-- dump date 20140618_194101 -- class Genbank::misc_feature -- table misc_feature_note -- id note 679935000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 679935000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 679935000003 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 679935000004 Walker A motif; other site 679935000005 ATP binding site [chemical binding]; other site 679935000006 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 679935000007 Walker B motif; other site 679935000008 arginine finger; other site 679935000009 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 679935000010 DnaA box-binding interface [nucleotide binding]; other site 679935000011 HTH domain; Region: HTH_11; pfam08279 679935000012 WYL domain; Region: WYL; pfam13280 679935000013 Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]; Region: {ManC}; COG0662 679935000014 primosome assembly protein PriA; Provisional; Region: PRK14873 679935000015 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 679935000016 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 679935000017 catalytic triad [active] 679935000018 The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent; Region: Oxidoreductase_nitrogenase; cl02775 679935000019 recombinase A; Provisional; Region: recA; PRK09354 679935000020 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 679935000021 hexamer interface [polypeptide binding]; other site 679935000022 Walker A motif; other site 679935000023 ATP binding site [chemical binding]; other site 679935000024 Walker B motif; other site 679935000025 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 679935000026 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 679935000027 Zn2+ binding site [ion binding]; other site 679935000028 Mg2+ binding site [ion binding]; other site 679935000029 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 679935000030 synthetase active site [active] 679935000031 NTP binding site [chemical binding]; other site 679935000032 metal binding site [ion binding]; metal-binding site 679935000033 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 679935000034 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 679935000035 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 679935000036 nucleotide binding site/active site [active] 679935000037 HIT family signature motif; other site 679935000038 catalytic residue [active] 679935000039 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 679935000040 non-specific DNA binding site [nucleotide binding]; other site 679935000041 salt bridge; other site 679935000042 sequence-specific DNA binding site [nucleotide binding]; other site 679935000043 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 679935000044 CoenzymeA binding site [chemical binding]; other site 679935000045 subunit interaction site [polypeptide binding]; other site 679935000046 PHB binding site; other site 679935000047 CAAX protease self-immunity; Region: Abi; pfam02517 679935000048 ABC-type Zn2+ transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: ZnuA; COG4531 679935000049 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 679935000050 intersubunit interface [polypeptide binding]; other site 679935000051 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 679935000052 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 679935000053 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935000054 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935000055 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935000056 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935000057 putative transposase OrfB; Reviewed; Region: PHA02517 679935000058 HTH-like domain; Region: HTH_21; pfam13276 679935000059 Integrase core domain; Region: rve; pfam00665 679935000060 Integrase core domain; Region: rve_2; pfam13333 679935000061 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 679935000062 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 679935000063 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 679935000064 HlyD family secretion protein; Region: HlyD_3; pfam13437 679935000065 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 679935000066 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 679935000067 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 679935000068 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 679935000069 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 679935000070 POT family; Region: PTR2; cl17359 679935000071 1,4-alpha-glucan-branching enzyme; Region: PLN02447 679935000072 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 679935000073 Alpha amylase catalytic domain found in bacterial and eukaryotic branching enzymes; Region: AmyAc_bac_euk_BE; cd11321 679935000074 active site 679935000075 catalytic site [active] 679935000076 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 679935000077 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 679935000078 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 679935000079 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 679935000080 N-ethylammeline chlorohydrolase; Provisional; Region: PRK06038 679935000081 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 679935000082 active site 679935000083 putative substrate binding pocket [chemical binding]; other site 679935000084 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 679935000085 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 679935000086 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 679935000087 Family of unknown function (DUF490); Region: DUF490; pfam04357 679935000088 UGMP family protein; Validated; Region: PRK09604 679935000089 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 679935000090 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 679935000091 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 679935000092 FMN binding site [chemical binding]; other site 679935000093 substrate binding site [chemical binding]; other site 679935000094 putative catalytic residue [active] 679935000095 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 679935000096 Terminase-like family; Region: Terminase_6; pfam03237 679935000097 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 679935000098 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 679935000099 non-specific DNA binding site [nucleotide binding]; other site 679935000100 salt bridge; other site 679935000101 sequence-specific DNA binding site [nucleotide binding]; other site 679935000102 Predicted transcriptional regulator [Transcription]; Region: COG2932 679935000103 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 679935000104 Catalytic site [active] 679935000105 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 679935000106 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 679935000107 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 679935000108 dimer interface [polypeptide binding]; other site 679935000109 PYR/PP interface [polypeptide binding]; other site 679935000110 TPP binding site [chemical binding]; other site 679935000111 substrate binding site [chemical binding]; other site 679935000112 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 679935000113 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 679935000114 TPP-binding site [chemical binding]; other site 679935000115 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 679935000116 catalytic residues [active] 679935000117 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 679935000118 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 679935000119 active site 679935000120 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C; pfam03174 679935000121 PA14 domain; Region: PA14; cl08459 679935000122 Sulfatase; Region: Sulfatase; cl17466 679935000123 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 679935000124 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935000125 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 679935000126 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 679935000127 active site 679935000128 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 679935000129 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935000130 Secretin and TonB N terminus short domain; Region: STN; pfam07660 679935000131 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935000132 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935000133 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 679935000134 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935000135 FecR protein; Region: FecR; pfam04773 679935000136 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935000137 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935000138 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 679935000139 DNA binding residues [nucleotide binding] 679935000140 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935000141 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935000142 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 679935000143 DNA binding residues [nucleotide binding] 679935000144 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935000145 FecR protein; Region: FecR; pfam04773 679935000146 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935000147 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935000148 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 679935000149 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 679935000150 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935000151 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 679935000152 active site 679935000153 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935000154 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 679935000155 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 679935000156 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935000157 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 679935000158 DNA binding residues [nucleotide binding] 679935000159 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935000160 FecR protein; Region: FecR; pfam04773 679935000161 Secretin and TonB N terminus short domain; Region: STN; pfam07660 679935000162 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935000163 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935000164 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 679935000165 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 679935000166 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935000167 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 679935000168 active site 679935000169 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935000170 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 679935000171 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935000172 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 679935000173 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935000174 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 679935000175 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935000176 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 679935000177 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 679935000178 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 679935000179 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 679935000180 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 679935000181 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 679935000182 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 679935000183 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 679935000184 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 679935000185 active site 679935000186 Fn3 associated; Region: Fn3_assoc; pfam13287 679935000187 PA14 domain; Region: PA14; cl08459 679935000188 potassium/proton antiporter; Reviewed; Region: PRK05326 679935000189 TrkA-C domain; Region: TrkA_C; pfam02080 679935000190 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 679935000191 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed; Region: PRK13188 679935000192 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 679935000193 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 679935000194 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 679935000195 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 679935000196 active site 679935000197 Sm and related proteins; Region: Sm_like; cl00259 679935000198 Sm1 motif; other site 679935000199 hexamer interface [polypeptide binding]; other site 679935000200 RNA binding site [nucleotide binding]; other site 679935000201 transcription termination factor NusA; Region: NusA; TIGR01953 679935000202 NusA N-terminal domain; Region: NusA_N; pfam08529 679935000203 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 679935000204 RNA binding site [nucleotide binding]; other site 679935000205 homodimer interface [polypeptide binding]; other site 679935000206 NusA-like KH domain; Region: KH_5; pfam13184 679935000207 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 679935000208 G-X-X-G motif; other site 679935000209 translation initiation factor IF-2; Region: IF-2; TIGR00487 679935000210 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 679935000211 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 679935000212 G1 box; other site 679935000213 putative GEF interaction site [polypeptide binding]; other site 679935000214 GTP/Mg2+ binding site [chemical binding]; other site 679935000215 Switch I region; other site 679935000216 G2 box; other site 679935000217 G3 box; other site 679935000218 Switch II region; other site 679935000219 G4 box; other site 679935000220 G5 box; other site 679935000221 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 679935000222 Translation-initiation factor 2; Region: IF-2; pfam11987 679935000223 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 679935000224 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 679935000225 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 679935000226 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 679935000227 phosphonoacetate hydrolase; Region: hydr_PhnA; TIGR02335 679935000228 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 679935000229 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 679935000230 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; pfam05708 679935000231 MgtC family; Region: MgtC; pfam02308 679935000232 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 679935000233 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 679935000234 23S rRNA binding site [nucleotide binding]; other site 679935000235 L21 binding site [polypeptide binding]; other site 679935000236 L13 binding site [polypeptide binding]; other site 679935000237 M6 family metalloprotease domain; Region: M6dom_TIGR03296 679935000238 H+ Antiporter protein; Region: 2A0121; TIGR00900 679935000239 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 679935000240 Beta-lactamase superfamily domain; Region: Lactamase_B_3; pfam13483 679935000241 Heavy-metal-associated domain; Region: HMA; pfam00403 679935000242 metal-binding site [ion binding] 679935000243 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935000244 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 679935000245 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 679935000246 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 679935000247 DEAD-like helicases superfamily; Region: DEXDc; smart00487 679935000248 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 679935000249 ATP binding site [chemical binding]; other site 679935000250 ATP binding site [chemical binding]; other site 679935000251 putative Mg++ binding site [ion binding]; other site 679935000252 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 679935000253 nucleotide binding region [chemical binding]; other site 679935000254 ATP-binding site [chemical binding]; other site 679935000255 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 679935000256 catalytic site [active] 679935000257 putative active site [active] 679935000258 putative substrate binding site [chemical binding]; other site 679935000259 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 679935000260 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 679935000261 putative RNA binding site [nucleotide binding]; other site 679935000262 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 679935000263 S-adenosylmethionine binding site [chemical binding]; other site 679935000264 Predicted transcriptional regulators [Transcription]; Region: COG1733 679935000265 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 679935000266 membrane protein insertase; Provisional; Region: PRK01318 679935000267 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 679935000268 CTP synthetase; Validated; Region: pyrG; PRK05380 679935000269 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 679935000270 Catalytic site [active] 679935000271 active site 679935000272 UTP binding site [chemical binding]; other site 679935000273 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 679935000274 active site 679935000275 putative oxyanion hole; other site 679935000276 catalytic triad [active] 679935000277 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 679935000278 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 679935000279 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 679935000280 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 679935000281 Domain of Unknown Function (DUF349); Region: DUF349; pfam03993 679935000282 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 679935000283 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 679935000284 active site 679935000285 phosphorylation site [posttranslational modification] 679935000286 intermolecular recognition site; other site 679935000287 dimerization interface [polypeptide binding]; other site 679935000288 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 679935000289 DNA binding site [nucleotide binding] 679935000290 gamma-glutamyl kinase; Provisional; Region: PRK05429 679935000291 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 679935000292 nucleotide binding site [chemical binding]; other site 679935000293 homotetrameric interface [polypeptide binding]; other site 679935000294 putative phosphate binding site [ion binding]; other site 679935000295 putative allosteric binding site; other site 679935000296 PUA domain; Region: PUA; pfam01472 679935000297 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 679935000298 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 679935000299 putative catalytic cysteine [active] 679935000300 Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]; Region: CrcB; COG0239 679935000301 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 679935000302 propionate/acetate kinase; Provisional; Region: PRK12379 679935000303 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 679935000304 butyrate kinase; Provisional; Region: PRK03011 679935000305 colanic acid exporter; Provisional; Region: PRK10459 679935000306 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 679935000307 pyruvate kinase; Provisional; Region: PRK05826 679935000308 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 679935000309 domain interfaces; other site 679935000310 active site 679935000311 Dehydroquinase class II; Region: DHquinase_II; pfam01220 679935000312 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 679935000313 trimer interface [polypeptide binding]; other site 679935000314 active site 679935000315 dimer interface [polypeptide binding]; other site 679935000316 thiamine monophosphate kinase; Provisional; Region: PRK05731 679935000317 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 679935000318 ATP binding site [chemical binding]; other site 679935000319 dimerization interface [polypeptide binding]; other site 679935000320 Septum formation initiator; Region: DivIC; cl17659 679935000321 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 679935000322 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 679935000323 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 679935000324 active site 679935000325 electron transport complex, RnfABCDGE type, A subunit; Region: rnfA; TIGR01943 679935000326 electron transport complex RsxE subunit; Provisional; Region: PRK12405 679935000327 FMN-binding domain; Region: FMN_bind; cl01081 679935000328 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 679935000329 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 679935000330 SLBB domain; Region: SLBB; pfam10531 679935000331 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 679935000332 ferredoxin; Validated; Region: PRK07118 679935000333 4Fe-4S binding domain; Region: Fer4; pfam00037 679935000334 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 679935000335 NAD synthetase; Provisional; Region: PRK13981 679935000336 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 679935000337 multimer interface [polypeptide binding]; other site 679935000338 active site 679935000339 catalytic triad [active] 679935000340 protein interface 1 [polypeptide binding]; other site 679935000341 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 679935000342 homodimer interface [polypeptide binding]; other site 679935000343 NAD binding pocket [chemical binding]; other site 679935000344 ATP binding pocket [chemical binding]; other site 679935000345 Mg binding site [ion binding]; other site 679935000346 active-site loop [active] 679935000347 Cupin domain; Region: Cupin_2; cl17218 679935000348 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 679935000349 Putative zinc ribbon domain; Region: DUF164; pfam02591 679935000350 Uncharacterized conserved protein [Function unknown]; Region: COG0327 679935000351 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 679935000352 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 679935000353 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 679935000354 DNA binding residues [nucleotide binding] 679935000355 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 679935000356 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 679935000357 S-adenosylmethionine binding site [chemical binding]; other site 679935000358 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; pfam13636 679935000359 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 679935000360 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 679935000361 Substrate-binding site [chemical binding]; other site 679935000362 Substrate specificity [chemical binding]; other site 679935000363 GH3 auxin-responsive promoter; Region: GH3; pfam03321 679935000364 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 679935000365 TrkA-N domain; Region: TrkA_N; pfam02254 679935000366 TrkA-C domain; Region: TrkA_C; pfam02080 679935000367 TrkA-N domain; Region: TrkA_N; pfam02254 679935000368 TrkA-C domain; Region: TrkA_C; pfam02080 679935000369 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 679935000370 active site 679935000371 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 679935000372 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 679935000373 Response regulator receiver domain; Region: Response_reg; pfam00072 679935000374 active site 679935000375 phosphorylation site [posttranslational modification] 679935000376 intermolecular recognition site; other site 679935000377 dimerization interface [polypeptide binding]; other site 679935000378 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 679935000379 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 679935000380 META domain; Region: META; pfam03724 679935000381 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 679935000382 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 679935000383 dimer interface [polypeptide binding]; other site 679935000384 PYR/PP interface [polypeptide binding]; other site 679935000385 