 dimer interface [polypeptide binding]; other site 295405009545 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 295405009546 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 295405009547 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 295405009548 Outer membrane efflux protein; Region: OEP; pfam02321 295405009549 Outer membrane efflux protein; Region: OEP; pfam02321 295405009550 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405009551 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405009552 Histidine kinase; Region: His_kinase; pfam06580 295405009553 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 295405009554 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 295405009555 active site 295405009556 phosphorylation site [posttranslational modification] 295405009557 intermolecular recognition site; other site 295405009558 dimerization interface [polypeptide binding]; other site 295405009559 LytTr DNA-binding domain; Region: LytTR; pfam04397 295405009560 [FeFe] hydrogenase, group B1/B3; Region: FeFe_hydrog_B1; TIGR04105 295405009561 4Fe-4S binding domain; Region: Fer4; cl02805 295405009562 4Fe-4S binding domain; Region: Fer4; pfam00037 295405009563 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 295405009564 [FeFe] hydrogenase H-cluster radical SAM maturase HydE; Region: rSAM_HydE; TIGR03956 295405009565 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 295405009566 FeS/SAM binding site; other site 295405009567 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 295405009568 [FeFe] hydrogenase H-cluster radical SAM maturase HydG; Region: rSAM_HydG; TIGR03955 295405009569 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 295405009570 FeS/SAM binding site; other site 295405009571 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 295405009572 [FeFe] hydrogenase H-cluster maturation GTPase HydF; Region: GTP_HydF; TIGR03918 295405009573 E. coli Ras-like protein (Era)-like GTPase; Region: Era_like; cd00880 295405009574 G1 box; other site 295405009575 GTP/Mg2+ binding site [chemical binding]; other site 295405009576 Switch I region; other site 295405009577 G2 box; other site 295405009578 Switch II region; other site 295405009579 G3 box; other site 295405009580 G4 box; other site 295405009581 G5 box; other site 295405009582 Glycosyl hydrolases family 35; Region: Glyco_hydro_35; pfam01301 295405009583 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405009584 sugar binding site [chemical binding]; other site 295405009585 phosphoglucosamine mutase; Region: Arch_GlmM; TIGR03990 295405009586 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 295405009587 active site 295405009588 substrate binding site [chemical binding]; other site 295405009589 metal binding site [ion binding]; metal-binding site 295405009590 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 295405009591 DHH family; Region: DHH; pfam01368 295405009592 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 295405009593 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 295405009594 Competence protein; Region: Competence; pfam03772 295405009595 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 295405009596 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 295405009597 substrate binding site [chemical binding]; other site 295405009598 hexamer interface [polypeptide binding]; other site 295405009599 metal binding site [ion binding]; metal-binding site 295405009600 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 295405009601 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 295405009602 putative active site [active] 295405009603 substrate binding site [chemical binding]; other site 295405009604 putative cosubstrate binding site; other site 295405009605 catalytic site [active] 295405009606 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 295405009607 substrate binding site [chemical binding]; other site 295405009608 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 295405009609 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 295405009610 Cl- selectivity filter; other site 295405009611 Cl- binding residues [ion binding]; other site 295405009612 pore gating glutamate residue; other site 295405009613 dimer interface [polypeptide binding]; other site 295405009614 FOG: CBS domain [General function prediction only]; Region: COG0517 295405009615 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 295405009616 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 295405009617 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 295405009618 active site 295405009619 Domain of unknown function (DUF4114); Region: DUF4114; pfam13448 295405009620 Protein of unknown function (DUF1703); Region: DUF1703; pfam08011 295405009621 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 295405009622 Protein of unknown function (DUF3380); Region: DUF3380; pfam11860 295405009623 Bacterial sugar transferase; Region: Bac_transf; pfam02397 295405009624 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 295405009625 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 295405009626 inhibitor-cofactor binding pocket; inhibition site 295405009627 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405009628 catalytic residue [active] 295405009629 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 295405009630 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 295405009631 Coenzyme A binding pocket [chemical binding]; other site 295405009632 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 295405009633 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405009634 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 295405009635 putative glycosyl transferase; Provisional; Region: PRK10125 295405009636 GDP-fucose protein O-fucosyltransferase and related proteins; Region: O-FucT_like; cl16914 295405009637 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405009638 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 295405009639 putative ADP-binding pocket [chemical binding]; other site 295405009640 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 295405009641 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 295405009642 active site 295405009643 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 295405009644 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 295405009645 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 295405009646 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405009647 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 295405009648 putative NAD(P) binding site [chemical binding]; other site 295405009649 active site 295405009650 putative substrate binding site [chemical binding]; other site 295405009651 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 295405009652 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405009653 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 295405009654 UpxZ family of transcription anti-terminator antagonists; Region: UpxZ; pfam06603 295405009655 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 295405009656 Domain of unknown function (DUF4373); Region: DUF4373; pfam14297 295405009657 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 295405009658 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 295405009659 DHH family; Region: DHH; pfam01368 295405009660 DHHA1 domain; Region: DHHA1; pfam02272 295405009661 DEAD-like helicases superfamily; Region: DEXDc; smart00487 295405009662 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 295405009663 ATP binding site [chemical binding]; other site 295405009664 putative Mg++ binding site [ion binding]; other site 295405009665 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 295405009666 nucleotide binding region [chemical binding]; other site 295405009667 ATP-binding site [chemical binding]; other site 295405009668 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 295405009669 putative DNA binding site [nucleotide binding]; other site 295405009670 putative Zn2+ binding site [ion binding]; other site 295405009671 TPR repeat; Region: TPR_11; pfam13414 295405009672 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 295405009673 binding surface 295405009674 TPR motif; other site 295405009675 Tetratricopeptide repeat; Region: TPR_16; pfam13432 295405009676 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 295405009677 binding surface 295405009678 TPR motif; other site 295405009679 TPR repeat; Region: TPR_11; pfam13414 295405009680 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 295405009681 TPR motif; other site 295405009682 TPR repeat; Region: TPR_11; pfam13414 295405009683 binding surface 295405009684 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 295405009685 putative substrate translocation pore; other site 295405009686 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 295405009687 catalytic site [active] 295405009688 BNR repeat-like domain; Region: BNR_2; pfam13088 295405009689 Asp-box motif; other site 295405009690 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 295405009691 Asp-box motif; other site 295405009692 catalytic site [active] 295405009693 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405009694 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405009695 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405009696 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405009697 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405009698 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 295405009699 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 295405009700 Class I aldolases; Region: Aldolase_Class_I; cl17187 295405009701 catalytic residue [active] 295405009702 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 295405009703 DNA-binding site [nucleotide binding]; DNA binding site 295405009704 Transcriptional regulators [Transcription]; Region: FadR; COG2186 295405009705 FCD domain; Region: FCD; pfam07729 295405009706 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 295405009707 Prephenate dehydratase; Region: PDT; pfam00800 295405009708 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 295405009709 putative L-Phe binding site [chemical binding]; other site 295405009710 LL-diaminopimelate aminotransferase; Provisional; Region: PRK09276 295405009711 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 295405009712 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405009713 homodimer interface [polypeptide binding]; other site 295405009714 catalytic residue [active] 295405009715 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 295405009716 Chorismate mutase type II; Region: CM_2; smart00830 295405009717 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 295405009718 Alanine dehydrogenase/PNT, C-terminal domain; Region: AlaDh_PNT_C; smart01002 295405009719 prephenate dehydrogenase; Validated; Region: PRK08507 295405009720 DNA primase, catalytic core; Region: dnaG; TIGR01391 295405009721 CHC2 zinc finger; Region: zf-CHC2; pfam01807 295405009722 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 295405009723 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 295405009724 active site 295405009725 metal binding site [ion binding]; metal-binding site 295405009726 interdomain interaction site; other site 295405009727 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 295405009728 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405009729 Sulfatase; Region: Sulfatase; pfam00884 295405009730 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405009731 Sulfatase; Region: Sulfatase; pfam00884 295405009732 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405009733 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405009734 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405009735 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405009736 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405009737 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 295405009738 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405009739 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405009740 FecR protein; Region: FecR; pfam04773 295405009741 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405009742 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405009743 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 295405009744 DNA binding residues [nucleotide binding] 295405009745 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 295405009746 homodecamer interface [polypeptide binding]; other site 295405009747 GTP cyclohydrolase I; Provisional; Region: PLN03044 295405009748 active site 295405009749 putative catalytic site residues [active] 295405009750 zinc binding site [ion binding]; other site 295405009751 GTP-CH-I/GFRP interaction surface; other site 295405009752 Sporulation related domain; Region: SPOR; pfam05036 295405009753 triosephosphate isomerase; Provisional; Region: PRK14567 295405009754 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 295405009755 substrate binding site [chemical binding]; other site 295405009756 dimer interface [polypeptide binding]; other site 295405009757 catalytic triad [active] 295405009758 DoxX; Region: DoxX; pfam07681 295405009759 Domain of Unknown Function (DUF1599); Region: DUF1599; pfam07659 295405009760 Domain of Unknown Function (DUF1599); Region: DUF1599; pfam07659 295405009761 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 295405009762 Peptidase family M23; Region: Peptidase_M23; pfam01551 295405009763 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 295405009764 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 295405009765 active site 295405009766 multimer interface [polypeptide binding]; other site 295405009767 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 295405009768 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 295405009769 generic binding surface II; other site 295405009770 ssDNA binding site; other site 295405009771 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 295405009772 ATP binding site [chemical binding]; other site 295405009773 putative Mg++ binding site [ion binding]; other site 295405009774 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 295405009775 nucleotide binding region [chemical binding]; other site 295405009776 ATP-binding site [chemical binding]; other site 295405009777 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 295405009778 substrate binding site; other site 295405009779 dimer interface; other site 295405009780 DJ-1 family protein; Region: not_thiJ; TIGR01383 295405009781 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 295405009782 conserved cys residue [active] 