TPP binding site [chemical binding]; other site 679935000386 substrate binding site [chemical binding]; other site 679935000387 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 679935000388 Domain of unknown function; Region: EKR; smart00890 679935000389 4Fe-4S binding domain; Region: Fer4_6; pfam12837 679935000390 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 679935000391 TPP-binding site [chemical binding]; other site 679935000392 dimer interface [polypeptide binding]; other site 679935000393 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 679935000394 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 679935000395 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 679935000396 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 679935000397 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 679935000398 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 679935000399 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 679935000400 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 679935000401 S-adenosylmethionine binding site [chemical binding]; other site 679935000402 Superfamily II DNA helicase [DNA replication, recombination, and repair]; Region: RecQ; COG0514 679935000403 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 679935000404 ATP binding site [chemical binding]; other site 679935000405 putative Mg++ binding site [ion binding]; other site 679935000406 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 679935000407 nucleotide binding region [chemical binding]; other site 679935000408 ATP-binding site [chemical binding]; other site 679935000409 RQC domain; Region: RQC; pfam09382 679935000410 HRDC domain; Region: HRDC; pfam00570 679935000411 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 679935000412 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 679935000413 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 679935000414 Walker A/P-loop; other site 679935000415 ATP binding site [chemical binding]; other site 679935000416 Q-loop/lid; other site 679935000417 ABC transporter signature motif; other site 679935000418 Walker B; other site 679935000419 D-loop; other site 679935000420 H-loop/switch region; other site 679935000421 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 679935000422 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 679935000423 hinge; other site 679935000424 active site 679935000425 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 679935000426 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cl00323 679935000427 Tetramer interface [polypeptide binding]; other site 679935000428 active site 679935000429 FMN-binding site [chemical binding]; other site 679935000430 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 679935000431 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 679935000432 S-adenosylmethionine binding site [chemical binding]; other site 679935000433 RecX family; Region: RecX; pfam02631 679935000434 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 679935000435 Peptidase family M23; Region: Peptidase_M23; pfam01551 679935000436 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 679935000437 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 679935000438 active site 679935000439 phosphorylation site [posttranslational modification] 679935000440 intermolecular recognition site; other site 679935000441 dimerization interface [polypeptide binding]; other site 679935000442 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 679935000443 active site 679935000444 Int/Topo IB signature motif; other site 679935000445 DNA binding site [nucleotide binding] 679935000446 Protein of unknown function (DUF2693); Region: DUF2693; pfam10902 679935000447 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 679935000448 dimer interface [polypeptide binding]; other site 679935000449 ssDNA binding site [nucleotide binding]; other site 679935000450 tetramer (dimer of dimers) interface [polypeptide binding]; other site 679935000451 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 679935000452 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 679935000453 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 679935000454 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 679935000455 isoleucyl-tRNA synthetase; Region: ileS; TIGR00392 679935000456 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 679935000457 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 679935000458 cofactor binding site; other site 679935000459 DNA binding site [nucleotide binding] 679935000460 substrate interaction site [chemical binding]; other site 679935000461 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 679935000462 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935000463 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935000464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935000465 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935000466 putative transposase OrfB; Reviewed; Region: PHA02517 679935000467 HTH-like domain; Region: HTH_21; pfam13276 679935000468 Integrase core domain; Region: rve; pfam00665 679935000469 Integrase core domain; Region: rve_2; pfam13333 679935000470 Type IV secretory system Conjugative DNA transfer; Region: T4SS-DNA_transf; pfam02534 679935000471 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 679935000472 Bacteroides conjugation system ATPase, TraG family; Region: Bac_Flav_CT_G; TIGR03783 679935000473 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 679935000474 Domain of unknown function (DUF4141); Region: DUF4141; pfam13605 679935000475 Bacteroides conjugative transposon TraM protein; Region: Bac_Flav_CT_M; TIGR03779 679935000476 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 679935000477 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 679935000478 ORF6N domain; Region: ORF6N; pfam10543 679935000479 ORF6N domain; Region: ORF6N; pfam10543 679935000480 Major fimbrial subunit protein (FimA); Region: P_gingi_FimA; pfam06321 679935000481 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 679935000482 ORF6N domain; Region: ORF6N; pfam10543 679935000483 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 679935000484 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 679935000485 Peptidase family M23; Region: Peptidase_M23; pfam01551 679935000486 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 679935000487 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 679935000488 P-loop; other site 679935000489 Magnesium ion binding site [ion binding]; other site 679935000490 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 679935000491 Magnesium ion binding site [ion binding]; other site 679935000492 Initiator Replication protein; Region: Rep_3; pfam01051 679935000493 30S ribosomal protein S16; Provisional; Region: rpsP; PRK14521 679935000494 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 679935000495 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 679935000496 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 679935000497 Ligand Binding Site [chemical binding]; other site 679935000498 tRNA-specific 2-thiouridylase MnmA; Reviewed; Region: mnmA; PRK00143 679935000499 Uncharacterized protein conserved in bacteria [Function unknown]; Region: MmcQ; COG2315 679935000500 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 679935000501 non-specific DNA binding site [nucleotide binding]; other site 679935000502 salt bridge; other site 679935000503 sequence-specific DNA binding site [nucleotide binding]; other site 679935000504 pyruvate phosphate dikinase; Provisional; Region: PRK09279 679935000505 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 679935000506 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 679935000507 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 679935000508 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 679935000509 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 679935000510 putative transposase OrfB; Reviewed; Region: PHA02517 679935000511 HTH-like domain; Region: HTH_21; pfam13276 679935000512 Integrase core domain; Region: rve; pfam00665 679935000513 Integrase core domain; Region: rve_2; pfam13333 679935000514 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 679935000515 active site 679935000516 catalytic residues [active] 679935000517 metal binding site [ion binding]; metal-binding site 679935000518 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 679935000519 glycyl-tRNA synthetase; Provisional; Region: PRK04173 679935000520 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 679935000521 motif 1; other site 679935000522 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 679935000523 active site 679935000524 motif 2; other site 679935000525 motif 3; other site 679935000526 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 679935000527 anticodon binding site; other site 679935000528 hypothetical protein; Reviewed; Region: PRK00024 679935000529 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 679935000530 MPN+ (JAMM) motif; other site 679935000531 Zinc-binding site [ion binding]; other site 679935000532 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 679935000533 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 679935000534 dimerization interface [polypeptide binding]; other site 679935000535 active site 679935000536 metal binding site [ion binding]; metal-binding site 679935000537 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 679935000538 dsRNA binding site [nucleotide binding]; other site 679935000539 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 679935000540 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 679935000541 dimer interface [polypeptide binding]; other site 679935000542 active site 679935000543 acyl carrier protein; Provisional; Region: acpP; PRK00982 679935000544 Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E; Region: GAT1_Peptidase_E; cd03146 679935000545 active site pocket [active] 679935000546 oxyanion hole [active] 679935000547 catalytic triad [active] 679935000548 active site nucleophile [active] 679935000549 prephenate dehydrogenase; Validated; Region: PRK08507 679935000550 Prephenate dehydrogenase; Region: PDH; pfam02153 679935000551 hypothetical protein; Reviewed; Region: PRK12497 679935000552 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 679935000553 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 679935000554 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 679935000555 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 679935000556 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 679935000557 dimer interface [polypeptide binding]; other site 679935000558 ADP-ribose binding site [chemical binding]; other site 679935000559 active site 679935000560 nudix motif; other site 679935000561 metal binding site [ion binding]; metal-binding site 679935000562 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 679935000563 Acyltransferase family; Region: Acyl_transf_3; pfam01757 679935000564 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 679935000565 putative FMN binding site [chemical binding]; other site 679935000566 NADPH bind site [chemical binding]; other site 679935000567 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 679935000568 4Fe-4S binding domain; Region: Fer4; cl02805 679935000569 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 679935000570 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 679935000571 Coenzyme A binding pocket [chemical binding]; other site 679935000572 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 679935000573 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 679935000574 Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism]; Region: CutC; COG3142 679935000575 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 679935000576 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 679935000577 putative dimer interface [polypeptide binding]; other site 679935000578 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 679935000579 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 679935000580 ligand binding site [chemical binding]; other site 679935000581 flexible hinge region; other site 679935000582 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 679935000583 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 679935000584 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 679935000585 active site 679935000586 catalytic residues [active] 679935000587 metal binding site [ion binding]; metal-binding site 679935000588 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 679935000589 Coenzyme A binding pocket [chemical binding]; other site 679935000590 37-kD nucleoid-associated bacterial protein; Region: NA37; pfam04245 679935000591 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 679935000592 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 679935000593 FMN binding site [chemical binding]; other site 679935000594 substrate binding site [chemical binding]; other site 679935000595 putative catalytic residue [active] 679935000596 short chain dehydrogenase; Provisional; Region: PRK07024 679935000597 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 679935000598 NAD(P) binding site [chemical binding]; other site 679935000599 active site 679935000600 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 679935000601 Cyclic nucleotide-binding domain; Region: cNMP_binding; pfam00027 679935000602 ligand binding site [chemical binding]; other site 679935000603 flexible hinge region; other site 679935000604 Domain of unknown function (DUF4379); Region: DUF4379; pfam14311 679935000605 hypothetical protein; Region: PHA00684 679935000606 TPR repeat; Region: TPR_11; pfam13414 679935000607 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 679935000608 binding surface 679935000609 TPR motif; other site 679935000610 TPR repeat; Region: TPR_11; pfam13414 679935000611 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 679935000612 binding surface 679935000613 TPR motif; other site 679935000614 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 679935000615 TPR motif; other site 679935000616 binding surface 679935000617 TPR repeat; Region: TPR_11; pfam13414 679935000618 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 679935000619 binding surface 679935000620 TPR motif; other site 679935000621 TPR repeat; Region: TPR_11; pfam13414 679935000622 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 679935000623 catalytic motif [active] 679935000624 Catalytic residue [active] 679935000625 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 679935000626 TPR motif; other site 679935000627 TPR repeat; Region: TPR_11; pfam13414 679935000628 binding surface 679935000629 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 679935000630 Domain of unknown function, B. Theta Gene description (DUF3871); Region: DUF3871; pfam12987 679935000631 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 679935000632 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 679935000633 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 679935000634 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 679935000635 active site 679935000636 DNA binding site [nucleotide binding] 679935000637 Int/Topo IB signature motif; other site 679935000638 Domain of unknown function (DUF4302); Region: DUF4302; pfam14135 679935000639 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 679935000640 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935000641 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935000642 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935000643 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 679935000644 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 679935000645 Lipocalin-like domain; Region: Lipocalin_4; pfam13648 679935000646 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 679935000647 active site 679935000648 catalytic residues [active] 679935000649 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 679935000650 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 679935000651 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935000652 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935000653 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935000654 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935000655 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 679935000656 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 679935000657 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 679935000658 Int/Topo IB signature motif; other site 679935000659 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935000660 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935000661 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 679935000662 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 679935000663 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935000664 Domain of unknown function (DUF4302); Region: DUF4302; pfam14135 679935000665 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 679935000666 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 679935000667 Flavodoxins [Energy production and conversion]; Region: FldA; COG0716 679935000668 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 679935000669 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 679935000670 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 679935000671 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 679935000672 Domain of unknown function (DUF386); Region: DUF386; cl01047 679935000673 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; Region: EEP-2; cd09084 679935000674 putative catalytic site [active] 679935000675 putative metal binding site [ion binding]; other site 679935000676 putative phosphate binding site [ion binding]; other site 679935000677 Rhomboid family; Region: Rhomboid; pfam01694 679935000678 DNA mismatch repair protein MutL; Region: mutl; TIGR00585 679935000679 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 679935000680 ATP binding site [chemical binding]; other site 679935000681 Mg2+ binding site [ion binding]; other site 679935000682 G-X-G motif; other site 679935000683 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 679935000684 ATP binding site [chemical binding]; other site 679935000685 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 679935000686 chaperone protein DnaJ; Provisional; Region: PRK14289 679935000687 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 679935000688 HSP70 interaction site [polypeptide binding]; other site 679935000689 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 679935000690 substrate binding site [polypeptide binding]; other site 679935000691 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 679935000692 Zn binding sites [ion binding]; other site 679935000693 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 679935000694 dimer interface [polypeptide binding]; other site 679935000695 GrpE; Region: GrpE; pfam01025 679935000696 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 679935000697 dimer interface [polypeptide binding]; other site 679935000698 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 679935000699 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 679935000700 putative SAM binding site [chemical binding]; other site 679935000701 homodimer interface [polypeptide binding]; other site 679935000702 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional; Region: PRK11930 679935000703 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 679935000704 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 679935000705 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 679935000706 active site 679935000707 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 679935000708 dimer interface [polypeptide binding]; other site 679935000709 substrate binding site [chemical binding]; other site 679935000710 catalytic residues [active] 679935000711 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 679935000712 MutS domain III; Region: MutS_III; pfam05192 679935000713 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935000714 Walker A/P-loop; other site 679935000715 ATP binding site [chemical binding]; other site 679935000716 Q-loop/lid; other site 679935000717 ABC transporter signature motif; other site 679935000718 Walker B; other site 679935000719 D-loop; other site 679935000720 H-loop/switch region; other site 679935000721 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 679935000722 Smr domain; Region: Smr; pfam01713 679935000723 virulence factor Mce family protein; Region: Mtu_fam_mce; TIGR00996 679935000724 mce related protein; Region: MCE; pfam02470 679935000725 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 679935000726 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 679935000727 active site 679935000728 metal binding site [ion binding]; metal-binding site 679935000729 Sporulation related domain; Region: SPOR; cl10051 679935000730 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 679935000731 Surface antigen; Region: Bac_surface_Ag; pfam01103 679935000732 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 679935000733 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 679935000734 Nitroreductase family; Region: Nitroreductase; pfam00881 679935000735 FMN binding site [chemical binding]; other site 679935000736 dimer interface [polypeptide binding]; other site 679935000737 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 679935000738 Coenzyme A binding pocket [chemical binding]; other site 679935000739 nucleoside transporter; Region: 2A0110; TIGR00889 679935000740 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 679935000741 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 679935000742 active site 679935000743 Zn binding site [ion binding]; other site 679935000744 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 679935000745 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 679935000746 active site 679935000747 Zn binding site [ion binding]; other site 679935000748 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 679935000749 RNA methyltransferase, RsmE family; Region: TIGR00046 679935000750 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 679935000751 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 679935000752 Hydrogenase 4 membrane component (E) [Energy production and conversion]; Region: HyfE; cl17899 679935000753 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 679935000754 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 679935000755 NADH dehydrogenase subunit D; Validated; Region: PRK06075; cl17338 679935000756 Ni,Fe-hydrogenase III large subunit [Energy production and conversion]; Region: HycE; COG3261 679935000757 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 679935000758 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl17194 679935000759 Chromate transporter; Region: Chromate_transp; pfam02417 679935000760 Chromate transporter; Region: Chromate_transp; pfam02417 679935000761 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 679935000762 beta-D-galactosidase; Reviewed; Region: lacZ; PRK09525 679935000763 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 679935000764 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 679935000765 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 679935000766 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 679935000767 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 679935000768 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 679935000769 Peptidase family U32; Region: Peptidase_U32; pfam01136 679935000770 Collagenase; Region: DUF3656; pfam12392 679935000771 seryl-tRNA synthetase; Provisional; Region: PRK05431 679935000772 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 679935000773 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 679935000774 dimer interface [polypeptide binding]; other site 679935000775 active site 679935000776 motif 1; other site 679935000777 motif 2; other site 679935000778 motif 3; other site 679935000779 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 679935000780 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 679935000781 Protein of unknown function (DUF1343); Region: DUF1343; pfam07075 679935000782 peptide chain release factor 2; Validated; Region: prfB; PRK00578 679935000783 This domain is found in peptide chain release factors; Region: PCRF; smart00937 679935000784 RF-1 domain; Region: RF-1; pfam00472 679935000785 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 679935000786 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 679935000787 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 679935000788 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 679935000789 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 679935000790 active site 679935000791 HIGH motif; other site 679935000792 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 679935000793 KMSKS motif; other site 679935000794 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 679935000795 tRNA binding surface [nucleotide binding]; other site 679935000796 anticodon binding site; other site 679935000797 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 679935000798 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 679935000799 ATP binding site [chemical binding]; other site 679935000800 Mg++ binding site [ion binding]; other site 679935000801 motif III; other site 679935000802 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 679935000803 nucleotide binding region [chemical binding]; other site 679935000804 ATP-binding site [chemical binding]; other site 679935000805 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 679935000806 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 679935000807 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 679935000808 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 679935000809 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C; pfam03174 679935000810 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 679935000811 Protein of unknown function (DUF2723); Region: DUF2723; pfam11028 679935000812 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 679935000813 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 679935000814 acyl-activating enzyme (AAE) consensus motif; other site 679935000815 putative AMP binding site [chemical binding]; other site 679935000816 putative active site [active] 679935000817 putative CoA binding site [chemical binding]; other site 679935000818 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 679935000819 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 679935000820 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 679935000821 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 679935000822 nucleoside/Zn binding site; other site 679935000823 dimer interface [polypeptide binding]; other site 679935000824 catalytic motif [active] 679935000825 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 679935000826 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 679935000827 dimer interface [polypeptide binding]; other site 679935000828 anticodon binding site; other site 679935000829 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 679935000830 homodimer interface [polypeptide binding]; other site 679935000831 motif 1; other site 679935000832 active site 679935000833 motif 2; other site 679935000834 GAD domain; Region: GAD; pfam02938 679935000835 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 679935000836 active site 679935000837 motif 3; other site 679935000838 recombination factor protein RarA; Reviewed; Region: PRK13342 679935000839 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 679935000840 Walker A motif; other site 679935000841 ATP binding site [chemical binding]; other site 679935000842 Walker B motif; other site 679935000843 arginine finger; other site 679935000844 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 679935000845 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 679935000846 active site 679935000847 metal binding site [ion binding]; metal-binding site 679935000848 homotetramer interface [polypeptide binding]; other site 679935000849 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 679935000850 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 679935000851 Walker A motif; other site 679935000852 ATP binding site [chemical binding]; other site 679935000853 Walker B motif; other site 679935000854 arginine finger; other site 679935000855 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 679935000856 Walker A motif; other site 679935000857 ATP binding site [chemical binding]; other site 679935000858 Walker B motif; other site 679935000859 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 679935000860 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 679935000861 TPR motif; other site 679935000862 Tetratricopeptide repeat; Region: TPR_12; pfam13424 679935000863 binding surface 679935000864 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935000865 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 679935000866 dimer interface [polypeptide binding]; other site 679935000867 phosphorylation site [posttranslational modification] 679935000868 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 679935000869 ATP binding site [chemical binding]; other site 679935000870 Mg2+ binding site [ion binding]; other site 679935000871 G-X-G motif; other site 679935000872 multidrug efflux protein; Reviewed; Region: PRK01766 679935000873 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 679935000874 cation binding site [ion binding]; other site 679935000875 PSP1 C-terminal conserved region; Region: PSP1; cl00770 679935000876 GldH lipoprotein; Region: GldH_lipo; cl11905 679935000877 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 679935000878 S-adenosylmethionine binding site [chemical binding]; other site 679935000879 Penicillinase repressor; Region: Pencillinase_R; pfam03965 679935000880 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 679935000881 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935000882 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935000883 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 679935000884 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 679935000885 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 679935000886 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 679935000887 ligand binding site [chemical binding]; other site 679935000888 active site 679935000889 UGI interface [polypeptide binding]; other site 679935000890 catalytic site [active] 679935000891 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 679935000892 UbiA prenyltransferase family; Region: UbiA; pfam01040 679935000893 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 679935000894 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935000895 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 679935000896 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 679935000897 DNA binding residues [nucleotide binding] 679935000898 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 679935000899 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 679935000900 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 679935000901 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 679935000902 S-adenosylmethionine synthetase; Validated; Region: PRK05250 679935000903 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 679935000904 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 679935000905 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 679935000906 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 679935000907 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935000908 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 679935000909 DNA binding residues [nucleotide binding] 679935000910 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 679935000911 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 679935000912 Int/Topo IB signature motif; other site 679935000913 Plasmid recombination enzyme; Region: Mob_Pre; pfam01076 679935000914 Protein of unknown function (DUF1266); Region: DUF1266; pfam06889 679935000915 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 679935000916 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 679935000917 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 679935000918 TPP-binding site [chemical binding]; other site 679935000919 dimer interface [polypeptide binding]; other site 679935000920 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 679935000921 PYR/PP interface [polypeptide binding]; other site 679935000922 dimer interface [polypeptide binding]; other site 679935000923 TPP binding site [chemical binding]; other site 679935000924 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 679935000925 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 679935000926 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 679935000927 Walker A motif; other site 679935000928 ATP binding site [chemical binding]; other site 679935000929 Walker B motif; other site 679935000930 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 679935000931 Clp protease; Region: CLP_protease; pfam00574 679935000932 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 679935000933 oligomer interface [polypeptide binding]; other site 679935000934 active site residues [active] 679935000935 Bacterial trigger factor protein (TF); Region: Trigger_N; pfam05697 679935000936 Glutamine cyclotransferase [Posttranslational modification, protein turnover, chaperones]; Region: COG3823 679935000937 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 679935000938 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 679935000939 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 679935000940 substrate binding pocket [chemical binding]; other site 679935000941 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 679935000942 B12 binding site [chemical binding]; other site 679935000943 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 679935000944 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 679935000945 FAD binding site [chemical binding]; other site 679935000946 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 679935000947 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 679935000948 metal binding site [ion binding]; metal-binding site 679935000949 dimer interface [polypeptide binding]; other site 679935000950 ribonuclease R; Region: RNase_R; TIGR02063 679935000951 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 679935000952 RNB domain; Region: RNB; pfam00773 679935000953 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 679935000954 RNA binding site [nucleotide binding]; other site 679935000955 menaquinone biosynthesis protein, SCO4550 family; Region: mena_SCO4550; TIGR03699 679935000956 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 679935000957 FeS/SAM binding site; other site 679935000958 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 679935000959 Uncharacterized conserved protein [Function unknown]; Region: COG3538 679935000960 Protein of unknown function (DUF1237); Region: DUF1237; pfam06824 679935000961 Glycosyl hydrolase family 76; Region: Glyco_hydro_76; pfam03663 679935000962 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 679935000963 active site 679935000964 catalytic triad [active] 679935000965 oxyanion hole [active] 679935000966 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 679935000967 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 679935000968 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 679935000969 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935000970 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 679935000971 ATP binding site [chemical binding]; other site 679935000972 Mg2+ binding site [ion binding]; other site 679935000973 G-X-G motif; other site 679935000974 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 679935000975 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 679935000976 active site 679935000977 phosphorylation site [posttranslational modification] 679935000978 intermolecular recognition site; other site 679935000979 dimerization interface [polypeptide binding]; other site 679935000980 Helix-turn-helix domain; Region: HTH_18; pfam12833 679935000981 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935000982 Glycosyl hydrolase family 76; Region: Glyco_hydro_76; pfam03663 679935000983 SusE outer membrane protein; Region: SusE; pfam14292 679935000984 SusE outer membrane protein; Region: SusE; pfam14292 679935000985 SusE outer membrane protein; Region: SusE; pfam14292 679935000986 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935000987 SusD family; Region: SusD; pfam07980 679935000988 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935000989 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935000990 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935000991 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 679935000992 Alpha-mannosidase [Carbohydrate transport and metabolism]; Region: AMS1; COG0383 679935000993 N-terminal catalytic domain of endoplasmic reticulum(ER)/cytosolic class II alpha-mannosidases; glycoside hydrolase family 38 (GH38); Region: GH38N_AMII_ER_cytosolic; cd10789 679935000994 active site 679935000995 catalytic site [active] 679935000996 Alpha mannosidase, middle domain; Region: Alpha-mann_mid; smart00872 679935000997 V-type ATP synthase subunit K; Validated; Region: PRK06558 679935000998 ATP synthase subunit C; Region: ATP-synt_C; pfam00137 679935000999 V-type ATP synthase subunit I; Validated; Region: PRK05771 679935001000 V-type ATP synthase subunit D; Provisional; Region: PRK02195 679935001001 V-type ATP synthase subunit B; Provisional; Region: PRK02118 679935001002 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 679935001003 Walker A motif homologous position; other site 679935001004 Walker B motif; other site 679935001005 V-type ATP synthase subunit A; Provisional; Region: PRK04192 679935001006 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 679935001007 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 679935001008 Walker A motif/ATP binding site; other site 679935001009 Walker B motif; other site 679935001010 Protein of unknown function (DUF2764); Region: DUF2764; pfam10962 679935001011 V-type ATP synthase subunit E; Provisional; Region: PRK01558 679935001012 V-type ATP synthase subunit E; Provisional; Region: PRK01005 679935001013 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 679935001014 dimerization interface [polypeptide binding]; other site 679935001015 putative Zn2+ binding site [ion binding]; other site 679935001016 putative DNA binding site [nucleotide binding]; other site 679935001017 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 679935001018 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 679935001019 nucleotide binding site [chemical binding]; other site 679935001020 Domain of unknown function (DUF4301); Region: DUF4301; pfam14134 679935001021 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 679935001022 FAD binding domain; Region: FAD_binding_4; pfam01565 679935001023 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 679935001024 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 679935001025 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 679935001026 Ligand Binding Site [chemical binding]; other site 679935001027 TilS substrate C-terminal domain; Region: TilS_C; smart00977 679935001028 DNA polymerase III, delta subunit [DNA replication, recombination, and repair]; Region: HolA; COG1466 679935001029 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 679935001030 substrate-cofactor binding pocket; other site 679935001031 homodimer interface [polypeptide binding]; other site 679935001032 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 679935001033 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935001034 catalytic residue [active] 679935001035 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 679935001036 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 679935001037 active site 679935001038 nucleotide binding site [chemical binding]; other site 679935001039 HIGH motif; other site 679935001040 KMSKS motif; other site 679935001041 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 679935001042 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 679935001043 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 679935001044 trimer interface [polypeptide binding]; other site 679935001045 active site 679935001046 UDP-GlcNAc binding site [chemical binding]; other site 679935001047 lipid binding site [chemical binding]; lipid-binding site 679935001048 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 679935001049 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 679935001050 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 679935001051 catalytic residues [active] 679935001052 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 679935001053 active site 679935001054 putative DNA-binding cleft [nucleotide binding]; other site 679935001055 dimer interface [polypeptide binding]; other site 679935001056 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 679935001057 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 679935001058 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 679935001059 catalytic residues [active] 679935001060 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 679935001061 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 679935001062 non-specific DNA binding site [nucleotide binding]; other site 679935001063 salt bridge; other site 679935001064 sequence-specific DNA binding site [nucleotide binding]; other site 679935001065 Protein involved in cell division [Cell division and chromosome partitioning]; Region: Fic; COG2184 679935001066 Fic/DOC family; Region: Fic; cl00960 679935001067 Transposase, Mutator family; Region: Transposase_mut; pfam00872 679935001068 MULE transposase domain; Region: MULE; pfam10551 679935001069 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 679935001070 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001071 replicative DNA helicase; Region: DnaB; TIGR00665 679935001072 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 679935001073 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 679935001074 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 679935001075 Walker A motif; other site 679935001076 ATP binding site [chemical binding]; other site 679935001077 Walker A motif; other site 679935001078 ATP binding site [chemical binding]; other site 679935001079 Walker B motif; other site 679935001080 DNA binding loops [nucleotide binding] 679935001081 Domain of unknown function (DUF4373); Region: DUF4373; pfam14297 679935001082 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001083 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 679935001084 active site 679935001085 DNA binding site [nucleotide binding] 679935001086 Int/Topo IB signature motif; other site 679935001087 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 679935001088 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 679935001089 catalytic residues [active] 679935001090 [FeFe] hydrogenase, group B1/B3; Region: FeFe_hydrog_B1; TIGR04105 679935001091 MarR family; Region: MarR; pfam01047 679935001092 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 679935001093 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935001094 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935001095 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935001096 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935001097 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935001098 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 679935001099 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935001100 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935001101 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935001102 Plasmid recombination enzyme; Region: Mob_Pre; pfam01076 679935001103 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 679935001104 Int/Topo IB signature motif; other site 679935001105 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 679935001106 dimer interface [polypeptide binding]; other site 679935001107 PYR/PP interface [polypeptide binding]; other site 679935001108 TPP binding site [chemical binding]; other site 679935001109 substrate binding site [chemical binding]; other site 679935001110 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 679935001111 TPP-binding site; other site 679935001112 indolepyruvate oxidoreductase subunit beta; Reviewed; Region: PRK06853 679935001113 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 679935001114 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 679935001115 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935001116 homodimer interface [polypeptide binding]; other site 679935001117 catalytic residue [active] 679935001118 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 679935001119 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 679935001120 Coenzyme A transferase; Region: CoA_trans; cl17247 679935001121 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 679935001122 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 679935001123 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 679935001124 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 679935001125 motif II; other site 679935001126 Peptidase S46; Region: Peptidase_S46; pfam10459 679935001127 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 679935001128 4Fe-4S binding domain; Region: Fer4_5; pfam12801 679935001129 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 679935001130 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 679935001131 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 679935001132 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 679935001133 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 679935001134 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935001135 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 679935001136 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 679935001137 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 679935001138 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 679935001139 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 679935001140 Walker A/P-loop; other site 679935001141 ATP binding site [chemical binding]; other site 679935001142 Q-loop/lid; other site 679935001143 ABC transporter signature motif; other site 679935001144 Walker B; other site 679935001145 D-loop; other site 679935001146 H-loop/switch region; other site 679935001147 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 679935001148 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 679935001149 FtsX-like permease family; Region: FtsX; pfam02687 679935001150 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 679935001151 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 679935001152 FtsX-like permease family; Region: FtsX; pfam02687 679935001153 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 679935001154 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 679935001155 HlyD family secretion protein; Region: HlyD_3; pfam13437 679935001156 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 679935001157 putative transporter; Validated; Region: PRK03818 679935001158 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 679935001159 TrkA-C domain; Region: TrkA_C; pfam02080 679935001160 TrkA-C domain; Region: TrkA_C; pfam02080 679935001161 AspT/YidE/YbjL