295405009783 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 295405009784 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 295405009785 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 295405009786 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 295405009787 active site 295405009788 hydrophilic channel; other site 295405009789 dimerization interface [polypeptide binding]; other site 295405009790 catalytic residues [active] 295405009791 active site lid [active] 295405009792 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK01911 295405009793 ATP-NAD kinase; Region: NAD_kinase; pfam01513 295405009794 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405009795 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405009796 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 295405009797 DNA binding residues [nucleotide binding] 295405009798 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405009799 FecR protein; Region: FecR; pfam04773 295405009800 fec operon regulator FecR; Reviewed; Region: PRK09774 295405009801 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405009802 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405009803 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405009804 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405009805 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405009806 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405009807 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405009808 SusD family; Region: SusD; pfam07980 295405009809 Putative glycoside hydrolase xylanase; Region: Xylanase; pfam13201 295405009810 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 295405009811 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; pfam03372 295405009812 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 295405009813 putative catalytic site [active] 295405009814 putative phosphate binding site [ion binding]; other site 295405009815 putative metal binding site [ion binding]; other site 295405009816 Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms]; Region: MecR1; COG4219 295405009817 copper transport repressor, CopY/TcrY family; Region: CopY_TcrY; TIGR02698 295405009818 Penicillinase repressor; Region: Pencillinase_R; pfam03965 295405009819 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 295405009820 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 295405009821 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 295405009822 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 295405009823 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 295405009824 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 295405009825 Tricorn protease; serine protease family S41; Region: Peptidase_S41_TRI; cd07562 295405009826 Domain interface; other site 295405009827 Peptide binding site; other site 295405009828 Active site tetrad [active] 295405009829 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 295405009830 malate dehydrogenase; Reviewed; Region: PRK06223 295405009831 dimer interface [polypeptide binding]; other site 295405009832 NAD(P) binding site [chemical binding]; other site 295405009833 tetramer (dimer of dimers) interface [polypeptide binding]; other site 295405009834 substrate binding site [chemical binding]; other site 295405009835 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 295405009836 FecR protein; Region: FecR; pfam04773 295405009837 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405009838 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405009839 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 295405009840 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 295405009841 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405009842 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 295405009843 Outer membrane efflux protein; Region: OEP; pfam02321 295405009844 Outer membrane efflux protein; Region: OEP; pfam02321 295405009845 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 295405009846 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 295405009847 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405009848 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 295405009849 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 295405009850 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 295405009851 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 295405009852 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 295405009853 Members of the SGNH-hydrolase superfamily, 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_like_4; cd04501 295405009854 active site 295405009855 catalytic triad [active] 295405009856 oxyanion hole [active] 295405009857 SGNH_hydrolase subfamily. SGNH hydrolases are 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...; Region: SGNH_hydrolase_like_2; cd01834 295405009858 active site 295405009859 catalytic triad [active] 295405009860 oxyanion hole [active] 295405009861 Penicillinase repressor; Region: Pencillinase_R; pfam03965 295405009862 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 295405009863 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 295405009864 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 295405009865 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 295405009866 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 295405009867 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405009868 catalytic residues [active] 295405009869 Domain of unknown function DUF59; Region: DUF59; pfam01883 295405009870 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 295405009871 tRNA (guanine-N(7)-)-methyltransferase; Reviewed; Region: trmB; PRK00121 295405009872 Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]; Region: COG1237 295405009873 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 295405009874 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 295405009875 homodimer interface [polypeptide binding]; other site 295405009876 substrate-cofactor binding pocket; other site 295405009877 catalytic residue [active] 295405009878 Exonuclease VII small subunit; Region: Exonuc_VII_S; pfam02609 295405009879 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 295405009880 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 295405009881 generic binding surface II; other site 295405009882 generic binding surface I; other site 295405009883 Peptidase S8 family domain, uncharacterized subfamily 9; Region: Peptidases_S8_9; cd07493 295405009884 active site 295405009885 catalytic triad [active] 295405009886 tRNA-specific 2-thiouridylase MnmA; Provisional; Region: PRK14664 295405009887 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 295405009888 Ligand Binding Site [chemical binding]; other site 295405009889 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 295405009890 homotrimer interaction site [polypeptide binding]; other site 295405009891 zinc binding site [ion binding]; other site 295405009892 CDP-binding sites; other site 295405009893 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 295405009894 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 295405009895 redox-sensing transcriptional repressor Rex; Provisional; Region: PRK05472 295405009896 Putative DNA-binding protein N-terminus; Region: Put_DNA-bind_N; pfam06971 295405009897 CoA binding domain; Region: CoA_binding; pfam02629 295405009898 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 295405009899 putative rRNA binding site [nucleotide binding]; other site 295405009900 elongation factor Ts; Provisional; Region: tsf; PRK09377 295405009901 Elongation factor TS; Region: EF_TS; pfam00889 295405009902 Elongation factor TS; Region: EF_TS; pfam00889 295405009903 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 295405009904 rRNA interaction site [nucleotide binding]; other site 295405009905 S8 interaction site; other site 295405009906 putative laminin-1 binding site; other site 295405009907 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 295405009908 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 295405009909 23S rRNA interface [nucleotide binding]; other site 295405009910 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 295405009911 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 295405009912 putative dimer interface [polypeptide binding]; other site 295405009913 putative anticodon binding site; other site 295405009914 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 295405009915 homodimer interface [polypeptide binding]; other site 295405009916 motif 1; other site 295405009917 motif 2; other site 295405009918 active site 295405009919 motif 3; other site 295405009920 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 295405009921 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 295405009922 RNA binding surface [nucleotide binding]; other site 295405009923 Pseudouridine synthases, RsuA subfamily; Region: PseudoU_synth_RsuA_like; cd02870 295405009924 active site 295405009925 adenylosuccinate lyase; Provisional; Region: PRK09285 295405009926 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 295405009927 tetramer interface [polypeptide binding]; other site 295405009928 active site 295405009929 Glycosyl hydrolases family 35; Region: Glyco_hydro_35; pfam01301 295405009930 maltose O-acetyltransferase; Provisional; Region: PRK10092 295405009931 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 295405009932 active site 295405009933 substrate binding site [chemical binding]; other site 295405009934 trimer interface [polypeptide binding]; other site 295405009935 CoA binding site [chemical binding]; other site 295405009936 hypothetical protein; Validated; Region: PRK02101 295405009937 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 295405009938 beta-N-acetylglucosaminidase; Region: NAGidase; pfam07555 295405009939 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405009940 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 295405009941 Calx-beta domain; Region: Calx-beta; cl02522 295405009942 TPR repeat; Region: TPR_11; pfam13414 295405009943 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 295405009944 TPR motif; other site 295405009945 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 295405009946 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 295405009947 ligand binding site [chemical binding]; other site 295405009948 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 295405009949 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405009950 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405009951 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 295405009952 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 295405009953 active site 295405009954 DNA binding site [nucleotide binding] 295405009955 Int/Topo IB signature motif; other site 295405009956 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 295405009957 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 295405009958 carbamoyl-phosphate synthase, large subunit; Region: CPSaseII_lrg; TIGR01369 295405009959 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 295405009960 ATP-grasp domain; Region: ATP-grasp_4; cl17255 295405009961 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 295405009962 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 295405009963 ATP-grasp domain; Region: ATP-grasp_4; cl17255 295405009964 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 295405009965 probable substrate binding site [chemical binding]; other site 295405009966 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 295405009967 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 295405009968 active site 295405009969 HIGH motif; other site 295405009970 dimer interface [polypeptide binding]; other site 295405009971 KMSKS motif; other site 295405009972 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 295405009973 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 295405009974 ligand binding site [chemical binding]; other site 295405009975 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 295405009976 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405009977 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 295405009978 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39B; cd02418 295405009979 putative active site [active] 295405009980 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 295405009981 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 295405009982 Walker A/P-loop; other site 295405009983 ATP binding site [chemical binding]; other site 295405009984 Q-loop/lid; other site 295405009985 ABC transporter signature motif; other site 295405009986 Walker B; other site 295405009987 D-loop; other site 295405009988 H-loop/switch region; other site 295405009989 LanC-like proteins. LanC is the cyclase enzyme of the lanthionine synthetase. Lanthionine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as a precursor peptide and then post-translationally modified to contain...; Region: LanC_like; cl04955 295405009990 Sulfotransferase family; Region: Sulfotransfer_2; pfam03567 295405009991 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 295405009992 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 295405009993 active site 295405009994 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 295405009995 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 295405009996 active site 295405009997 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 295405009998 ligand binding site; other site 295405009999 tetramer interface; other site 295405010000 pseudo-rSAM protein, GG-Bacteroidales system; Region: pseudo_rSAM_GG; TIGR04150 295405010001 Domain of unknown function (DUF4008); Region: DUF4008; cl14869 295405010002 radical SAM peptide maturase, GG-Bacteroidales family; Region: GG_samocin_CFB; TIGR04148 295405010003 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 295405010004 FeS/SAM binding site; other site 295405010005 radical SAM/SPASM domain Clo7bot peptide maturase; Region: rSAM_Clo7bot; TIGR04334 295405010006 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 295405010007 FeS/SAM binding site; other site 295405010008 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 295405010009 Domain present in PSD-95, Dlg, and ZO-1/2; Region: PDZ; smart00228 295405010010 natural product precursor, GG-Bacteroidales family; Region: GG_sam_targ_CFB; TIGR04149 295405010011 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 295405010012 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 295405010013 natural product precursor, GG-Bacteroidales family; Region: GG_sam_targ_CFB; TIGR04149 295405010014 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 295405010015 glycosyltransferase, GG-Bacteroidales peptide system; Region: glyco_rSAM_CFB; TIGR04157 295405010016 Lanthionine synthetase C-like protein; Region: LANC_like; pfam05147 295405010017 N-terminal domain of galactosyltransferase; Region: Glyco_transf_7C; pfam02709 295405010018 LanC-like proteins. LanC is the cyclase enzyme of the lanthionine synthetase. Lanthionine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as a precursor peptide and then post-translationally modified to contain...; Region: LanC_like; cl04955 295405010019 Domain of unknown function (DUF3244); Region: DUF3244; pfam11589 295405010020 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405010021 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 295405010022 binding surface 295405010023 TPR motif; other site 295405010024 Integrase core domain; Region: rve; pfam00665 295405010025 Integrase core domain; Region: rve_3; pfam13683 295405010026 Uncharacterized protein conserved in bacteria (DUF2136); Region: DUF2136; pfam09907 295405010027 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 295405010028 sequence-specific DNA binding site [nucleotide binding]; other site 295405010029 salt bridge; other site 295405010030 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 295405010031 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 295405010032 ATP binding site [chemical binding]; other site 295405010033 Mg2+ binding site [ion binding]; other site 295405010034 G-X-G motif; other site 295405010035 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 295405010036 ATP binding site [chemical binding]; other site 295405010037 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 295405010038 OstA-like protein; Region: OstA_2; pfam13100 295405010039 Rotavirus RNA-binding Protein 53 (NS53); Region: Rota_NS53; pfam00981 295405010040 OstA-like protein; Region: OstA; cl00844 295405010041 OstA-like protein; Region: OstA_2; pfam13100 295405010042 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 295405010043 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 295405010044 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 295405010045 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 295405010046 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 295405010047 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 295405010048 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 295405010049 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 295405010050 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 295405010051 active site 295405010052 Superfamily II DNA helicase [DNA replication, recombination, and repair]; Region: RecQ; COG0514 295405010053 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 295405010054 ATP binding site [chemical binding]; other site 295405010055 putative Mg++ binding site [ion binding]; other site 295405010056 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 295405010057 nucleotide binding region [chemical binding]; other site 295405010058 ATP-binding site [chemical binding]; other site 295405010059 RQC domain; Region: RQC; pfam09382 295405010060 HRDC domain; Region: HRDC; pfam00570 295405010061 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 295405010062 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 295405010063 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 295405010064 Walker A motif; other site 295405010065 ATP binding site [chemical binding]; other site 295405010066 Walker B motif; other site 295405010067 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 295405010068 Clp protease; Region: CLP_protease; pfam00574 295405010069 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 295405010070 oligomer interface [polypeptide binding]; other site 295405010071 active site residues [active] 295405010072 trigger factor; Region: tig; TIGR00115 295405010073 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 295405010074 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 295405010075 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 295405010076 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 295405010077 Walker A/P-loop; other site 295405010078 ATP binding site [chemical binding]; other site 295405010079 Q-loop/lid; other site 295405010080 ABC transporter signature motif; other site 295405010081 Walker B; other site 295405010082 D-loop; other site 295405010083 H-loop/switch region; other site 295405010084 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 295405010085 Permease; Region: Permease; pfam02405 295405010086 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 295405010087 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 295405010088 Walker A/P-loop; other site 295405010089 ATP binding site [chemical binding]; other site 295405010090 Q-loop/lid; other site 295405010091 ABC transporter signature motif; other site 295405010092 Walker B; other site 295405010093 D-loop; other site 295405010094 H-loop/switch region; other site 295405010095 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 295405010096 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 295405010097 active site 295405010098 phosphorylation site [posttranslational modification] 295405010099 intermolecular recognition site; other site 295405010100 dimerization interface [polypeptide binding]; other site 295405010101 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 295405010102 DNA binding residues [nucleotide binding] 295405010103 dimerization interface [polypeptide binding]; other site 295405010104 GTP-binding protein Der; Reviewed; Region: PRK00093 295405010105 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 295405010106 G1 box; other site 295405010107 GTP/Mg2+ binding site [chemical binding]; other site 295405010108 Switch I region; other site 295405010109 G2 box; other site 295405010110 Switch II region; other site 295405010111 G3 box; other site 295405010112 G4 box; other site 295405010113 G5 box; other site 295405010114 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 295405010115 G1 box; other site 295405010116 GTP/Mg2+ binding site [chemical binding]; other site 295405010117 Switch I region; other site 295405010118 G2 box; other site 295405010119 G3 box; other site 295405010120 Switch II region; other site 295405010121 G4 box; other site 295405010122 G5 box; other site 295405010123 GTPase Era; Reviewed; Region: era; PRK00089 295405010124 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 295405010125 G1 box; other site 295405010126 GTP/Mg2+ binding site [chemical binding]; other site 295405010127 Switch I region; other site 295405010128 G2 box; other site 295405010129 Switch II region; other site 295405010130 G3 box; other site 295405010131 G4 box; other site 295405010132 G5 box; other site 295405010133 KH domain; Region: KH_2; pfam07650 295405010134 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 295405010135 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 295405010136 dimer interface [polypeptide binding]; other site 295405010137 active site 295405010138 CoA binding pocket [chemical binding]; other site 295405010139 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 295405010140 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 295405010141 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 295405010142 FAD binding site [chemical binding]; other site 295405010143 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 295405010144 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 295405010145 DNA polymerase III subunit delta'; Validated; Region: PRK08058 295405010146 PSP1 C-terminal conserved region; Region: PSP1; cl00770 295405010147 gliding motility-associated lipoprotein GldH; Region: GldH_lipo; TIGR03511 295405010148 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 295405010149 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 295405010150 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 295405010151 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 295405010152 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 295405010153 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 295405010154 rod shape-determining protein MreC; Provisional; Region: PRK13922 295405010155 rod shape-determining protein MreC; Region: MreC; pfam04085 295405010156 rod shape-determining protein MreB; Provisional; Region: PRK13927 295405010157 MreB and similar proteins; Region: MreB_like; cd10225 295405010158 nucleotide binding site [chemical binding]; other site 295405010159 Mg binding site [ion binding]; other site 295405010160 putative protofilament interaction site [polypeptide binding]; other site 295405010161 RodZ interaction site [polypeptide binding]; other site 295405010162 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 295405010163 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 295405010164 purine monophosphate binding site [chemical binding]; other site 295405010165 dimer interface [polypeptide binding]; other site 295405010166 putative catalytic residues [active] 295405010167 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 295405010168 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 295405010169 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 295405010170 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 295405010171 active site 295405010172 Zn binding site [ion binding]; other site 295405010173 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 295405010174 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 295405010175 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 295405010176 ABC transporter; Region: ABC_tran_2; pfam12848 295405010177 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 295405010178 MG2 domain; Region: A2M_N; pfam01835 295405010179 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405010180 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 295405010181 active site 295405010182 Surface antigen; Region: Bac_surface_Ag; pfam01103 295405010183 Family of unknown function (DUF490); Region: DUF490; pfam04357 295405010184 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405010185 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 295405010186 dimer interface [polypeptide binding]; other site 295405010187 phosphorylation site [posttranslational modification] 295405010188 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 295405010189 ATP binding site [chemical binding]; other site 295405010190 Mg2+ binding site [ion binding]; other site 295405010191 G-X-G motif; other site 295405010192 Response regulator receiver domain; Region: Response_reg; pfam00072 295405010193 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 295405010194 active site 295405010195 phosphorylation site [posttranslational modification] 295405010196 intermolecular recognition site; other site 295405010197 dimerization interface [polypeptide binding]; other site 295405010198 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 295405010199 multidrug efflux protein; Reviewed; Region: PRK01766 295405010200 cation binding site [ion binding]; other site 295405010201 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 295405010202 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 295405010203 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 295405010204 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 295405010205 active site 295405010206 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 295405010207 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 295405010208 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 295405010209 active site 295405010210 phosphorylation site [posttranslational modification] 295405010211 intermolecular recognition site; other site 295405010212 dimerization interface [polypeptide binding]; other site 295405010213 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 295405010214 Walker A motif; other site 295405010215 ATP binding site [chemical binding]; other site 295405010216 Walker B motif; other site 295405010217 arginine finger; other site 295405010218 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 295405010219 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 295405010220 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 295405010221 active site 295405010222 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 295405010223 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 295405010224 NAD(P) binding site [chemical binding]; other site 295405010225 homotetramer interface [polypeptide binding]; other site 295405010226 homodimer interface [polypeptide binding]; other site 295405010227 active site 295405010228 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 295405010229 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 295405010230 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4200 295405010231 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 295405010232 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 295405010233 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 295405010234 Walker A/P-loop; other site 295405010235 ATP binding site [chemical binding]; other site 295405010236 Q-loop/lid; other site 295405010237 ABC transporter signature motif; other site 295405010238 Walker B; other site 295405010239 D-loop; other site 295405010240 H-loop/switch region; other site 295405010241 Erythromycin esterase; Region: Erythro_esteras; cl17110 295405010242 Erythromycin esterase; Region: Erythro_esteras; cl17110 295405010243 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 295405010244 DNA-binding site [nucleotide binding]; DNA binding site 295405010245 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 295405010246 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 295405010247 Walker A/P-loop; other site 295405010248 ATP binding site [chemical binding]; other site 295405010249 Q-loop/lid; other site 295405010250 ABC transporter signature motif; other site 295405010251 Walker B; other site 295405010252 D-loop; other site 295405010253 H-loop/switch region; other site 295405010254 TPR repeat; Region: TPR_11; pfam13414 295405010255 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 295405010256 TPR motif; other site 295405010257 binding surface 295405010258 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 295405010259 binding surface 295405010260 TPR motif; other site 295405010261 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 295405010262 binding surface 295405010263 TPR motif; other site 295405010264 PBP superfamily domain; Region: PBP_like_2; pfam12849 295405010265 