antiporter duplication domain; Region: YidE_YbjL_dupl; TIGR01625 679935001162 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 679935001163 Mechanosensitive ion channel; Region: MS_channel; pfam00924 679935001164 Ultra-violet resistance protein B; Region: UvrB; pfam12344 679935001165 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 679935001166 nudix motif; other site 679935001167 MFS transport protein AraJ; Provisional; Region: PRK10091 679935001168 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 679935001169 putative substrate translocation pore; other site 679935001170 OstA-like protein; Region: OstA_2; pfam13100 679935001171 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 679935001172 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 679935001173 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 679935001174 CAAX protease self-immunity; Region: Abi; pfam02517 679935001175 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 679935001176 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 679935001177 P-loop; other site 679935001178 Magnesium ion binding site [ion binding]; other site 679935001179 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 679935001180 Magnesium ion binding site [ion binding]; other site 679935001181 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 679935001182 ParB-like nuclease domain; Region: ParB; smart00470 679935001183 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 679935001184 N-acetyl-D-glucosamine binding site [chemical binding]; other site 679935001185 catalytic residue [active] 679935001186 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 679935001187 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 679935001188 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 679935001189 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 679935001190 trmE is a tRNA modification GTPase; Region: trmE; cd04164 679935001191 G1 box; other site 679935001192 G1 box; other site 679935001193 GTP/Mg2+ binding site [chemical binding]; other site 679935001194 GTP/Mg2+ binding site [chemical binding]; other site 679935001195 Switch I region; other site 679935001196 G2 box; other site 679935001197 Switch II region; other site 679935001198 G3 box; other site 679935001199 G4 box; other site 679935001200 G5 box; other site 679935001201 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 679935001202 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 679935001203 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 679935001204 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 679935001205 Int/Topo IB signature motif; other site 679935001206 DNA-damage-inducible protein D; Provisional; Region: dinD; PRK11525 679935001207 BRO family, N-terminal domain; Region: Bro-N; pfam02498 679935001208 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001209 Helix-turn-helix domain; Region: HTH_39; pfam14090 679935001210 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935001211 AAA domain; Region: AAA_23; pfam13476 679935001212 Walker A/P-loop; other site 679935001213 ATP binding site [chemical binding]; other site 679935001214 RecT family; Region: RecT; cl04285 679935001215 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 679935001216 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 679935001217 RT_Bac_retron_I: 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_I; cd01646 679935001218 putative active site [active] 679935001219 putative NTP binding site [chemical binding]; other site 679935001220 putative nucleic acid binding site [nucleotide binding]; other site 679935001221 Predicted periplasmic lipoprotein (DUF2279); Region: DUF2279; cl11574 679935001222 Mrr N-terminal domain; Region: Mrr_N; pfam14338 679935001223 Restriction endonuclease; Region: Mrr_cat; pfam04471 679935001224 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001225 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001226 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 679935001227 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 679935001228 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 679935001229 Int/Topo IB signature motif; other site 679935001230 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 679935001231 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 679935001232 Int/Topo IB signature motif; other site 679935001233 Virulence protein [General function prediction only]; Region: COG3943 679935001234 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001235 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001236 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001237 Protein of unknown function (DUF4099); Region: DUF4099; pfam13351 679935001238 Protein of unknown function (DUF3945); Region: DUF3945; pfam13101 679935001239 DNA topoisomerase III; Provisional; Region: PRK07726 679935001240 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 679935001241 active site 679935001242 putative interdomain interaction site [polypeptide binding]; other site 679935001243 putative metal-binding site [ion binding]; other site 679935001244 putative nucleotide binding site [chemical binding]; other site 679935001245 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 679935001246 domain I; other site 679935001247 DNA binding groove [nucleotide binding] 679935001248 phosphate binding site [ion binding]; other site 679935001249 domain II; other site 679935001250 domain III; other site 679935001251 nucleotide binding site [chemical binding]; other site 679935001252 catalytic site [active] 679935001253 domain IV; other site 679935001254 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 679935001255 Methyltransferase domain; Region: Methyltransf_26; pfam13659 679935001256 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 679935001257 DEAD-like helicases superfamily; Region: DEXDc; smart00487 679935001258 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 679935001259 helicase superfamily c-terminal domain; Region: HELICc; smart00490 679935001260 ATP-binding site [chemical binding]; other site 679935001261 Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]; Region: FusA; COG0480 679935001262 Tet(M)-like family includes Tet(M), Tet(O), Tet(W), and OtrA, containing tetracycline resistant proteins; Region: TetM_like; cd04168 679935001263 G1 box; other site 679935001264 putative GEF interaction site [polypeptide binding]; other site 679935001265 GTP/Mg2+ binding site [chemical binding]; other site 679935001266 Switch I region; other site 679935001267 G2 box; other site 679935001268 G3 box; other site 679935001269 Switch II region; other site 679935001270 G4 box; other site 679935001271 G5 box; other site 679935001272 Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome...; Region: Tet_II; cd03690 679935001273 EF-G_domain IV_RPP domain is a part of bacterial ribosomal protected proteins (RPP) family. RPPs such as tetracycline resistance proteins Tet(M) and Tet(O) mediate tetracycline resistance in both gram-positive and -negative species. Tetracyclines inhibit...; Region: Tet_like_IV; cd01684 679935001274 Tet_C: C-terminus of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to the C terminal domains of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a...; Region: Tet_C; cd03711 679935001275 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935001276 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 679935001277 dimer interface [polypeptide binding]; other site 679935001278 phosphorylation site [posttranslational modification] 679935001279 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 679935001280 ATP binding site [chemical binding]; other site 679935001281 Mg2+ binding site [ion binding]; other site 679935001282 G-X-G motif; other site 679935001283 Response regulator receiver domain; Region: Response_reg; pfam00072 679935001284 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 679935001285 active site 679935001286 phosphorylation site [posttranslational modification] 679935001287 intermolecular recognition site; other site 679935001288 dimerization interface [polypeptide binding]; other site 679935001289 Domain of unknown function, B. Theta Gene description (DUF3873); Region: DUF3873; pfam12989 679935001290 PcfJ-like protein; Region: PcfJ; pfam14284 679935001291 PcfK-like protein; Region: PcfK; pfam14058 679935001292 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001293 AAA domain; Region: AAA_25; pfam13481 679935001294 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 679935001295 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 679935001296 Int/Topo IB signature motif; other site 679935001297 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 679935001298 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 679935001299 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 679935001300 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 679935001301 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 679935001302 Transposase, Mutator family; Region: Transposase_mut; pfam00872 679935001303 MULE transposase domain; Region: MULE; pfam10551 679935001304 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 679935001305 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 679935001306 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 679935001307 Virulence protein [General function prediction only]; Region: COG3943 679935001308 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 679935001309 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 679935001310 HsdM N-terminal domain; Region: HsdM_N; pfam12161 679935001311 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 679935001312 S-adenosylmethionine binding site [chemical binding]; other site 679935001313 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 679935001314 T5orf172 domain; Region: T5orf172; pfam10544 679935001315 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 679935001316 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 679935001317 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 679935001318 ATP binding site [chemical binding]; other site 679935001319 putative Mg++ binding site [ion binding]; other site 679935001320 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 679935001321 salt bridge; other site 679935001322 non-specific DNA binding site [nucleotide binding]; other site 679935001323 sequence-specific DNA binding site [nucleotide binding]; other site 679935001324 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 679935001325 AAA domain; Region: AAA_14; pfam13173 679935001326 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 679935001327 Archaea bacterial proteins of unknown function; Region: DUF234; pfam03008 679935001328 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 679935001329 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 679935001330 non-specific DNA binding site [nucleotide binding]; other site 679935001331 salt bridge; other site 679935001332 sequence-specific DNA binding site [nucleotide binding]; other site 679935001333 SEC-C motif; Region: SEC-C; pfam02810 679935001334 DoxX; Region: DoxX; pfam07681 679935001335 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 679935001336 alpha-1,2-mannosidase, putative; Region: aman2_put; TIGR01180 679935001337 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 679935001338 Predicted membrane protein [Function unknown]; Region: COG1238 679935001339 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 679935001340 Coenzyme A binding pocket [chemical binding]; other site 679935001341 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 679935001342 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 679935001343 Ferritin-like domain; Region: Ferritin; pfam00210 679935001344 ferroxidase diiron center [ion binding]; other site 679935001345 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935001346 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935001347 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935001348 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935001349 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935001350 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935001351 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935001352 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 679935001353 dimer interface [polypeptide binding]; other site 679935001354 phosphorylation site [posttranslational modification] 679935001355 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 679935001356 ATP binding site [chemical binding]; other site 679935001357 Mg2+ binding site [ion binding]; other site 679935001358 G-X-G motif; other site 679935001359 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 679935001360 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 679935001361 active site 679935001362 phosphorylation site [posttranslational modification] 679935001363 intermolecular recognition site; other site 679935001364 dimerization interface [polypeptide binding]; other site 679935001365 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 679935001366 DNA binding site [nucleotide binding] 679935001367 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 679935001368 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 679935001369 dimer interface [polypeptide binding]; other site 679935001370 active site 679935001371 CoA binding pocket [chemical binding]; other site 679935001372 putative phosphate acyltransferase; Provisional; Region: PRK05331 679935001373 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 679935001374 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 679935001375 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 679935001376 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 679935001377 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 679935001378 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 679935001379 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 679935001380 Walker A/P-loop; other site 679935001381 ATP binding site [chemical binding]; other site 679935001382 Q-loop/lid; other site 679935001383 ABC transporter signature motif; other site 679935001384 Walker B; other site 679935001385 D-loop; other site 679935001386 H-loop/switch region; other site 679935001387 Permease; Region: Permease; pfam02405 679935001388 adenylosuccinate lyase; Provisional; Region: PRK09285 679935001389 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 679935001390 tetramer interface [polypeptide binding]; other site 679935001391 active site 679935001392 putative glutamate/gamma-aminobutyrate antiporter; Region: put_Glu_GABA_T; TIGR03813 679935001393 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935001394 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935001395 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 679935001396 DNA binding residues [nucleotide binding] 679935001397 FecR protein; Region: FecR; pfam04773 679935001398 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935001399 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935001400 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935001401 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 679935001402 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935001403 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935001404 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935001405 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 679935001406 putative catalytic site [active] 679935001407 putative metal binding site [ion binding]; other site 679935001408 putative phosphate binding site [ion binding]; other site 679935001409 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 679935001410 putative catalytic site [active] 679935001411 putative metal binding site [ion binding]; other site 679935001412 putative phosphate binding site [ion binding]; other site 679935001413 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935001414 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 679935001415 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 679935001416 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 679935001417 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 679935001418 Protein export membrane protein; Region: SecD_SecF; cl14618 679935001419 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 679935001420 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 679935001421 HlyD family secretion protein; Region: HlyD_3; pfam13437 679935001422 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935001423 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935001424 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 679935001425 DNA binding residues [nucleotide binding] 679935001426 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935001427 FecR protein; Region: FecR; pfam04773 679935001428 Secretin and TonB N terminus short domain; Region: STN; pfam07660 679935001429 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935001430 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935001431 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 679935001432 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935001433 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 679935001434 Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins; Region: GDPD_AtGDE_like; cd08566 679935001435 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 679935001436 putative active site [active] 679935001437 catalytic site [active] 679935001438 putative metal binding site [ion binding]; other site 679935001439 oligomer interface [polypeptide binding]; other site 679935001440 FOG: PKD repeat [General function prediction only]; Region: COG3291 679935001441 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 679935001442 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 679935001443 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 679935001444 active site 679935001445 PQQ-like domain; Region: PQQ_2; pfam13360 679935001446 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 679935001447 putative catalytic site [active] 679935001448 putative metal binding site [ion binding]; other site 679935001449 putative phosphate binding site [ion binding]; other site 679935001450 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 679935001451 Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins; Region: GDPD_AtGDE_like; cd08566 679935001452 putative active site [active] 679935001453 catalytic site [active] 679935001454 putative metal binding site [ion binding]; other site 679935001455 oligomer interface [polypeptide binding]; other site 679935001456 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 679935001457 putative catalytic site [active] 679935001458 putative metal binding site [ion binding]; other site 679935001459 putative phosphate binding site [ion binding]; other site 679935001460 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 679935001461 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 679935001462 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 679935001463 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 679935001464 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001465 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935001466 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935001467 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935001468 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935001469 Initiator Replication protein; Region: Rep_3; cl17676 679935001470 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 679935001471 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 679935001472 P-loop; other site 679935001473 Magnesium ion binding site [ion binding]; other site 679935001474 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 679935001475 Magnesium ion binding site [ion binding]; other site 679935001476 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 679935001477 Peptidase family M23; Region: Peptidase_M23; pfam01551 679935001478 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 679935001479 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 679935001480 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4185 679935001481 AAA domain; Region: AAA_33; pfam13671 679935001482 Archaeal ATPase; Region: Arch_ATPase; pfam01637 679935001483 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 679935001484 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 679935001485 active site 679935001486 DNA binding site [nucleotide binding] 679935001487 Int/Topo IB signature motif; other site 679935001488 SprT-like family; Region: SprT-like; pfam10263 679935001489 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001490 VirE N-terminal domain; Region: VirE_N; pfam08800 679935001491 Primase C terminal 2 (PriCT-2); Region: PriCT_2; pfam08707 679935001492 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 679935001493 Type IV pilin PilA; Region: Pilin_PilA; pfam14245 679935001494 putative transposase OrfB; Reviewed; Region: PHA02517 679935001495 HTH-like domain; Region: HTH_21; pfam13276 679935001496 Integrase core domain; Region: rve; pfam00665 679935001497 Integrase core domain; Region: rve_3; pfam13683 679935001498 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 679935001499 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 679935001500 P-loop; other site 679935001501 Magnesium ion binding site [ion binding]; other site 679935001502 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 679935001503 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 679935001504 Domain of unknown function (DUF4134); Region: DUF4134; pfam13572 679935001505 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 679935001506 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 679935001507 putative active site [active] 679935001508 putative NTP binding site [chemical binding]; other site 679935001509 putative nucleic acid binding site [nucleotide binding]; other site 679935001510 Type II intron maturase; Region: Intron_maturas2; pfam01348 679935001511 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 679935001512 active site 679935001513 Domain of unknown function (DUF4133); Region: DUF4133; pfam13571 679935001514 N-terminal domain of reverse transcriptase; Region: RVT_N; pfam13655 679935001515 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 679935001516 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 679935001517 putative active site [active] 679935001518 putative NTP binding site [chemical binding]; other site 679935001519 putative nucleic acid binding site [nucleotide binding]; other site 679935001520 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 679935001521 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 679935001522 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 679935001523 putative active site [active] 679935001524 putative NTP binding site [chemical binding]; other site 679935001525 putative nucleic acid binding site [nucleotide binding]; other site 679935001526 Type II intron maturase; Region: Intron_maturas2; pfam01348 679935001527 Domain of unknown function, B. Theta Gene description (DUF3876); Region: DUF3876; pfam12992 679935001528 Domain of unknown function (DUF4141); Region: DUF4141; pfam13605 679935001529 Bacteroides conjugative transposon TraJ protein; Region: Bac_Flav_CT_J; TIGR03782 679935001530 Bacteroides conjugative transposon TraK protein; Region: Bac_Flav_CT_K; TIGR03781 679935001531 Bacteroides conjugative transposon TraM protein; Region: Bac_Flav_CT_M; TIGR03779 679935001532 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 679935001533 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 679935001534 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935001535 AAA domain; Region: AAA_21; pfam13304 679935001536 Walker A/P-loop; other