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 295405010266 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 295405010267 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 295405010268 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 295405010269 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 295405010270 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 295405010271 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 295405010272 SGNH_peri1; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known...; Region: SGNH_hydrolase_peri1; cd01825 295405010273 active site 295405010274 catalytic triad [active] 295405010275 oxyanion hole [active] 295405010276 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 295405010277 SGNH_peri1; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known...; Region: SGNH_hydrolase_peri1; cd01825 295405010278 active site 295405010279 oxyanion hole [active] 295405010280 catalytic triad [active] 295405010281 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 295405010282 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405010283 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 295405010284 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405010285 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 295405010286 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 295405010287 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 295405010288 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 295405010289 active sites [active] 295405010290 tetramer interface [polypeptide binding]; other site 295405010291 Formiminotransferase-cyclodeaminase; Region: FTCD_C; pfam04961 295405010292 imidazolonepropionase; Validated; Region: PRK09356 295405010293 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 295405010294 active site 295405010295 Glutamate formiminotransferase [Amino acid transport and metabolism]; Region: COG3643 295405010296 Formiminotransferase domain, N-terminal subdomain; Region: FTCD_N; pfam07837 295405010297 Formiminotransferase domain; Region: FTCD; pfam02971 295405010298 urocanate hydratase; Provisional; Region: PRK05414 295405010299 MutS domain III; Region: MutS_III; pfam05192 295405010300 DNA-binding domain of DNA mismatch repair MUTS family; Region: MUTSd; smart00533 295405010301 ATP-binding cassette domain of MutS-like homolog; Region: ABC_MutS-like; cd03283 295405010302 Walker A/P-loop; other site 295405010303 ATP binding site [chemical binding]; other site 295405010304 Q-loop/lid; other site 295405010305 ABC transporter signature motif; other site 295405010306 Walker B; other site 295405010307 D-loop; other site 295405010308 H-loop/switch region; other site 295405010309 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 295405010310 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 295405010311 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 295405010312 alphaNTD - beta interaction site [polypeptide binding]; other site 295405010313 alphaNTD homodimer interface [polypeptide binding]; other site 295405010314 alphaNTD - beta' interaction site [polypeptide binding]; other site 295405010315 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 295405010316 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 295405010317 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 295405010318 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 295405010319 RNA binding surface [nucleotide binding]; other site 295405010320 30S ribosomal protein S11; Validated; Region: PRK05309 295405010321 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 295405010322 30S ribosomal protein S13; Region: bact_S13; TIGR03631 295405010323 Ribosomal protein L36; Region: Ribosomal_L36; pfam00444 295405010324 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 295405010325 rRNA binding site [nucleotide binding]; other site 295405010326 predicted 30S ribosome binding site; other site 295405010327 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 295405010328 active site 295405010329 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 295405010330 SecY translocase; Region: SecY; pfam00344 295405010331 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 295405010332 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 295405010333 23S rRNA binding site [nucleotide binding]; other site 295405010334 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 295405010335 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 295405010336 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 295405010337 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 295405010338 5S rRNA interface [nucleotide binding]; other site 295405010339 L27 interface [polypeptide binding]; other site 295405010340 23S rRNA interface [nucleotide binding]; other site 295405010341 L5 interface [polypeptide binding]; other site 295405010342 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 295405010343 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 295405010344 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 295405010345 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 295405010346 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 295405010347 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 295405010348 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 295405010349 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 295405010350 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 295405010351 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 295405010352 RNA binding site [nucleotide binding]; other site 295405010353 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 295405010354 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 295405010355 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 295405010356 23S rRNA interface [nucleotide binding]; other site 295405010357 putative translocon interaction site; other site 295405010358 signal recognition particle (SRP54) interaction site; other site 295405010359 L23 interface [polypeptide binding]; other site 295405010360 trigger factor interaction site; other site 295405010361 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 295405010362 23S rRNA interface [nucleotide binding]; other site 295405010363 5S rRNA interface [nucleotide binding]; other site 295405010364 putative antibiotic binding site [chemical binding]; other site 295405010365 L25 interface [polypeptide binding]; other site 295405010366 L27 interface [polypeptide binding]; other site 295405010367 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 295405010368 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 295405010369 G-X-X-G motif; other site 295405010370 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 295405010371 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 295405010372 putative translocon binding site; other site 295405010373 protein-rRNA interface [nucleotide binding]; other site 295405010374 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 295405010375 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 295405010376 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 295405010377 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 295405010378 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 295405010379 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 295405010380 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 295405010381 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 295405010382 elongation factor G; Reviewed; Region: PRK12739 295405010383 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 295405010384 G1 box; other site 295405010385 putative GEF interaction site [polypeptide binding]; other site 295405010386 GTP/Mg2+ binding site [chemical binding]; other site 295405010387 Switch I region; other site 295405010388 G2 box; other site 295405010389 G3 box; other site 295405010390 Switch II region; other site 295405010391 G4 box; other site 295405010392 G5 box; other site 295405010393 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 295405010394 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 295405010395 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 295405010396 30S ribosomal protein S7; Validated; Region: PRK05302 295405010397 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 295405010398 S17 interaction site [polypeptide binding]; other site 295405010399 S8 interaction site; other site 295405010400 16S rRNA interaction site [nucleotide binding]; other site 295405010401 streptomycin interaction site [chemical binding]; other site 295405010402 23S rRNA interaction site [nucleotide binding]; other site 295405010403 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 295405010404 Protein of unknown function (DUF3467); Region: DUF3467; pfam11950 295405010405 Acyltransferase family; Region: Acyl_transf_3; pfam01757 295405010406 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 295405010407 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 295405010408 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 295405010409 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 295405010410 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 295405010411 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 295405010412 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 295405010413 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 295405010414 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 295405010415 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 295405010416 DNA binding site [nucleotide binding] 295405010417 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 295405010418 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 295405010419 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 295405010420 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 295405010421 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 295405010422 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 295405010423 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 295405010424 RPB3 interaction site [polypeptide binding]; other site 295405010425 RPB1 interaction site [polypeptide binding]; other site 295405010426 RPB11 interaction site [polypeptide binding]; other site 295405010427 RPB10 interaction site [polypeptide binding]; other site 295405010428 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 295405010429 core dimer interface [polypeptide binding]; other site 295405010430 peripheral dimer interface [polypeptide binding]; other site 295405010431 L10 interface [polypeptide binding]; other site 295405010432 L11 interface [polypeptide binding]; other site 295405010433 putative EF-Tu interaction site [polypeptide binding]; other site 295405010434 putative EF-G interaction site [polypeptide binding]; other site 295405010435 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 295405010436 23S rRNA interface [nucleotide binding]; other site 295405010437 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 295405010438 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 295405010439 mRNA/rRNA interface [nucleotide binding]; other site 295405010440 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 295405010441 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 295405010442 23S rRNA interface [nucleotide binding]; other site 295405010443 L7/L12 interface [polypeptide binding]; other site 295405010444 putative thiostrepton binding site; other site 295405010445 L25 interface [polypeptide binding]; other site 295405010446 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 295405010447 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 295405010448 putative homodimer interface [polypeptide binding]; other site 295405010449 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 295405010450 heterodimer interface [polypeptide binding]; other site 295405010451 homodimer interface [polypeptide binding]; other site 295405010452 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 295405010453 elongation factor Tu; Reviewed; Region: PRK12735 295405010454 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 295405010455 G1 box; other site 295405010456 GEF interaction site [polypeptide binding]; other site 295405010457 GTP/Mg2+ binding site [chemical binding]; other site 295405010458 Switch I region; other site 295405010459 G2 box; other site 295405010460 G3 box; other site 295405010461 Switch II region; other site 295405010462 G4 box; other site 295405010463 G5 box; other site 295405010464 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 295405010465 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 295405010466 Antibiotic Binding Site [chemical binding]; other site 295405010467 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 295405010468 30S subunit binding site; other site 295405010469 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 295405010470 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 295405010471 active site 295405010472 Int/Topo IB signature motif; other site 295405010473 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 295405010474 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 295405010475 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 295405010476 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 295405010477 active site 295405010478 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 295405010479 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 295405010480 trimer interface [polypeptide binding]; other site 295405010481 putative metal binding site [ion binding]; other site 295405010482 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 295405010483 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 295405010484 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 295405010485 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 295405010486 HIGH motif; other site 295405010487 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 295405010488 active site 295405010489 KMSKS motif; other site 295405010490 Predicted membrane-associated HD superfamily hydrolase [General function prediction only]; Region: COG1480 295405010491 7TM receptor with intracellular HD hydrolase; Region: 7TM-7TMR_HD; pfam07698 295405010492 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 295405010493 Zn2+ binding site [ion binding]; other site 295405010494 Mg2+ binding site [ion binding]; other site 295405010495 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 295405010496 Low molecular weight phosphatase family; Region: LMWPc; cd00115 295405010497 active site 295405010498 Domain of unknown function (DUF4091); Region: DUF4091; pfam13320 295405010499 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 295405010500 primosomal protein N' Region: priA; TIGR00595 295405010501 ATP binding site [chemical binding]; other site 295405010502 putative Mg++ binding site [ion binding]; other site 295405010503 helicase superfamily c-terminal domain; Region: HELICc; smart00490 295405010504 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 295405010505 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 295405010506 Aspartase; Region: Aspartase; cd01357 295405010507 active sites [active] 295405010508 tetramer interface [polypeptide binding]; other site 295405010509 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 295405010510 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK09412 295405010511 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 295405010512 active site 295405010513 homodimer interface [polypeptide binding]; other site 295405010514 homotetramer interface [polypeptide binding]; other site 295405010515 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 295405010516 Transposase; Region: DEDD_Tnp_IS110; pfam01548 295405010517 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 295405010518 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 295405010519 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 295405010520 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 295405010521 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 295405010522 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 295405010523 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 295405010524 Transposase; Region: DEDD_Tnp_IS110; pfam01548 295405010525 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 295405010526 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 295405010527 active site 295405010528 DNA binding site [nucleotide binding] 295405010529 Int/Topo IB signature motif; other site 295405010530 DNA binding domain, excisionase family; Region: excise; TIGR01764 295405010531 AAA domain; Region: AAA_25; pfam13481 295405010532 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 295405010533 Walker A motif; other site 295405010534 ATP binding site [chemical binding]; other site 295405010535 Walker B motif; other site 295405010536 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 295405010537 Trp docking motif [polypeptide binding]; other site 295405010538 active site 295405010539 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405010540 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 295405010541 dimer interface [polypeptide binding]; other site 295405010542 phosphorylation site [posttranslational modification] 295405010543 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 295405010544 ATP binding site [chemical binding]; other site 295405010545 Mg2+ binding site [ion binding]; other site 295405010546 G-X-G motif; other site 295405010547 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 295405010548 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 295405010549 active site 295405010550 phosphorylation site [posttranslational modification] 295405010551 intermolecular recognition site; other site 295405010552 dimerization interface [polypeptide binding]; other site 295405010553 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405010554 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405010555 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 295405010556 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 295405010557 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 295405010558 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 295405010559 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 295405010560 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 295405010561 Walker A motif; other site 295405010562 ATP binding site [chemical binding]; other site 295405010563 Walker B motif; other site 295405010564 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 295405010565 Integrase core domain; Region: rve; pfam00665 295405010566 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 295405010567 catalytic site [active] 295405010568 BNR repeat-like domain; Region: BNR_2; pfam13088 295405010569 Asp-box motif; other site 295405010570 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3666 295405010571 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 295405010572 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 295405010573 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 295405010574 putative active cleft [active] 295405010575 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 295405010576 Major Facilitator Superfamily; Region: MFS_1; pfam07690 295405010577 putative substrate translocation pore; other site 295405010578 cyclically-permuted mutarotase family protein; Region: mutarot_permut; TIGR03548 295405010579 Galactose oxidase, central domain; Region: Kelch_3; cl02701 295405010580 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405010581 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405010582 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405010583 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 295405010584 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405010585 SusD family; Region: SusD; pfam07980 295405010586 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 295405010587 active site 295405010588 catalytic residues [active] 295405010589 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 295405010590 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 295405010591 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 295405010592 active site 295405010593 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C; pfam03174 295405010594 PA14 domain; Region: PA14; cl08459 295405010595 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 295405010596 active site 295405010597 catalytic residues [active] 295405010598 Glycosyl hydrolases family 35; Region: Glyco_hydro_35; pfam01301 295405010599 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405010600 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405010601 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 295405010602 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405010603 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405010604 SusD family; Region: SusD; pfam07980 295405010605 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 295405010606 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 295405010607 RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons; Region: RT_like; cl02808 295405010608 RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons; Region: RT_like; cl02808 295405010609 NTP binding site [chemical binding]; other site 295405010610 Helix-turn-helix domain; Region: HTH_28; pfam13518 295405010611 Domain of unknown function (DUF4373); Region: DUF4373; pfam14297 295405010612 AAA domain; Region: AAA_14; pfam13173 295405010613 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 295405010614 Plasmid recombination enzyme; Region: Mob_Pre; pfam01076 295405010615 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 295405010616 Helix-turn-helix domain; Region: HTH_17; cl17695 295405010617 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 295405010618 active site 295405010619 catalytic residues [active] 295405010620 DNA binding site [nucleotide binding] 295405010621 Int/Topo IB signature motif; other site 295405010622 Protein of unknown function (DUF2795); Region: DUF2795; pfam11387 295405010623 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 295405010624 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405010625 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 295405010626 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 295405010627 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 295405010628 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 295405010629 active site 295405010630 catalytic residues [active] 295405010631 DNA binding site [nucleotide binding] 295405010632 Int/Topo IB signature motif; other site 295405010633 Protein of unknown function (DUF2961); Region: DUF2961; pfam11175 295405010634 FRG domain; Region: FRG; pfam08867 295405010635 Amidohydrolase; Region: Amidohydro_2; pfam04909 295405010636 VirE N-terminal domain; Region: VirE_N; pfam08800 295405010637 Virulence-associated protein E; Region: VirE; pfam05272 295405010638 Domain of unknonw function from B. Theta Gene description (DUF3874); Region: DUF3874; pfam12990 295405010639 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 295405010640 sialate O-acetylesterase_like family of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: sialate_O-acetylesterase_like1; cd01827 295405010641 active site 295405010642 catalytic triad [active] 295405010643 oxyanion hole [active] 295405010644 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 295405010645 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 295405010646 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; cd00229 295405010647 active site 295405010648 catalytic triad [active] 295405010649 oxyanion hole [active] 295405010650 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 295405010651 dimer interface [polypeptide binding]; other site 295405010652 ADP-ribose binding site [chemical binding]; other site 295405010653 active site 295405010654 nudix motif; other site 295405010655 metal binding site [ion binding]; metal-binding site 295405010656 Histidine kinase; Region: His_kinase; pfam06580 295405010657 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 295405010658 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 295405010659 active site 295405010660 phosphorylation site [posttranslational modification] 295405010661 intermolecular recognition site; other site 295405010662 dimerization interface [polypeptide binding]; other site 295405010663 LytTr DNA-binding domain; Region: LytTR; smart00850 295405010664 4Fe-4S binding domain; Region: Fer4_5; pfam12801 295405010665 4Fe-4S binding domain; Region: Fer4_5; pfam12801 295405010666 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 295405010667 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 295405010668 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 295405010669 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 295405010670 Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only]; Region: COG1453 295405010671 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 295405010672 active site 295405010673 catalytic tetrad [active] 295405010674 Domain of unknown function (DUF1893); Region: TM1506; pfam08973 295405010675 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 295405010676 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 295405010677 N-terminal plug; other site 295405010678 ligand-binding site [chemical binding]; other site 295405010679 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 295405010680 Protein of unknown function (DUF1349); Region: DUF1349; pfam07081 295405010681 maltose O-acetyltransferase; Provisional; Region: PRK10092 295405010682 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 295405010683 active site 295405010684 substrate binding site [chemical binding]; other site 295405010685 trimer interface [polypeptide binding]; other site 295405010686 CoA binding site [chemical binding]; other site 295405010687 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 295405010688 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 295405010689 DNA binding residues [nucleotide binding] 295405010690 dimerization interface [polypeptide binding]; other site 295405010691 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 295405010692 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 295405010693 DNA binding site [nucleotide binding] 295405010694 active site 295405010695 Cupin domain; Region: Cupin_2; pfam07883 295405010696 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405010697 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405010698 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK12315 295405010699 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 295405010700 TPP-binding site; other site 295405010701 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 295405010702 PYR/PP interface [polypeptide binding]; other site 295405010703 dimer interface [polypeptide binding]; other site 295405010704 TPP binding site [chemical binding]; other site 295405010705 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 295405010706 flavodoxin; Provisional; Region: PRK07116 295405010707 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 295405010708 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 295405010709 Fic/DOC family; Region: Fic; pfam02661 295405010710 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 295405010711 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 295405010712 ORF6N domain; Region: ORF6N; pfam10543 295405010713 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 295405010714 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 295405010715 Substrate binding site; other site 295405010716 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 295405010717 nucleotide binding site/active site [active] 295405010718 HIT family signature motif; other site 295405010719 catalytic residue [active] 295405010720 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 295405010721 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 295405010722 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 295405010723 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 295405010724 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 295405010725 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405010726 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 295405010727 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 295405010728 RNase E interface [polypeptide binding]; other site 295405010729 trimer interface [polypeptide binding]; other site 295405010730 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 295405010731 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 295405010732 RNase E interface [polypeptide binding]; other site 295405010733 trimer interface [polypeptide binding]; other site 295405010734 active site 295405010735 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 295405010736 putative nucleic acid binding region [nucleotide binding]; other site 295405010737 G-X-X-G motif; other site 295405010738 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 295405010739 RNA binding site [nucleotide binding]; other site 295405010740 domain