site 679935001537 ATP binding site [chemical binding]; other site 679935001538 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935001539 ABC transporter signature motif; other site 679935001540 Walker B; other site 679935001541 D-loop; other site 679935001542 H-loop/switch region; other site 679935001543 Protein of unknown function DUF262; Region: DUF262; pfam03235 679935001544 Protein of unknown function DUF262; Region: DUF262; pfam03235 679935001545 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 679935001546 non-specific DNA binding site [nucleotide binding]; other site 679935001547 salt bridge; other site 679935001548 sequence-specific DNA binding site [nucleotide binding]; other site 679935001549 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935001550 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935001551 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935001552 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 679935001553 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 679935001554 S-adenosylmethionine binding site [chemical binding]; other site 679935001555 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 679935001556 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 679935001557 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 679935001558 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 679935001559 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 679935001560 ATP binding site [chemical binding]; other site 679935001561 putative Mg++ binding site [ion binding]; other site 679935001562 Plasmid recombination enzyme; Region: Mob_Pre; pfam01076 679935001563 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 679935001564 Helix-turn-helix domain; Region: HTH_17; cl17695 679935001565 Protein of unknown function (DUF2795); Region: DUF2795; pfam11387 679935001566 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 679935001567 active site 679935001568 intersubunit interactions; other site 679935001569 catalytic residue [active] 679935001570 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 679935001571 IHF - DNA interface [nucleotide binding]; other site 679935001572 IHF dimer interface [polypeptide binding]; other site 679935001573 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 679935001574 Domain of unknown function (DUF4120); Region: DUF4120; pfam13496 679935001575 Domain of unknown function (DUF4121); Region: DUF4121; pfam13497 679935001576 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 679935001577 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 679935001578 ParB-like nuclease domain; Region: ParB; smart00470 679935001579 AAA domain; Region: AAA_21; pfam13304 679935001580 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 679935001581 S-adenosylmethionine binding site [chemical binding]; other site 679935001582 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935001583 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001584 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 679935001585 Int/Topo IB signature motif; other site 679935001586 ORF6N domain; Region: ORF6N; pfam10543 679935001587 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 679935001588 Ras GTPase Activating Domain; Region: RasGAP; cl02569 679935001589 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 679935001590 Phage Tail Collar Domain; Region: Collar; pfam07484 679935001591 Phage-related minor tail protein; Region: PhageMin_Tail; pfam10145 679935001592 Protein of unknown function (DUF2586); Region: DUF2586; pfam10758 679935001593 Neisseria meningitidis TspB protein; Region: Neisseria_TspB; pfam05616 679935001594 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; cl02712 679935001595 amidase catalytic site [active] 679935001596 Zn binding residues [ion binding]; other site 679935001597 substrate binding site [chemical binding]; other site 679935001598 Caudovirus prohead protease; Region: Peptidase_U35; cl01521 679935001599 Uncharacterized conserved protein [Function unknown]; Region: COG5484 679935001600 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 679935001601 Protein of unknown function (DUF1320); Region: DUF1320; cl01818 679935001602 Protein of unknown function (DUF935); Region: DUF935; pfam06074 679935001603 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 679935001604 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 679935001605 chaperone protein DnaJ; Provisional; Region: PRK14301 679935001606 Bacteriophage Mu Gam like protein; Region: Phage_Mu_Gam; cl01825 679935001607 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 679935001608 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 679935001609 Walker A motif; other site 679935001610 ATP binding site [chemical binding]; other site 679935001611 Walker B motif; other site 679935001612 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 679935001613 AAA domain; Region: AAA_22; pfam13401 679935001614 Walker A motif; other site 679935001615 ATP binding site [chemical binding]; other site 679935001616 Walker B motif; other site 679935001617 Predicted transcriptional regulator [Transcription]; Region: COG2932 679935001618 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 679935001619 Catalytic site [active] 679935001620 nitrile hydratase, alpha subunit; Region: nitrile_alph; TIGR01323 679935001621 Bacteroides conjugative transposon TraN protein; Region: Bac_Flav_CT_N; TIGR03780 679935001622 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 679935001623 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 679935001624 Bacteroides conjugation system ATPase, TraG family; Region: Bac_Flav_CT_G; TIGR03783 679935001625 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 679935001626 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 679935001627 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 679935001628 ATP binding site [chemical binding]; other site 679935001629 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 679935001630 Walker B motif; other site 679935001631 D-alanyl-D-alanine carboxypeptidase; Provisional; Region: dacD; PRK11397 679935001632 putative transposase OrfB; Reviewed; Region: PHA02517 679935001633 HTH-like domain; Region: HTH_21; pfam13276 679935001634 Integrase core domain; Region: rve; pfam00665 679935001635 Integrase core domain; Region: rve_2; pfam13333 679935001636 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935001637 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935001638 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935001639 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935001640 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 679935001641 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 679935001642 cofactor binding site; other site 679935001643 DNA binding site [nucleotide binding] 679935001644 substrate interaction site [chemical binding]; other site 679935001645 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 679935001646 isoleucyl-tRNA synthetase; Region: ileS; TIGR00392 679935001647 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 679935001648 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 679935001649 Protein of unknown function (DUF2693); Region: DUF2693; pfam10902 679935001650 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 679935001651 active site 679935001652 DNA binding site [nucleotide binding] 679935001653 Int/Topo IB signature motif; other site 679935001654 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935001655 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935001656 Leucine-rich repeat (LRR) protein [Function unknown]; Region: COG4886 679935001657 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935001658 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935001659 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 679935001660 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 679935001661 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 679935001662 Uncharacterized conserved protein [Function unknown]; Region: COG1479 679935001663 Protein of unknown function DUF262; Region: DUF262; pfam03235 679935001664 Uncharacterized conserved protein [Function unknown]; Region: COG3472 679935001665 Domain of unknown function, B. Theta Gene description (DUF3871); Region: DUF3871; pfam12987 679935001666 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 679935001667 AAA domain; Region: AAA_21; pfam13304 679935001668 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935001669 ABC transporter signature motif; other site 679935001670 Walker B; other site 679935001671 D-loop; other site 679935001672 H-loop/switch region; other site 679935001673 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 679935001674 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 679935001675 active site 679935001676 DNA binding site [nucleotide binding] 679935001677 Int/Topo IB signature motif; other site 679935001678 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 679935001679 ferredoxin-NADP(+) reductase subunit alpha; Reviewed; Region: PRK06222 679935001680 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 679935001681 FAD binding pocket [chemical binding]; other site 679935001682 FAD binding motif [chemical binding]; other site 679935001683 phosphate binding motif [ion binding]; other site 679935001684 beta-alpha-beta structure motif; other site 679935001685 NAD binding pocket [chemical binding]; other site 679935001686 Iron coordination center [ion binding]; other site 679935001687 putative oxidoreductase; Provisional; Region: PRK12831 679935001688 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 679935001689 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 679935001690 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 679935001691 Lipocalin-like; Region: Lipocalin_3; pfam12702 679935001692 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 679935001693 Predicted periplasmic protein [Function unknown]; Region: COG3698 679935001694 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 679935001695 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 679935001696 putative active site [active] 679935001697 Protein of unknown function (DUF4254); Region: DUF4254; pfam14063 679935001698 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 679935001699 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 679935001700 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 679935001701 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 679935001702 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 679935001703 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 679935001704 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 679935001705 DNA binding site [nucleotide binding] 679935001706 active site 679935001707 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 679935001708 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 679935001709 NADH:ubiquinone oxidoreductase subunit 4 (chain M) [Energy production and conversion]; Region: NuoM; COG1008 679935001710 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 679935001711 NADH:ubiquinone oxidoreductase subunit 5 (chain L)/Multisubunit Na+/H+ antiporter, MnhA subunit [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NuoL; COG1009 679935001712 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 679935001713 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 679935001714 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 679935001715 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 679935001716 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 679935001717 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 679935001718 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 679935001719 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 679935001720 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 679935001721 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; pfam00329 679935001722 NADH dehydrogenase subunit D; Validated; Region: PRK06075; cl17338 679935001723 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 679935001724 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl17194 679935001725 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 679935001726 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 679935001727 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935001728 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 679935001729 active site 679935001730 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935001731 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 679935001732 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 679935001733 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 679935001734 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935001735 Secretin and TonB N terminus short domain; Region: STN; pfam07660 679935001736 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935001737 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935001738 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 679935001739 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935001740 FecR protein; Region: FecR; pfam04773 679935001741 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935001742 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935001743 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 679935001744 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 679935001745 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 679935001746 Rubredoxin [Energy production and conversion]; Region: COG1773 679935001747 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 679935001748 iron binding site [ion binding]; other site 679935001749 tryptophanase/L-cysteine desulfhydrase, PLP-dependent; Provisional; Region: tnaA; PRK13238 679935001750 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 679935001751 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 679935001752 catalytic residue [active] 679935001753 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 679935001754 Class I aldolases; Region: Aldolase_Class_I; cl17187 679935001755 catalytic residue [active] 679935001756 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 679935001757 active site 679935001758 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 679935001759 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935001760 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 679935001761 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 679935001762 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 679935001763 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935001764 Secretin and TonB N terminus short domain; Region: STN; pfam07660 679935001765 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935001766 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935001767 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935001768 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 679935001769 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935001770 FecR protein; Region: FecR; pfam04773 679935001771 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935001772 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935001773 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 679935001774 DNA binding residues [nucleotide binding] 679935001775 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 679935001776 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 679935001777 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 679935001778 Transglycosylase; Region: Transgly; pfam00912 679935001779 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 679935001780 Predicted Zn-dependent protease (DUF2268); Region: DUF2268; cl02316 679935001781 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 679935001782 putative rRNA binding site [nucleotide binding]; other site 679935001783 Pyrococcus aspartate kinase subunit, putative; Region: AspKin_pair; TIGR02078 679935001784 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 679935001785 nucleotide binding site [chemical binding]; other site 679935001786 substrate binding site [chemical binding]; other site 679935001787 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 679935001788 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 679935001789 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 679935001790 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 679935001791 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 679935001792 trimer interface [polypeptide binding]; other site 679935001793 active site 679935001794 substrate binding site [chemical binding]; other site 679935001795 CoA binding site [chemical binding]; other site 679935001796 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 679935001797 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 679935001798 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 679935001799 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 679935001800 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 679935001801 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 679935001802 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 679935001803 UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: WecC; COG0677 679935001804 NAD binding site [chemical binding]; other site 679935001805 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 679935001806 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 679935001807 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 679935001808 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 679935001809 Int/Topo IB signature motif; other site 679935001810 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935001811 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935001812 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935001813 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 679935001814 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 679935001815 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 679935001816 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935001817 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 679935001818 dimer interface [polypeptide binding]; other site 679935001819 phosphorylation site [posttranslational modification] 679935001820 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 679935001821 ATP binding site [chemical binding]; other site 679935001822 Mg2+ binding site [ion binding]; other site 679935001823 G-X-G motif; other site 679935001824 Response regulator receiver domain; Region: Response_reg; pfam00072 679935001825 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 679935001826 active site 679935001827 phosphorylation site [posttranslational modification] 679935001828 intermolecular recognition site; other site 679935001829 dimerization interface [polypeptide binding]; other site 679935001830 Helix-turn-helix domain; Region: HTH_18; pfam12833 679935001831 PKD domain; Region: PKD; pfam00801 679935001832 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 679935001833 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935001834 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935001835 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 679935001836 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 679935001837 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 679935001838 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935001839 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 679935001840 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 679935001841 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 679935001842 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 679935001843 Right handed beta helix region; Region: Beta_helix; pfam13229 679935001844 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 679935001845 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 679935001846 inhibitor-cofactor binding pocket; inhibition site 679935001847 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935001848 catalytic residue [active] 679935001849 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 679935001850 lipoyl attachment site [posttranslational modification]; other site 679935001851 malate dehydrogenase; Reviewed; Region: PRK06223 679935001852 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 679935001853 dimer interface [polypeptide binding]; other site 679935001854 NAD(P) binding site [chemical binding]; other site 679935001855 tetramer (dimer of dimers) interface [polypeptide binding]; other site 679935001856 substrate binding site [chemical binding]; other site 679935001857 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935001858 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 679935001859 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 679935001860 N-terminal plug; other site 679935001861 ligand-binding site [chemical binding]; other site 679935001862 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 679935001863 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 679935001864 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 679935001865 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 679935001866 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 679935001867 putative active site [active] 679935001868 catalytic site [active] 679935001869 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 679935001870 putative active site [active] 679935001871 catalytic site [active] 679935001872 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 679935001873 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 679935001874 Flavoprotein; Region: Flavoprotein; pfam02441 679935001875 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 679935001876 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 679935001877 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 679935001878 Walker A/P-loop; other site 679935001879 ATP binding site [chemical binding]; other site 679935001880 Q-loop/lid; other site 679935001881 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 679935001882 ABC transporter signature motif; other site 679935001883 Walker B; other site 679935001884 D-loop; other site 679935001885 H-loop/switch region; other site 679935001886 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 679935001887 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 679935001888 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 679935001889 ring oligomerisation interface [polypeptide binding]; other site 679935001890 ATP/Mg binding site [chemical binding]; other site 679935001891 stacking interactions; other site 679935001892 hinge regions; other site 679935001893 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 679935001894 oligomerisation interface [polypeptide binding]; other site 679935001895 mobile loop; other site 679935001896 roof hairpin; other site 679935001897 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 679935001898 Int/Topo IB signature motif; other site 679935001899 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001900 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001901 Archaeal ATPase; Region: Arch_ATPase; pfam01637 679935001902 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 679935001903 ligand binding site [chemical binding]; other site 679935001904 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 679935001905 binding surface 679935001906 TPR motif; other site 679935001907 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 679935001908 Domain of unknown function (DUF1896); Region: DUF1896; pfam08989 679935001909 Protein of unknown function (DUF4099); Region: DUF4099; pfam13351 679935001910 Protein of unknown function (DUF3945); Region: DUF3945; pfam13101 679935001911 Fic/DOC family; Region: Fic; pfam02661 679935001912 YWFCY protein; Region: YWFCY; pfam14293 679935001913 AAA-like domain; Region: AAA_10; pfam12846 679935001914 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 679935001915 putative transposase OrfB; Reviewed; Region: PHA02517 679935001916 HTH-like domain; Region: HTH_21; pfam13276 679935001917 Integrase core domain; Region: rve; pfam00665 679935001918 Integrase core domain; Region: rve_3; pfam13683 679935001919 RteC protein; Region: RteC; pfam09357 679935001920 Protein of unknown function (DUF805); Region: DUF805; pfam05656 679935001921 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935001922 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935001923 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935001924 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935001925 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935001926 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 679935001927 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935001928 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 679935001929 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 679935001930 RT_Bac_retron_I: 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_I; cd01646 679935001931 putative active site [active] 679935001932 putative NTP binding site [chemical binding]; other site 679935001933 NTP binding site [chemical binding]; other site 679935001934 putative nucleic acid binding site [nucleotide binding]; other site 679935001935 Major fimbrial subunit protein (FimA); Region: P_gingi_FimA; pfam06321 679935001936 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 679935001937 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 679935001938 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 679935001939 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 679935001940 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 679935001941 ligand binding site [chemical binding]; other site 679935001942 putative transporter; Validated; Region: PRK03818 679935001943 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 679935001944 TrkA-C domain; Region: TrkA_C; pfam02080 679935001945 TrkA-C domain; Region: TrkA_C; pfam02080 679935001946 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 679935001947 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 679935001948 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 679935001949 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 679935001950 P-loop; other site 679935001951 Magnesium ion binding site [ion binding]; other site 679935001952 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 679935001953 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 679935001954 Domain of unknown function (DUF4134); Region: DUF4134; pfam13572 679935001955 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 679935001956 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 679935001957 putative active site [active] 679935001958 putative NTP binding site [chemical binding]; other site 679935001959 putative nucleic acid binding site [nucleotide binding]; other site 679935001960 Type II intron maturase; Region: Intron_maturas2; pfam01348 679935001961 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 679935001962 active site 679935001963 Domain of unknown function (DUF4133); Region: DUF4133; pfam13571 679935001964 Domain of unknown function, B. Theta Gene description (DUF3876); Region: DUF3876; pfam12992 679935001965 Domain of unknown function (DUF4141); Region: DUF4141; pfam13605 679935001966 Bacteroides conjugative transposon TraJ protein; Region: Bac_Flav_CT_J; TIGR03782 679935001967 Bacteroides conjugative transposon TraK protein; Region: Bac_Flav_CT_K; TIGR03781 679935001968 Bacteroides conjugative transposon TraM protein; Region: Bac_Flav_CT_M; TIGR03779 679935001969 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 679935001970 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 679935001971 Predicted phosphoadenosine phosphosulfate sulfotransferase [General function prediction only]; Region: COG3969 679935001972 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 679935001973 Active Sites [active] 679935001974 Domain of unknown function (DUF3440); Region: DUF3440; pfam11922 679935001975 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 679935001976 ParB-like nuclease domain; Region: ParBc; pfam02195 679935001977 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 679935001978 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 679935001979 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 679935001980 active site 679935001981 DNA binding site [nucleotide binding] 679935001982 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 679935001983 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 679935001984 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 679935001985 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 679935001986 Catalytic site [active] 679935001987 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 679935001988 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 679935001989 Uncharacterized protein family (UPF0156); Region: RHH_2; pfam03693 679935001990 Domain of unknown function (DUF4120); Region: DUF4120; pfam13496 679935001991 Domain of unknown function (DUF4121); Region: DUF4121; pfam13497 679935001992 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 679935001993 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 679935001994 ParB-like nuclease domain; Region: ParB; smart00470 679935001995 Family description; Region: UvrD_C_2; pfam13538 679935001996 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935001997 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935001998 Inosine-uridine preferring nucleoside hydrolase; Region: IU_nuc_hydro; pfam01156 679935001999 active site 679935002000 FmdE, Molybdenum formylmethanofuran dehydrogenase operon; Region: FmdE; pfam02663 679935002001 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 679935002002 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 679935002003 N-terminal plug; other site 679935002004 ligand-binding site [chemical binding]; other site 679935002005 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 679935002006 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 679935002007 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 679935002008 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 679935002009 Walker A/P-loop; other site 679935002010 ATP binding site [chemical binding]; other site 679935002011 Q-loop/lid; other site 679935002012 ABC transporter signature motif; other site 679935002013 Walker B; other site 679935002014 D-loop; other site 679935002015 H-loop/switch region; other site 679935002016 cobalt ABC transporter, permease protein CbiQ; Region: CbiQ_TIGR; TIGR02454 679935002017 cobalt transport protein CbiM; Validated; Region: PRK06265 679935002018 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 679935002019 PDGLE domain; Region: PDGLE; pfam13190 679935002020 Urea transporter; Region: UT; cl01829 679935002021 UreD urease accessory protein; Region: UreD; cl00530 679935002022 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 679935002023 G1 box; other site 679935002024 GTP/Mg2+ binding site [chemical binding]; other site 679935002025 G2 box; other site 679935002026 Switch I region; other site 679935002027 Switch II region; other site 679935002028 G4 box; other site 679935002029 G5 box; other site 679935002030 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 679935002031 UreF; Region: UreF; pfam01730 679935002032 urease accessory protein UreE; Provisional; Region: ureE; PRK14711 679935002033 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cl03727 679935002034 dimer interface [polypeptide binding]; other site 679935002035 catalytic residues [active] 679935002036 urease subunit alpha; Reviewed; Region: ureC; PRK13207 679935002037 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 679935002038 subunit interactions [polypeptide binding]; other site 679935002039 active site 679935002040 flap region; other site 679935002041 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 679935002042 alpha-beta subunit interface [polypeptide binding]; other site 679935002043 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 679935002044 alpha-gamma subunit interface [polypeptide binding]; other site 679935002045 beta-gamma subunit interface [polypeptide binding]; other site 679935002046 Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]; Region: CrcB; COG0239 679935002047 enolase; Provisional; Region: eno; PRK00077 679935002048 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 679935002049 dimer interface [polypeptide binding]; other site 679935002050 metal binding site [ion binding]; metal-binding site 679935002051 substrate binding pocket [chemical binding]; other site 679935002052 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 679935002053 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 679935002054 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 679935002055 Int/Topo IB signature motif; other site 679935002056 Domain of unknown function (DUF4091); Region: DUF4091; pfam13320 679935002057 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 679935002058 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 679935002059 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 679935002060 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 679935002061 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 679935002062 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935002063 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 679935002064 dimer interface [polypeptide binding]; other site 679935002065 phosphorylation site [posttranslational modification] 679935002066 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 679935002067 ATP binding site [chemical binding]; other site 679935002068 Mg2+ binding site [ion binding]; other site 679935002069 G-X-G motif; other site 679935002070 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 679935002071 Response regulator receiver domain; Region: Response_reg; pfam00072 679935002072 active site 679935002073 phosphorylation site [posttranslational modification] 679935002074 intermolecular recognition site; other site 679935002075 dimerization interface [polypeptide binding]; other site 679935002076 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 679935002077 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935002078 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 679935002079 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 679935002080 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 679935002081 active site 679935002082 Fn3 associated; Region: Fn3_assoc; pfam13287 679935002083 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 679935002084 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 679935002085 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 679935002086 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 679935002087 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 679935002088 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 679935002089 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 679935002090 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 679935002091 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 679935002092 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 679935002093 active site 679935002094 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 679935002095 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 679935002096 Trehalose and maltose hydrolases (possible phosphorylases) [Carbohydrate transport and metabolism]; Region: ATH1; COG1554 679935002097 Glycosyl hydrolase family 65 central catalytic domain; Region: Glyco_hydro_65m; pfam03632 679935002098 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 679935002099 putative catalytic site [active] 679935002100 putative metal binding site [ion binding]; other site 679935002101 putative phosphate binding site [ion binding]; other site 679935002102 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 679935002103 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935002104 active site 679935002105 metal binding site [ion binding]; metal-binding site 679935002106 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935002107 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935002108 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 679935002109 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 679935002110 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 679935002111 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935002112 SusD family; Region: SusD; pfam07980 679935002113 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 679935002114 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; pfam00150 679935002115 Glycosyl hydrolase family 49; Region: Glyco_hydro_49; pfam03718 679935002116 Glycosyl hydrolase family 49; Region: Glyco_hydro_49; pfam03718 679935002117 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 679935002118 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 679935002119 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 679935002120 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 679935002121 active site 679935002122 Fn3 associated; Region: Fn3_assoc; pfam13287 679935002123 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935002124 FecR protein; Region: FecR; pfam04773 679935002125 Secretin and TonB N terminus short domain; Region: STN; pfam07660 679935002126 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935002127 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935002128 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935002129 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 679935002130 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 679935002131 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935002132 SusD family; Region: SusD; pfam07980 679935002133 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 679935002134 putative catalytic site [active] 679935002135 putative metal binding site [ion binding]; other site 679935002136 putative phosphate binding site [ion binding]; other site 679935002137 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935002138 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935002139 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935002140 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 679935002141 DNA binding residues [nucleotide binding] 679935002142 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 679935002143 Queuosine biosynthesis protein; Region: Queuosine_synth; pfam02547 679935002144 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 679935002145 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935002146 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 679935002147 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 679935002148 active site 679935002149 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 679935002150 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935002151 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935002152 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935002153 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 679935002154 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935002155 FecR protein; Region: FecR; pfam04773 679935002156 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935002157 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935002158 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 679935002159 DNA binding residues [nucleotide binding] 679935002160 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 679935002161 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 679935002162 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 679935002163 active site 679935002164 Fn3 associated; Region: Fn3_assoc; pfam13287 679935002165 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 679935002166 L-aspartate oxidase; Provisional; Region: PRK09077 679935002167 L-aspartate oxidase; Provisional; Region: PRK06175 679935002168 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 679935002169 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 679935002170 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 679935002171 G1 box; other site 679935002172 putative GEF interaction site [polypeptide binding]; other site 679935002173 GTP/Mg2+ binding site [chemical binding]; other site 679935002174 Switch I region; other site 679935002175 G2 box; other site 679935002176 G3 box; other site 679935002177 Switch II region; other site 679935002178 G4 box; other site 679935002179 G5 box; other site 679935002180 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 679935002181 Pirin-related protein [General function prediction only]; Region: COG1741 679935002182 Pirin; Region: Pirin; pfam02678 679935002183 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 679935002184 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 679935002185 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 679935002186 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 679935002187 putative ligand binding site [chemical binding]; other site 679935002188 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 679935002189 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 679935002190 ABC-ATPase subunit interface; other site 679935002191 dimer interface [polypeptide binding]; other site 679935002192 putative PBP binding regions; other site 679935002193 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 679935002194 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 679935002195 Walker A/P-loop; other site 679935002196 ATP binding site [chemical binding]; other site 679935002197 Q-loop/lid; other site 679935002198 ABC transporter signature motif; other site 679935002199 Walker B; other site 679935002200 D-loop; other site 679935002201 H-loop/switch region; other site 679935002202 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 679935002203 thiamine monophosphate kinase; Provisional; Region: PRK05731 679935002204 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 679935002205 ATP binding site [chemical binding]; other site 679935002206 dimerization interface [polypeptide binding]; other site 679935002207 adenylate kinase; Reviewed; Region: adk; PRK00279 679935002208 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 679935002209 AMP-binding site [chemical binding]; other site 679935002210 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 679935002211 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 679935002212 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 679935002213 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 679935002214 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 679935002215 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 679935002216 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 679935002217 EamA-like transporter family; Region: EamA; pfam00892 679935002218 YciF bacterial stress response protein, ferritin-like iron-binding domain; Region: YciF; cd07909 679935002219 dimerization interface [polypeptide binding]; other site 679935002220 metal binding site [ion binding]; metal-binding site 679935002221 DKNYY family; Region: DKNYY; pfam13644 679935002222 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 679935002223 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 679935002224 RNA binding site [nucleotide binding]; other site 679935002225 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 679935002226 RNA binding site [nucleotide binding]; other site 679935002227 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 679935002228 RNA binding site [nucleotide binding]; other site 679935002229 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 679935002230 RNA binding site [nucleotide binding]; other site 679935002231 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec5; cd05690 679935002232 RNA binding site [nucleotide binding]; other site 679935002233 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 679935002234 RNA binding site [nucleotide binding]; other site 679935002235 Escherichia coli UshA-like family, N-terminal metallophosphatase domain; Region: MPP_UshA_N_like; cd00845 679935002236 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 679935002237 active site 679935002238 metal binding site [ion binding]; metal-binding site 679935002239 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 679935002240 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 679935002241 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 679935002242 active site 679935002243 glycine dehydrogenase; Provisional; Region: PRK05367 679935002244 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 679935002245 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 679935002246 catalytic residue [active] 679935002247 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 679935002248 tetramer interface [polypeptide binding]; other site 679935002249 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935002250 catalytic residue [active] 679935002251 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 679935002252 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 679935002253 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 679935002254 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 679935002255 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 679935002256 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 679935002257 putative trimer interface [polypeptide binding]; other site 679935002258 putative CoA binding site [chemical binding]; other site 679935002259 von Willebrand factor (vWF) type A domain; Region: VWA; smart00327 679935002260 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 679935002261 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 679935002262 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 679935002263 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 679935002264 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 679935002265 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 679935002266 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 679935002267 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 679935002268 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 679935002269 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 679935002270 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 679935002271 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 679935002272 active site 679935002273 dimer interface [polypeptide binding]; other site 679935002274 motif 1; other site 679935002275 motif 2; other site 679935002276 motif 3; other site 679935002277 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 679935002278 anticodon binding site; other site 679935002279 translation initiation factor IF-3; Region: infC; TIGR00168 679935002280 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 679935002281 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 679935002282 Acyl-protein synthetase, LuxE; Region: LuxE; pfam04443 679935002283 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 679935002284 ligand binding site; other site 679935002285 tetramer interface; other site 679935002286 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 679935002287 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 679935002288 active site 679935002289 Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: LpqC; COG3509 679935002290 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 679935002291 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 679935002292 Clp amino terminal domain; Region: Clp_N; pfam02861 679935002293 Clp amino terminal domain; Region: Clp_N; pfam02861 679935002294 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 