interface; other site 295405010741 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405010742 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405010743 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 295405010744 DNA binding residues [nucleotide binding] 295405010745 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405010746 FecR protein; Region: FecR; pfam04773 295405010747 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405010748 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405010749 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405010750 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405010751 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 295405010752 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 295405010753 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 295405010754 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405010755 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 295405010756 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 295405010757 The C-terminal domain of uncharacterized bacterial proteins; Region: Bvu_2165_C_like; cd12843 295405010758 butyrate kinase; Provisional; Region: PRK03011 295405010759 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 295405010760 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 295405010761 active site 295405010762 catalytic residues [active] 295405010763 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 295405010764 dimer interface [polypeptide binding]; other site 295405010765 catalytic triad [active] 295405010766 M28 Zn-Peptidases; Region: M28_like_6; cd08656 295405010767 Peptidase family M28; Region: Peptidase_M28; pfam04389 295405010768 metal binding site [ion binding]; metal-binding site 295405010769 Cysteine desulfurase SufE subunit [Posttranslational modification, protein turnover, chaperones]; Region: sufE; COG2166 295405010770 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 295405010771 non-specific DNA binding site [nucleotide binding]; other site 295405010772 salt bridge; other site 295405010773 sequence-specific DNA binding site [nucleotide binding]; other site 295405010774 CAAX protease self-immunity; Region: Abi; pfam02517 295405010775 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 295405010776 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 295405010777 active site 295405010778 Riboflavin kinase; Region: Flavokinase; pfam01687 295405010779 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 295405010780 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 295405010781 motif II; other site 295405010782 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 295405010783 plasma-membrane calcium-translocating P-type ATPase; Region: ATPase-IIB_Ca; TIGR01517 295405010784 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 295405010785 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 295405010786 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 295405010787 motif II; other site 295405010788 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 295405010789 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 295405010790 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405010791 dimer interface [polypeptide binding]; other site 295405010792 phosphorylation site [posttranslational modification] 295405010793 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 295405010794 ATP binding site [chemical binding]; other site 295405010795 Mg2+ binding site [ion binding]; other site 295405010796 G-X-G motif; other site 295405010797 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 295405010798 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 295405010799 active site 295405010800 phosphorylation site [posttranslational modification] 295405010801 intermolecular recognition site; other site 295405010802 dimerization interface [polypeptide binding]; other site 295405010803 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 295405010804 Rubredoxin; Region: Rubredoxin; pfam00301 295405010805 iron binding site [ion binding]; other site 295405010806 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 295405010807 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 295405010808 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 295405010809 PhoU domain; Region: PhoU; pfam01895 295405010810 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 295405010811 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 295405010812 active site 295405010813 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405010814 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 295405010815 ATP binding site [chemical binding]; other site 295405010816 Mg2+ binding site [ion binding]; other site 295405010817 G-X-G motif; other site 295405010818 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 295405010819 putative catalytic site [active] 295405010820 putative metal binding site [ion binding]; other site 295405010821 putative phosphate binding site [ion binding]; other site 295405010822 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 295405010823 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 295405010824 active site 295405010825 metal binding site [ion binding]; metal-binding site 295405010826 Domain of Unknown Function with PDB structure (DUF3857); Region: DUF3857; pfam12969 295405010827 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 295405010828 Domain of Unknown Function with PDB structure (DUF3858); Region: DUF3858; pfam12970 295405010829 Domain of Unknown Function with PDB structure (DUF3857); Region: DUF3857; pfam12969 295405010830 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 295405010831 DNA-binding protein, histone-like, putative; Region: HU_rel; TIGR01201 295405010832 Aminopeptidase P, N-terminal domain; Region: AMP_N; smart01011 295405010833 proline aminopeptidase P II; Provisional; Region: PRK10879 295405010834 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 295405010835 active site 295405010836 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 295405010837 RNA polymerase sigma-54 factor; Region: rpoN_sigma; TIGR02395 295405010838 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 295405010839 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 295405010840 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 295405010841 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 295405010842 lipoyl attachment site [posttranslational modification]; other site 295405010843 AIR carboxylase; Region: AIRC; pfam00731 295405010844 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional; Region: PRK02048 295405010845 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 295405010846 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 295405010847 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 295405010848 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 295405010849 Glycosyl hydrolase family 43; Region: GH43_3; cd08982 295405010850 active site 295405010851 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 295405010852 sugar binding site [chemical binding]; other site 295405010853 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 295405010854 Interdomain contacts; other site 295405010855 Cytokine receptor motif; other site 295405010856 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5368 295405010857 Putative glucoamylase; Region: Glycoamylase; pfam10091 295405010858 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405010859 starch binding outer membrane protein SusD; Region: SusD; cd08977 295405010860 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405010861 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405010862 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 295405010863 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 295405010864 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 295405010865 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 295405010866 Flagellar FliJ protein; Region: FliJ; pfam02050 295405010867 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 295405010868 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 295405010869 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 295405010870 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 295405010871 protein binding site [polypeptide binding]; other site 295405010872 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 295405010873 Catalytic dyad [active] 295405010874 Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor.The physiological function of AK is associated with the regulation of extracellular...; Region: adenosine_kinase; cd01168 295405010875 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 295405010876 substrate binding site [chemical binding]; other site 295405010877 ATP binding site [chemical binding]; other site 295405010878 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 295405010879 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 295405010880 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405010881 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405010882 SusD family; Region: SusD; pfam07980 295405010883 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405010884 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405010885 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405010886 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 295405010887 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 295405010888 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 295405010889 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405010890 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 295405010891 dimer interface [polypeptide binding]; other site 295405010892 phosphorylation site [posttranslational modification] 295405010893 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 295405010894 ATP binding site [chemical binding]; other site 295405010895 Mg2+ binding site [ion binding]; other site 295405010896 G-X-G motif; other site 295405010897 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 295405010898 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 295405010899 active site 295405010900 phosphorylation site [posttranslational modification] 295405010901 intermolecular recognition site; other site 295405010902 dimerization interface [polypeptide binding]; other site 295405010903 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 295405010904 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405010905 glycyl-radical enzyme activating protein family; Region: PFLE_PFLC; TIGR02494 295405010906 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 295405010907 FeS/SAM binding site; other site 295405010908 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 295405010909 D-xylose transporter XylE; Provisional; Region: xylE; PRK10077 295405010910 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 295405010911 putative substrate translocation pore; other site 295405010912 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 295405010913 active site 295405010914 catalytic residues [active] 295405010915 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 295405010916 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 295405010917 Uncharacterized conserved protein [Function unknown]; Region: COG1359 295405010918 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 295405010919 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 295405010920 active site 295405010921 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 295405010922 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 295405010923 active site 295405010924 dimerization interface [polypeptide binding]; other site 295405010925 He_PIG associated, NEW1 domain of bacterial glycohydrolase; Region: He_PIG_assoc; pfam10632 295405010926 Putative Ig domain; Region: He_PIG; pfam05345 295405010927 alpha-galactosidase; Region: PLN02808; cl17638 295405010928 N-terminal domain of galactosyltransferase; Region: Glyco_transf_7C; cl17476 295405010929 LicD family; Region: LicD; pfam04991 295405010930 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 295405010931 Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline; Region: PC_cytidylyltransferase; cd02523 295405010932 active site 295405010933 metal-binding site 295405010934 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 295405010935 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 295405010936 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405010937 homodimer interface [polypeptide binding]; other site 295405010938 catalytic residue [active] 295405010939 pseudo-rSAM protein, GG-Bacteroidales system; Region: pseudo_rSAM_GG; TIGR04150 295405010940 radical SAM peptide maturase, GG-Bacteroidales family; Region: GG_samocin_CFB; TIGR04148 295405010941 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 295405010942 FeS/SAM binding site; other site 295405010943 natural product precursor, GG-Bacteroidales family; Region: GG_sam_targ_CFB; TIGR04149 295405010944 glycosyltransferase, GG-Bacteroidales peptide system; Region: glyco_rSAM_CFB; TIGR04157 295405010945 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 295405010946 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 295405010947 Glycosyl transferase family 8; Region: Glyco_transf_8; pfam01501 295405010948 Ligand binding site; other site 295405010949 metal-binding site 295405010950 LytTr DNA-binding domain; Region: LytTR; smart00850 295405010951 Domain of unknown function (DUF4221); Region: DUF4221; pfam13970 295405010952 Gram-negative bacterial tonB protein; Region: TonB; cl10048 295405010953 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 295405010954 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 295405010955 nudix motif; other site 295405010956 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 295405010957 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 295405010958 binding surface 295405010959 TPR motif; other site 295405010960 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 295405010961 binding surface 295405010962 TPR motif; other site 295405010963 Tetratricopeptide repeat; Region: TPR_12; pfam13424 295405010964 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 295405010965 binding surface 295405010966 TPR motif; other site 295405010967 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 295405010968 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 295405010969 binding surface 295405010970 TPR motif; other site 295405010971 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 295405010972 DNA topoisomerase I; Provisional; Region: PRK08780 295405010973 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 295405010974 active site 295405010975 interdomain interaction site; other site 295405010976 putative metal-binding site [ion binding]; other site 295405010977 nucleotide binding site [chemical binding]; other site 295405010978 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 295405010979 domain I; other site 295405010980 DNA binding groove [nucleotide binding] 295405010981 phosphate binding site [ion binding]; other site 295405010982 domain II; other site 295405010983 domain III; other site 295405010984 nucleotide binding site [chemical binding]; other site 295405010985 catalytic site [active] 295405010986 domain IV; other site 295405010987 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 295405010988 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 295405010989 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 295405010990 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 295405010991 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 295405010992 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 295405010993 active site 295405010994 HIGH motif; other site 295405010995 nucleotide binding site [chemical binding]; other site 295405010996 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 295405010997 KMSK motif region; other site 295405010998 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 295405010999 tRNA binding surface [nucleotide binding]; other site 295405011000 anticodon binding site; other site 295405011001 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 295405011002 IHF dimer interface [polypeptide binding]; other site 295405011003 IHF - DNA interface [nucleotide binding]; other site 295405011004 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 295405011005 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 295405011006 sigma70 family sigma factor YlaC; Region: YlaC; pfam10777 295405011007 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; Region: EEP-2; cd09084 295405011008 putative catalytic site [active] 295405011009 putative metal binding site [ion binding]; other site 295405011010 putative phosphate binding site [ion binding]; other site 295405011011 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 295405011012 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 295405011013 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 295405011014 Protein export membrane protein; Region: SecD_SecF; pfam02355 295405011015 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 295405011016 IHF - DNA interface [nucleotide binding]; other site 295405011017 IHF dimer interface [polypeptide binding]; other site 295405011018 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 295405011019 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 295405011020 Helix-turn-helix domain; Region: HTH_18; pfam12833 295405011021 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 295405011022 active site 295405011023 DNA binding site [nucleotide binding] 295405011024 Int/Topo IB signature motif; other site 295405011025 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 295405011026 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 295405011027 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 295405011028 dimer interface [polypeptide binding]; other site 295405011029 PYR/PP interface [polypeptide binding]; other site 295405011030 TPP binding site [chemical binding]; other site 295405011031 substrate binding site [chemical binding]; other site 295405011032 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 295405011033 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 295405011034 TPP-binding site [chemical binding]; other site 295405011035 Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins; Region: GDPD_AtGDE_like; cd08566 295405011036 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 295405011037 putative active site [active] 295405011038 catalytic site [active] 295405011039 putative metal binding site [ion binding]; other site 295405011040 oligomer interface [polypeptide binding]; other site 295405011041 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 295405011042 active site 295405011043 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 295405011044 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 295405011045 active site 295405011046 substrate-binding site [chemical binding]; other site 295405011047 metal-binding site [ion binding] 295405011048 ATP binding site [chemical binding]; other site 295405011049 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405011050 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405011051 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405011052 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405011053 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405011054 SusD family; Region: SusD; pfam07980 295405011055 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405011056 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405011057 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405011058 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405011059 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405011060 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405011061 SusD family; Region: SusD; pfam07980 295405011062 Right handed beta helix region; Region: Beta_helix; pfam13229 295405011063 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 295405011064 Glycosyl hydrolase family 65 central catalytic domain; Region: Glyco_hydro_65m; pfam03632 295405011065 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405011066 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405011067 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405011068 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 295405011069 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 295405011070 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405011071 SusD family; Region: SusD; pfam07980 295405011072 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 295405011073 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 295405011074 G1 box; other site 295405011075 putative GEF interaction site [polypeptide binding]; other site 295405011076 GTP/Mg2+ binding site [chemical binding]; other site 295405011077 Switch I region; other site 295405011078 G2 box; other site 295405011079 G3 box; other site 295405011080 Switch II region; other site 295405011081 G4 box; other site 295405011082 G5 box; other site 295405011083 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 295405011084 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 295405011085 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 295405011086 16S/18S rRNA binding site [nucleotide binding]; other site 295405011087 S13e-L30e interaction site [polypeptide binding]; other site 295405011088 25S rRNA binding site [nucleotide binding]; other site 295405011089 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 295405011090 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 295405011091 non-specific DNA binding site [nucleotide binding]; other site 295405011092 salt bridge; other site 295405011093 sequence-specific DNA binding site [nucleotide binding]; other site 295405011094 Cupin domain; Region: Cupin_2; pfam07883 295405011095 AMP-binding domain protein; Validated; Region: PRK08315 295405011096 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 295405011097 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 295405011098 acyl-activating enzyme (AAE) consensus motif; other site 295405011099 putative AMP binding site [chemical binding]; other site 295405011100 putative active site [active] 295405011101 putative CoA binding site [chemical binding]; other site 295405011102 PAS fold; Region: PAS_4; pfam08448 295405011103 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 295405011104 PAS fold; Region: PAS_4; pfam08448 295405011105 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405011106 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 295405011107 dimer interface [polypeptide binding]; other site 295405011108 phosphorylation site [posttranslational modification] 295405011109 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 295405011110 ATP binding site [chemical binding]; other site 295405011111 Mg2+ binding site [ion binding]; other site 295405011112 G-X-G motif; other site 295405011113 Adenosylhomocysteinase; Provisional; Region: PTZ00075 295405011114 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 295405011115 homotetramer interface [polypeptide binding]; other site 295405011116 ligand binding site [chemical binding]; other site 295405011117 catalytic site [active] 295405011118 NAD binding site [chemical binding]; other site 295405011119 Bacterial membrane protein YfhO; Region: YfhO; pfam09586 295405011120 Bacterial membrane protein YfhO; Region: YfhO; pfam09586 295405011121 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 295405011122 Sulfatase; Region: Sulfatase; pfam00884 295405011123 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405011124 SusD family; Region: SusD; pfam07980 295405011125 Secretin and TonB N terminus short domain; Region: STN; pfam07660 295405011126 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405011127 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405011128 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405011129 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 295405011130 FecR protein; Region: FecR; pfam04773 295405011131 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 295405011132 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 295405011133 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405011134 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 295405011135 DNA binding residues [nucleotide binding] 295405011136 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 295405011137 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 295405011138 FtsX-like permease family; Region: FtsX; pfam02687 295405011139 Ribosome-binding factor A; Region: RBFA; pfam02033 295405011140 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 295405011141 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 295405011142 S-adenosylmethionine binding site [chemical binding]; other site 295405011143 pyruvate kinase; Provisional; Region: PRK05826 295405011144 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 295405011145 domain interfaces; other site 295405011146 active site 295405011147 Dehydroquinase class II; Region: DHquinase_II; pfam01220 295405011148 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 295405011149 trimer interface [polypeptide binding]; other site 295405011150 active site 295405011151 dimer interface [polypeptide binding]; other site 295405011152 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 295405011153 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 295405011154 active site 295405011155 Int/Topo IB signature motif; other site 295405011156 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 295405011157 TPR motif; other site 295405011158 binding surface 295405011159 Tetratricopeptide repeat; Region: TPR_16; pfam13432 295405011160 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 295405011161 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 295405011162 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 295405011163 catalytic residues [active] 295405011164 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 295405011165 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 295405011166 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 295405011167 Walker A motif; other site 295405011168 ATP binding site [chemical binding]; other site 295405011169 Walker B motif; other site 295405011170 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 295405011171 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 295405011172 LanC-like proteins. LanC is the cyclase enzyme of the lanthionine synthetase. Lanthionine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as a precursor peptide and then post-translationally modified to contain...; Region: LanC_like; cl04955 295405011173 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 295405011174 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 295405011175 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405011176 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 295405011177 dimer interface [polypeptide binding]; other site 295405011178 phosphorylation site [posttranslational modification] 295405011179 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 295405011180 ATP binding site [chemical binding]; other site 295405011181 Mg2+ binding site [ion binding]; other site 295405011182 G-X-G motif; other site 295405011183 Response regulator receiver domain; Region: Response_reg; pfam00072 295405011184 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 295405011185 active site 295405011186 phosphorylation site [posttranslational modification] 295405011187 intermolecular recognition site; other site 295405011188 dimerization interface [polypeptide binding]; other site 295405011189 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 295405011190 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405011191 radical SAM enzyme, rSAM/lipoprotein system; Region: rSAM_w_lipo; TIGR04133 295405011192 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 295405011193 FeS/SAM binding site; other site 295405011194 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 295405011195 putative lipoprotein, rSAM/lipoprotein system; Region: lipo_with_rSAM; TIGR04134 295405011196 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 295405011197 CoA binding domain; Region: CoA_binding_2; pfam13380 295405011198 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 295405011199 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 295405011200 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 295405011201 NVEALA protein; Region: NVEALA; pfam14055 295405011202 colanic acid exporter; Provisional; Region: PRK10459 295405011203 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 295405011204 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 295405011205 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405011206 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405011207 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 295405011208 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405011209 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 295405011210 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 