679935002295 Walker A motif; other site 679935002296 ATP binding site [chemical binding]; other site 679935002297 Walker B motif; other site 679935002298 arginine finger; other site 679935002299 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 679935002300 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 679935002301 Walker A motif; other site 679935002302 ATP binding site [chemical binding]; other site 679935002303 Walker B motif; other site 679935002304 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 679935002305 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14970 679935002306 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 679935002307 Walker A motif; other site 679935002308 ATP binding site [chemical binding]; other site 679935002309 Walker B motif; other site 679935002310 DNA polymerase III subunit delta'; Validated; Region: PRK08485 679935002311 arginine finger; other site 679935002312 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 679935002313 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 679935002314 active site 679935002315 HIGH motif; other site 679935002316 dimer interface [polypeptide binding]; other site 679935002317 KMSKS motif; other site 679935002318 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 679935002319 RNA binding surface [nucleotide binding]; other site 679935002320 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 679935002321 active site 679935002322 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 679935002323 Na2 binding site [ion binding]; other site 679935002324 putative substrate binding site 1 [chemical binding]; other site 679935002325 Na binding site 1 [ion binding]; other site 679935002326 putative substrate binding site 2 [chemical binding]; other site 679935002327 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935002328 active site 679935002329 metal binding site [ion binding]; metal-binding site 679935002330 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 679935002331 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 679935002332 homopentamer interface [polypeptide binding]; other site 679935002333 active site 679935002334 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 679935002335 TPR motif; other site 679935002336 binding surface 679935002337 TPR repeat; Region: TPR_11; pfam13414 679935002338 recombination protein F; Reviewed; Region: recF; PRK00064 679935002339 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935002340 Walker A/P-loop; other site 679935002341 ATP binding site [chemical binding]; other site 679935002342 Q-loop/lid; other site 679935002343 ABC transporter signature motif; other site 679935002344 Walker B; other site 679935002345 D-loop; other site 679935002346 H-loop/switch region; other site 679935002347 Protein of unknown function (DUF721); Region: DUF721; pfam05258 679935002348 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 679935002349 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 679935002350 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 679935002351 ligand binding site [chemical binding]; other site 679935002352 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 679935002353 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 679935002354 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 679935002355 active site 679935002356 dimer interface [polypeptide binding]; other site 679935002357 effector binding site; other site 679935002358 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 679935002359 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 679935002360 homotrimer interaction site [polypeptide binding]; other site 679935002361 putative active site [active] 679935002362 META domain; Region: META; pfam03724 679935002363 Malate/lactate dehydrogenases [Energy production and conversion]; Region: Mdh; COG0039 679935002364 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl17195 679935002365 NAD(P) binding site [chemical binding]; other site 679935002366 LDH/MDH dimer interface [polypeptide binding]; other site 679935002367 substrate binding site [chemical binding]; other site 679935002368 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935002369 active site 679935002370 metal binding site [ion binding]; metal-binding site 679935002371 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935002372 recombination protein RecR; Reviewed; Region: recR; PRK00076 679935002373 RecR protein; Region: RecR; pfam02132 679935002374 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 679935002375 putative active site [active] 679935002376 putative metal-binding site [ion binding]; other site 679935002377 tetramer interface [polypeptide binding]; other site 679935002378 Tetratricopeptide repeat; Region: TPR_16; pfam13432 679935002379 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 679935002380 TPR motif; other site 679935002381 binding surface 679935002382 Bacterial SH3 domain; Region: SH3_3; cl17532 679935002383 Oxygen tolerance; Region: BatD; pfam13584 679935002384 fumarate hydratase; Provisional; Region: PRK15389 679935002385 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 679935002386 Fumarase C-terminus; Region: Fumerase_C; pfam05683 679935002387 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 679935002388 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 679935002389 intersubunit interface [polypeptide binding]; other site 679935002390 active site 679935002391 zinc binding site [ion binding]; other site 679935002392 Na+ binding site [ion binding]; other site 679935002393 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935002394 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935002395 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935002396 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 679935002397 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 679935002398 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 679935002399 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 679935002400 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 679935002401 NAD(P) binding site [chemical binding]; other site 679935002402 active site 679935002403 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 679935002404 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 679935002405 Prephenate dehydratase; Region: PDT; pfam00800 679935002406 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 679935002407 putative L-Phe binding site [chemical binding]; other site 679935002408 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 679935002409 Chorismate mutase type II; Region: CM_2; smart00830 679935002410 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 679935002411 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 679935002412 active site 679935002413 phosphorylation site [posttranslational modification] 679935002414 intermolecular recognition site; other site 679935002415 dimerization interface [polypeptide binding]; other site 679935002416 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 679935002417 DNA binding site [nucleotide binding] 679935002418 Family of unknown function (DUF1028); Region: DUF1028; pfam06267 679935002419 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935002420 HAMP domain; Region: HAMP; pfam00672 679935002421 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 679935002422 dimer interface [polypeptide binding]; other site 679935002423 phosphorylation site [posttranslational modification] 679935002424 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 679935002425 ATP binding site [chemical binding]; other site 679935002426 Mg2+ binding site [ion binding]; other site 679935002427 G-X-G motif; other site 679935002428 Phosphate transporter family; Region: PHO4; cl00396 679935002429 Phosphate transporter family; Region: PHO4; cl00396 679935002430 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 679935002431 binding surface 679935002432 TPR motif; other site 679935002433 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 679935002434 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935002435 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 679935002436 Pyruvate formate lyase 1; Region: PFL1; cd01678 679935002437 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 679935002438 coenzyme A binding site [chemical binding]; other site 679935002439 active site 679935002440 catalytic residues [active] 679935002441 glycine loop; other site 679935002442 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 679935002443 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 679935002444 FeS/SAM binding site; other site 679935002445 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 679935002446 amino acid carrier protein; Region: agcS; TIGR00835 679935002447 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 679935002448 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 679935002449 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 679935002450 Sec-independent protein translocase protein (TatC); Region: TatC; pfam00902 679935002451 Sec-independent protein secretion pathway components [Intracellular trafficking and secretion]; Region: TatA; COG1826 679935002452 HEAT repeats; Region: HEAT_2; pfam13646 679935002453 Domain of Unknown Function (DUF1080); Region: DUF1080; pfam06439 679935002454 Domain of Unknown Function (DUF1080); Region: DUF1080; pfam06439 679935002455 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 679935002456 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 679935002457 Domain of Unknown Function (DUF1080); Region: DUF1080; pfam06439 679935002458 Domain of Unknown Function (DUF1080); Region: DUF1080; pfam06439 679935002459 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 679935002460 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 679935002461 active site 679935002462 catalytic site [active] 679935002463 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935002464 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935002465 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935002466 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935002467 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935002468 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 679935002469 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935002470 FecR protein; Region: FecR; pfam04773 679935002471 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935002472 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935002473 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 679935002474 DNA binding residues [nucleotide binding] 679935002475 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 679935002476 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 679935002477 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 679935002478 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 679935002479 HlyD family secretion protein; Region: HlyD_3; pfam13437 679935002480 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 679935002481 Helix-turn-helix domain; Region: HTH_18; pfam12833 679935002482 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935002483 Helix-turn-helix domain; Region: HTH_18; pfam12833 679935002484 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935002485 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 679935002486 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 679935002487 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 679935002488 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 679935002489 non-specific DNA binding site [nucleotide binding]; other site 679935002490 salt bridge; other site 679935002491 sequence-specific DNA binding site [nucleotide binding]; other site 679935002492 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 679935002493 non-specific DNA binding site [nucleotide binding]; other site 679935002494 salt bridge; other site 679935002495 sequence-specific DNA binding site [nucleotide binding]; other site 679935002496 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 679935002497 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 679935002498 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 679935002499 catalytic residue [active] 679935002500 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 679935002501 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 679935002502 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 679935002503 FeS/SAM binding site; other site 679935002504 Radical SAM superfamily; Region: Radical_SAM; pfam04055 679935002505 hypothetical protein; Validated; Region: PRK02101 679935002506 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 679935002507 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 679935002508 TPP-binding site; other site 679935002509 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 679935002510 PYR/PP interface [polypeptide binding]; other site 679935002511 dimer interface [polypeptide binding]; other site 679935002512 TPP binding site [chemical binding]; other site 679935002513 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 679935002514 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 679935002515 putative nucleotide binding site [chemical binding]; other site 679935002516 uridine monophosphate binding site [chemical binding]; other site 679935002517 homohexameric interface [polypeptide binding]; other site 679935002518 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 679935002519 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 679935002520 catalytic residues [active] 679935002521 ribosome recycling factor; Reviewed; Region: frr; PRK00083 679935002522 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 679935002523 hinge region; other site 679935002524 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 679935002525 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 679935002526 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 679935002527 active site 679935002528 substrate-binding site [chemical binding]; other site 679935002529 metal-binding site [ion binding] 679935002530 ATP binding site [chemical binding]; other site 679935002531 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 679935002532 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 679935002533 FeS/SAM binding site; other site 679935002534 HemN C-terminal domain; Region: HemN_C; pfam06969 679935002535 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 679935002536 Glycogen synthase; Region: Glycogen_syn; pfam05693 679935002537 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 679935002538 putative homodimer interface [polypeptide binding]; other site 679935002539 putative active site pocket [active] 679935002540 alpha-glucan phosphorylases; Region: more_P_ylases; TIGR02094 679935002541 Glycogen debranching enzyme N terminal; Region: GDE_N; pfam12439 679935002542 glycogen debranching enzyme, archaeal type, putative; Region: gde_arch; TIGR01561 679935002543 Amylo-alpha-1,6-glucosidase; Region: GDE_C; pfam06202 679935002544 Starch synthase catalytic domain; Region: Glyco_transf_5; pfam08323 679935002545 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 679935002546 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935002547 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 679935002548 Glycosyl hydrolase family 57; Region: Glyco_hydro_57; pfam03065 679935002549 putative active site [active] 679935002550 catalytic site [active] 679935002551 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 679935002552 sequence-specific DNA binding site [nucleotide binding]; other site 679935002553 salt bridge; other site 679935002554 Colicin V production protein; Region: Colicin_V; pfam02674 679935002555 GTPase RsgA; Reviewed; Region: PRK00098 679935002556 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 679935002557 RNA binding site [nucleotide binding]; other site 679935002558 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 679935002559 GTPase/Zn-binding domain interface [polypeptide binding]; other site 679935002560 GTP/Mg2+ binding site [chemical binding]; other site 679935002561 G4 box; other site 679935002562 G5 box; other site 679935002563 G1 box; other site 679935002564 Switch I region; other site 679935002565 G2 box; other site 679935002566 G3 box; other site 679935002567 Switch II region; other site 679935002568 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 679935002569 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 679935002570 Ornithine/acetylornithine aminotransferase [Amino acid transport and metabolism]; Region: ArgD; COG4992 679935002571 inhibitor-cofactor binding pocket; inhibition site 679935002572 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935002573 catalytic residue [active] 679935002574 endonuclease IV; Provisional; Region: PRK01060 679935002575 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 679935002576 AP (apurinic/apyrimidinic) site pocket; other site 679935002577 DNA interaction; other site 679935002578 Metal-binding active site; metal-binding site 679935002579 Protein of unknown function (DUF3078); Region: DUF3078; pfam11276 679935002580 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 679935002581 C-terminal peptidase (prc); Region: prc; TIGR00225 679935002582 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 679935002583 protein binding site [polypeptide binding]; other site 679935002584 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 679935002585 Catalytic dyad [active] 679935002586 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 679935002587 intersubunit interface [polypeptide binding]; other site 679935002588 active site 679935002589 catalytic residue [active] 679935002590 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 679935002591 ligand binding site [chemical binding]; other site 679935002592 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 679935002593 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 679935002594 RNase E interface [polypeptide binding]; other site 679935002595 trimer interface [polypeptide binding]; other site 679935002596 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 679935002597 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 679935002598 RNase E interface [polypeptide binding]; other site 679935002599 trimer interface [polypeptide binding]; other site 679935002600 active site 679935002601 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 679935002602 putative nucleic acid binding region [nucleotide binding]; other site 679935002603 G-X-X-G motif; other site 679935002604 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 679935002605 RNA binding site [nucleotide binding]; other site 679935002606 domain interface; other site 679935002607 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 679935002608 16S/18S rRNA binding site [nucleotide binding]; other site 679935002609 S13e-L30e interaction site [polypeptide binding]; other site 679935002610 25S rRNA binding site [nucleotide binding]; other site 679935002611 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 679935002612 ApbE family; Region: ApbE; pfam02424 679935002613 putative lipid kinase; Reviewed; Region: PRK13059 679935002614 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 679935002615 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 679935002616 Helix-turn-helix domain; Region: HTH_18; pfam12833 679935002617 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935002618 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 679935002619 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 679935002620 DNA binding site [nucleotide binding] 679935002621 Int/Topo IB signature motif; other site 679935002622 active site 679935002623 catalytic residues [active] 679935002624 Haemolysin XhlA; Region: XhlA; pfam10779 679935002625 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 679935002626 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 679935002627 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 679935002628 WbqC-like protein family; Region: WbqC; pfam08889 679935002629 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 679935002630 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 679935002631 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 679935002632 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 679935002633 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 679935002634 generic binding surface II; other site 679935002635 ssDNA binding site; other site 679935002636 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 679935002637 ATP binding site [chemical binding]; other site 679935002638 putative Mg++ binding site [ion binding]; other site 679935002639 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 679935002640 nucleotide binding region [chemical binding]; other site 679935002641 ATP-binding site [chemical binding]; other site 679935002642 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 679935002643 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 679935002644 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 679935002645 nucleotide binding site [chemical binding]; other site 679935002646 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 679935002647 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 679935002648 substrate binding pocket [chemical binding]; other site 679935002649 chain length determination region; other site 679935002650 substrate-Mg2+ binding site; other site 679935002651 catalytic residues [active] 679935002652 aspartate-rich region 1; other site 679935002653 active site lid residues [active] 679935002654 aspartate-rich region 2; other site 679935002655 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 679935002656 Peptidase family U32; Region: Peptidase_U32; pfam01136 679935002657 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 679935002658 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 679935002659 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 679935002660 Major Facilitator Superfamily; Region: MFS_1; pfam07690 679935002661 putative substrate translocation pore; other site 679935002662 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 679935002663 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 679935002664 dimer interface [polypeptide binding]; other site 679935002665 catalytic triad [active] 679935002666 Aminopeptidase P, N-terminal domain; Region: AMP_N; smart01011 679935002667 proline aminopeptidase P II; Provisional; Region: PRK10879 679935002668 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; cl00279 679935002669 active site 679935002670 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 679935002671 Menaquinone biosynthesis; Region: VitK2_biosynth; cl17475 679935002672 Predicted membrane protein [Function unknown]; Region: COG2311 679935002673 Protein of unknown function (DUF1624); Region: DUF1624; cl01394 679935002674 Protein of unknown function (DUF418); Region: DUF418; pfam04235 679935002675 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 679935002676 elongation factor G; Reviewed; Region: PRK12740 679935002677 G1 box; other site 679935002678 putative GEF interaction site [polypeptide binding]; other site 679935002679 GTP/Mg2+ binding site [chemical binding]; other site 679935002680 Switch I region; other site 679935002681 G2 box; other site 679935002682 G3 box; other site 679935002683 Switch II region; other site 679935002684 G4 box; other site 679935002685 G5 box; other site 679935002686 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 679935002687 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 679935002688 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 679935002689 Phosphate transporter family; Region: PHO4; cl00396 679935002690 Phosphate transporter family; Region: PHO4; cl00396 679935002691 