295405011211 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 295405011212 active site 295405011213 homodimer interface [polypeptide binding]; other site 295405011214 UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional; Region: wecC; PRK11064 295405011215 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 295405011216 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 295405011217 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 295405011218 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 295405011219 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 295405011220 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 295405011221 metal-binding site 295405011222 NAD-dependent deacetylase; Provisional; Region: PRK00481 295405011223 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 295405011224 NAD+ binding site [chemical binding]; other site 295405011225 substrate binding site [chemical binding]; other site 295405011226 Zn binding site [ion binding]; other site 295405011227 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 295405011228 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 295405011229 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 295405011230 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 295405011231 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 295405011232 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 295405011233 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 295405011234 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 295405011235 putative DNA binding site [nucleotide binding]; other site 295405011236 putative Zn2+ binding site [ion binding]; other site 295405011237 AsnC family; Region: AsnC_trans_reg; pfam01037 295405011238 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 295405011239 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 295405011240 active site 295405011241 phosphorylation site [posttranslational modification] 295405011242 intermolecular recognition site; other site 295405011243 dimerization interface [polypeptide binding]; other site 295405011244 LytTr DNA-binding domain; Region: LytTR; smart00850 295405011245 Histidine kinase; Region: His_kinase; pfam06580 295405011246 Outer membrane efflux protein; Region: OEP; pfam02321 295405011247 Outer membrane efflux protein; Region: OEP; pfam02321 295405011248 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 295405011249 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 295405011250 HlyD family secretion protein; Region: HlyD_3; pfam13437 295405011251 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 295405011252 Methyltransferase domain; Region: Methyltransf_18; pfam12847 295405011253 starch binding outer membrane protein SusD; Region: SusD; cl17845 295405011254 SusD family; Region: SusD; pfam07980 295405011255 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 295405011256 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405011257 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 295405011258 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 295405011259 Protein of unknown function (DUF2961); Region: DUF2961; pfam11175 295405011260 Protein of unknown function (DUF2961); Region: DUF2961; pfam11175 295405011261 Sugar (and other) transporter; Region: Sugar_tr; pfam00083 295405011262 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 295405011263 putative substrate translocation pore; other site 295405011264 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 295405011265 The C-terminal domain of uncharacterized bacterial proteins; Region: Bvu_2165_C_like; cd12843 295405011266 Periplasmic binding domain of two-component sensor kinase signaling systems; Region: PBP1_sensor_kinase_like; cd06308 295405011267 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 295405011268 putative ligand binding site [chemical binding]; other site 295405011269 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 295405011270 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 295405011271 dimer interface [polypeptide binding]; other site 295405011272 phosphorylation site [posttranslational modification] 295405011273 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 295405011274 ATP binding site [chemical binding]; other site 295405011275 Mg2+ binding site [ion binding]; other site 295405011276 G-X-G motif; other site 295405011277 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 295405011278 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 295405011279 active site 295405011280 phosphorylation site [posttranslational modification] 295405011281 intermolecular recognition site; other site 295405011282 dimerization interface [polypeptide binding]; other site 295405011283 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405011284 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405011285 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405011286 Glycosyl hydrolases family 32 N-terminal domain; Region: Glyco_hydro_32N; pfam00251 295405011287 Glycosyl hydrolase family 32, beta-fructosidases; Region: GH32_B_Fructosidase; cd08996 295405011288 substrate binding [chemical binding]; other site 295405011289 active site 295405011290 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 295405011291 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 295405011292 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 295405011293 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 295405011294 Homo sapiens acid phosphatase 5 and related proteins, metallophosphatase domain; Region: MPP_ACP5; cd07378 295405011295 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 295405011296 active site 295405011297 metal binding site [ion binding]; metal-binding site 295405011298 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 295405011299 Mechanosensitive ion channel; Region: MS_channel; pfam00924 295405011300 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 295405011301 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 295405011302 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 295405011303 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 295405011304 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 295405011305 ATP binding site [chemical binding]; other site 295405011306 Mg2+ binding site [ion binding]; other site 295405011307 G-X-G motif; other site 295405011308 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 295405011309 ATP binding site [chemical binding]; other site 295405011310 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 295405011311 active site 295405011312 putative metal-binding site [ion binding]; other site 295405011313 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 295405011314 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 295405011315 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 295405011316 active site 295405011317 (T/H)XGH motif; other site 295405011318 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 295405011319 C-terminal peptidase (prc); Region: prc; TIGR00225 295405011320 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 295405011321 protein binding site [polypeptide binding]; other site 295405011322 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 295405011323 Catalytic dyad [active] 295405011324 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 295405011325 active site 295405011326 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405011327 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 295405011328 succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family; Region: sdhC_b558_fam; TIGR02046 295405011329 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 295405011330 putative Iron-sulfur protein interface [polypeptide binding]; other site 295405011331 proximal heme binding site [chemical binding]; other site 295405011332 distal heme binding site [chemical binding]; other site 295405011333 putative dimer interface [polypeptide binding]; other site 295405011334 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07573 295405011335 L-aspartate oxidase; Provisional; Region: PRK06175 295405011336 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 295405011337 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated; Region: PRK07570 295405011338 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 295405011339 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 295405011340 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 295405011341 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 295405011342 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 295405011343 Domain of unknown function (DUF4374); Region: DUF4374; pfam14298 295405011344 Cna protein B-type domain; Region: Cna_B_2; pfam13715 295405011345 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 295405011346 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 295405011347 N-terminal plug; other site 295405011348 ligand-binding site [chemical binding]; other site 295405011349 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 295405011350 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 295405011351 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 295405011352 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 295405011353 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 295405011354 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 295405011355 DNA protecting protein DprA; Region: dprA; TIGR00732 295405011356 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 295405011357 active site 295405011358 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 295405011359 Class I aldolases; Region: Aldolase_Class_I; cl17187 295405011360 Peptidase family U32; Region: Peptidase_U32; pfam01136 295405011361 The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases; Region: URO-D_CIMS_like; cl00464 295405011362 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; pfam09832 295405011363 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 295405011364 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 295405011365 FMN binding site [chemical binding]; other site 295405011366 active site 295405011367 catalytic residues [active] 295405011368 substrate binding site [chemical binding]; other site 295405011369 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 295405011370 active site 295405011371 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 295405011372 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 295405011373 NAD(P) binding site [chemical binding]; other site 295405011374 active site 295405011375 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 295405011376 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 295405011377 ribonuclease R; Region: RNase_R; TIGR02063 295405011378 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 295405011379 RNB domain; Region: RNB; pfam00773 295405011380 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 295405011381 RNA binding site [nucleotide binding]; other site 295405011382 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 295405011383 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 295405011384 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 295405011385 DNA binding residues [nucleotide binding] 295405011386 Predicted flavin-nucleotide-binding protein [General function prediction only]; Region: COG3467 295405011387 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 295405011388 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 295405011389 dimer interface [polypeptide binding]; other site 295405011390 pyridoxal 5'-phosphate binding site [chemical binding]; other site 295405011391 catalytic residue [active] 295405011392 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 295405011393 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 295405011394 substrate binding pocket [chemical binding]; other site 295405011395 GTP-binding protein YchF; Reviewed; Region: PRK09601 295405011396 YchF GTPase; Region: YchF; cd01900 295405011397 G1 box; other site 295405011398 GTP/Mg2+ binding site [chemical binding]; other site 295405011399 Switch I region; other site 295405011400 G2 box; other site 295405011401 Switch II region; other site 295405011402 G3 box; other site 295405011403 G4 box; other site 295405011404 G5 box; other site 295405011405 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 295405011406 2-dehydropantoate 2-reductase; Region: apbA_panE; TIGR00745 295405011407 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 295405011408 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 295405011409 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 295405011410 Chloramphenicol O-acetyltransferase [Defense mechanisms]; Region: COG4845 295405011411 Chloramphenicol acetyltransferase; Region: CAT; smart01059 295405011412 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 295405011413 MutS domain I; Region: MutS_I; pfam01624 295405011414 MutS domain II; Region: MutS_II; pfam05188 295405011415 MutS domain III; Region: MutS_III; pfam05192 295405011416 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 295405011417 Walker A/P-loop; other site 295405011418 ATP binding site [chemical binding]; other site 295405011419 Q-loop/lid; other site 295405011420 ABC transporter signature motif; other site 295405011421 Walker B; other site 295405011422 D-loop; other site 295405011423 H-loop/switch region; other site 295405011424 leucyl-tRNA synthetase, eubacterial and mitochondrial family; Region: leuS_bact; TIGR00396 295405011425 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 295405011426 active site 295405011427 HIGH motif; other site 295405011428 nucleotide binding site [chemical binding]; other site 295405011429 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 295405011430 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 295405011431 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 295405011432 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 295405011433 active site 295405011434 KMSKS motif; other site 295405011435 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 295405011436 tRNA binding surface [nucleotide binding]; other site 295405011437 Uncharacterized conserved protein [Function unknown]; Region: COG1284 295405011438 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 295405011439 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 295405011440 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 295405011441 active site 295405011442 dimerization interface [polypeptide binding]; other site 295405011443 quinolinate synthetase; Provisional; Region: PRK09375