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 679935002692 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 679935002693 Coenzyme A binding pocket [chemical binding]; other site 679935002694 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 679935002695 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 679935002696 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 679935002697 hinge; other site 679935002698 active site 679935002699 thymidine kinase; Provisional; Region: PRK04296 679935002700 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 679935002701 DNA-binding site [nucleotide binding]; DNA binding site 679935002702 transcriptional regulator NanR; Provisional; Region: PRK03837 679935002703 FCD domain; Region: FCD; pfam07729 679935002704 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 679935002705 Carbon starvation protein CstA; Region: CstA; pfam02554 679935002706 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 679935002707 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 679935002708 DNA-binding site [nucleotide binding]; DNA binding site 679935002709 RNA-binding motif; other site 679935002710 RNA-binding proteins (RRM domain) [General function prediction only]; Region: COG0724 679935002711 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 679935002712 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 679935002713 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 679935002714 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 679935002715 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 679935002716 HlyD family secretion protein; Region: HlyD_3; pfam13437 679935002717 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 679935002718 dimer interface [polypeptide binding]; other site 679935002719 phosphorylation site [posttranslational modification] 679935002720 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 679935002721 ATP binding site [chemical binding]; other site 679935002722 Mg2+ binding site [ion binding]; other site 679935002723 G-X-G motif; other site 679935002724 Response regulator receiver domain; Region: Response_reg; pfam00072 679935002725 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 679935002726 active site 679935002727 phosphorylation site [posttranslational modification] 679935002728 intermolecular recognition site; other site 679935002729 dimerization interface [polypeptide binding]; other site 679935002730 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 679935002731 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 679935002732 active site 679935002733 phosphorylation site [posttranslational modification] 679935002734 intermolecular recognition site; other site 679935002735 dimerization interface [polypeptide binding]; other site 679935002736 Bacterial sugar transferase; Region: Bac_transf; pfam02397 679935002737 Outer membrane efflux protein; Region: OEP; pfam02321 679935002738 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 679935002739 O-antigen ligase like membrane protein; Region: O-antigen_lig; pfam13425 679935002740 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 679935002741 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 679935002742 Probable Catalytic site; other site 679935002743 metal-binding site 679935002744 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 679935002745 EpsO protein participates in the methanolan synthesis; Region: EpsO_like; cd06438 679935002746 DXD motif; other site 679935002747 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935002748 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 679935002749 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 679935002750 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 679935002751 trimer interface [polypeptide binding]; other site 679935002752 active site 679935002753 substrate binding site [chemical binding]; other site 679935002754 CoA binding site [chemical binding]; other site 679935002755 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 679935002756 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 679935002757 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935002758 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 679935002759 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 679935002760 CESA_like_1 is a member of the cellulose synthase (CESA) superfamily; Region: CESA_like_1; cd06439 679935002761 DXD motif; other site 679935002762 Response regulator receiver domain; Region: Response_reg; pfam00072 679935002763 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 679935002764 active site 679935002765 phosphorylation site [posttranslational modification] 679935002766 intermolecular recognition site; other site 679935002767 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935002768 dimerization interface [polypeptide binding]; other site 679935002769 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 679935002770 ATP binding site [chemical binding]; other site 679935002771 Mg2+ binding site [ion binding]; other site 679935002772 G-X-G motif; other site 679935002773 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; Region: EEP-2; cd09084 679935002774 putative catalytic site [active] 679935002775 putative metal binding site [ion binding]; other site 679935002776 putative phosphate binding site [ion binding]; other site 679935002777 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 679935002778 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 679935002779 NAD binding site [chemical binding]; other site 679935002780 putative substrate binding site 2 [chemical binding]; other site 679935002781 putative substrate binding site 1 [chemical binding]; other site 679935002782 active site 679935002783 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 679935002784 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 679935002785 substrate binding pocket [chemical binding]; other site 679935002786 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 679935002787 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 679935002788 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 679935002789 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 679935002790 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 679935002791 putative active site [active] 679935002792 catalytic triad [active] 679935002793 putative dimer interface [polypeptide binding]; other site 679935002794 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 679935002795 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 679935002796 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935002797 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935002798 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 679935002799 DNA binding residues [nucleotide binding] 679935002800 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935002801 FecR protein; Region: FecR; pfam04773 679935002802 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 679935002803 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935002804 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 679935002805 active site 679935002806 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935002807 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 679935002808 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 679935002809 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 679935002810 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 679935002811 active site 679935002812 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C_1; pfam13290 679935002813 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 679935002814 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 679935002815 Sulfatase; Region: Sulfatase; pfam00884 679935002816 Protein of unknown function (DUF3467); Region: DUF3467; pfam11950 679935002817 LysE type translocator; Region: LysE; cl00565 679935002818 cytidylate kinase; Provisional; Region: cmk; PRK00023 679935002819 AAA domain; Region: AAA_17; pfam13207 679935002820 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 679935002821 CMP-binding site; other site 679935002822 The sites determining sugar specificity; other site 679935002823 LytB protein; Region: LYTB; cl00507 679935002824 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 679935002825 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 679935002826 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 679935002827 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 679935002828 protein binding site [polypeptide binding]; other site 679935002829 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 679935002830 Catalytic dyad [active] 679935002831 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935002832 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 679935002833 ATP binding site [chemical binding]; other site 679935002834 Mg2+ binding site [ion binding]; other site 679935002835 G-X-G motif; other site 679935002836 Domain of unknown function (DUF4271); Region: DUF4271; pfam14093 679935002837 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 679935002838 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 679935002839 active site 679935002840 ribonuclease P; Reviewed; Region: rnpA; PRK01903 679935002841 Haemolytic domain; Region: Haemolytic; pfam01809 679935002842 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 679935002843 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 679935002844 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 679935002845 DNA binding residues [nucleotide binding] 679935002846 dimerization interface [polypeptide binding]; other site 679935002847 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 679935002848 Sulfatase; Region: Sulfatase; pfam00884 679935002849 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 679935002850 active site 679935002851 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 679935002852 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 679935002853 HflX GTPase family; Region: HflX; cd01878 679935002854 G1 box; other site 679935002855 GTP/Mg2+ binding site [chemical binding]; other site 679935002856 Switch I region; other site 679935002857 G2 box; other site 679935002858 G3 box; other site 679935002859 Switch II region; other site 679935002860 G4 box; other site 679935002861 G5 box; other site 679935002862 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 679935002863 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 679935002864 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14466 679935002865 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 679935002866 FeS/SAM binding site; other site 679935002867 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 679935002868 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 679935002869 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 679935002870 S-adenosylmethionine binding site [chemical binding]; other site 679935002871 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 679935002872 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 679935002873 non-specific DNA binding site [nucleotide binding]; other site 679935002874 salt bridge; other site 679935002875 sequence-specific DNA binding site [nucleotide binding]; other site 679935002876 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 679935002877 non-specific DNA binding site [nucleotide binding]; other site 679935002878 salt bridge; other site 679935002879 sequence-specific DNA binding site [nucleotide binding]; other site 679935002880 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 679935002881 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 679935002882 S-adenosylmethionine binding site [chemical binding]; other site 679935002883 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 679935002884 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935002885 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 679935002886 DNA binding residues [nucleotide binding] 679935002887 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 679935002888 active site 679935002889 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 679935002890 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 679935002891 Predicted permeases [General function prediction only]; Region: COG0795 679935002892 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 679935002893 putative menaquinone biosynthesis protein, SCO4494 family; Region: mena_SCO4494; TIGR03700 679935002894 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 679935002895 FeS/SAM binding site; other site 679935002896 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2815 679935002897 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 679935002898 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 679935002899 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 679935002900 RNA binding surface [nucleotide binding]; other site 679935002901 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 679935002902 active site 679935002903 uncharacterized radical SAM protein YgiQ; Region: SAM_YgiQ; TIGR03904 679935002904 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 679935002905 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 679935002906 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_6; cd04955 679935002907 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935002908 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935002909 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 679935002910 Acyltransferase family; Region: Acyl_transf_3; pfam01757 679935002911 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 679935002912 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 679935002913 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 679935002914 trimer interface [polypeptide binding]; other site 679935002915 active site 679935002916 substrate binding site [chemical binding]; other site 679935002917 CoA binding site [chemical binding]; other site 679935002918 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 679935002919 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 679935002920 Probable Catalytic site; other site 679935002921 metal-binding site 679935002922 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 679935002923 FMN binding site [chemical binding]; other site 679935002924 dimer interface [polypeptide binding]; other site 679935002925 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; cl09156 679935002926 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 679935002927 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 679935002928 active site 679935002929 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 679935002930 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 679935002931 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 679935002932 NAD binding site [chemical binding]; other site 679935002933 substrate binding site [chemical binding]; other site 679935002934 homodimer interface [polypeptide binding]; other site 679935002935 active site 679935002936 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 679935002937 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 679935002938 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 679935002939 NADP binding site [chemical binding]; other site 679935002940 active site 679935002941 putative substrate binding site [chemical binding]; other site 679935002942 putative lipopolysaccharide biosynthesis O-acetyl transferase WbbJ; Provisional; Region: PRK09677 679935002943 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 679935002944 trimer interface [polypeptide binding]; other site 679935002945 active site 679935002946 substrate binding site [chemical binding]; other site 679935002947 CoA binding site [chemical binding]; other site 679935002948 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 679935002949 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 679935002950 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 679935002951 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 679935002952 substrate binding site; other site 679935002953 tetramer interface; other site 679935002954 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 679935002955 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 679935002956 Mg++ binding site [ion binding]; other site 679935002957 putative catalytic motif [active] 679935002958 substrate binding site [chemical binding]; other site 679935002959 transcriptional activator RfaH; Region: RfaH; TIGR01955 679935002960 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 679935002961 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 679935002962 homodimer interface [polypeptide binding]; other site 679935002963 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 679935002964 active site 679935002965 DNA binding site [nucleotide binding] 679935002966 Int/Topo IB signature motif; other site 679935002967 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 679935002968 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 679935002969 Recombination protein O N terminal; Region: RecO_N; pfam11967 679935002970 Recombination protein O C terminal; Region: RecO_C; pfam02565 679935002971 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 679935002972 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 679935002973 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 679935002974 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 679935002975 active site 679935002976 Int/Topo IB signature motif; other site 679935002977 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 679935002978 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 679935002979 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935002980 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935002981 SusD family; Region: SusD; pfam07980 679935002982 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935002983 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935002984 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 679935002985 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 679935002986 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935002987 FecR protein; Region: FecR; pfam04773 679935002988 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935002989 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935002990 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 679935002991 DNA binding residues [nucleotide binding] 679935002992 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 679935002993 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 679935002994 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 679935002995 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 679935002996 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 679935002997 Amidohydrolase; Region: Amidohydro_4; pfam13147 679935002998 active site 679935002999 Domain of unknown function (DUF4296); Region: DUF4296; pfam14129 679935003000 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 679935003001 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 679935003002 Ribosome-binding factor A; Region: RBFA; pfam02033 679935003003 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 679935003004 Bacterial Ig-like domain; Region: Big_5; pfam13205 679935003005 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 679935003006 catalytic center binding site [active] 679935003007 ATP binding site [chemical binding]; other site 679935003008 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 679935003009 DNA polymerase III subunit delta'; Validated; Region: PRK08485 679935003010 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 679935003011 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 679935003012 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 679935003013 Domain of unknown function, B. Theta Gene description (DUF3868); Region: DUF3868; pfam12984 679935003014 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 679935003015 Major fimbrial subunit protein (FimA); Region: P_gingi_FimA; pfam06321 679935003016 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 679935003017 Mg2+ transporter Helicobacter pylori CorA-like subgroup; Region: HpCorA-like; cd12836 679935003018 Cl binding site [ion binding]; other site 679935003019 oligomer interface [polypeptide binding]; other site 679935003020 Menaquinone biosynthesis; Region: VitK2_biosynth; pfam02621 679935003021 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 679935003022 oligomer interface [polypeptide binding]; other site 679935003023 active site residues [active] 679935003024 Phage-related protein [Function unknown]; Region: COG4695; cl01923 679935003025 virion protein; Provisional; Region: V; PHA02564 679935003026 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 679935003027 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 679935003028 Competence protein; Region: Competence; pfam03772 679935003029 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 679935003030 S-adenosylmethionine binding site [chemical binding]; other site 679935003031 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 679935003032 Adenosine deaminase z-alpha domain; Region: z-alpha; cl02659 679935003033 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 679935003034 NAD(P) binding pocket [chemical binding]; other site 679935003035 Domain of unknown function (DUF2520); Region: DUF2520; pfam10728 679935003036 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 679935003037 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 679935003038 active site 679935003039 motif I; other site 679935003040 motif II; other site 679935003041 StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been...; Region: StaR_like; cd05804 679935003042 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 679935003043 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 679935003044 putative acyl-acceptor binding pocket; other site 679935003045 MraW methylase family; Region: Methyltransf_5; cl17771 679935003046 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 679935003047 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 679935003048 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 679935003049 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 679935003050 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 679935003051 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 679935003052 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 679935003053 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 679935003054 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 679935003055 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 679935003056 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 679935003057 Mg++ binding site [ion binding]; other site 679935003058 putative catalytic motif [active] 679935003059 putative substrate binding site [chemical binding]; other site 679935003060 UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]; Region: MurD; COG0771 679935003061 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 679935003062 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 679935003063 Bacterial cell division membrane protein [Cell division and chromosome partitioning]; Region: FtsW; COG0772 679935003064 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 679935003065 RNA binding surface [nucleotide binding]; other site 679935003066 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 679935003067 putative active site [active] 679935003068 catalytic residue [active] 679935003069 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 679935003070 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 679935003071 5S rRNA interface [nucleotide binding]; other site 679935003072 CTC domain interface [polypeptide binding]; other site 679935003073 L16 interface [polypeptide binding]; other site 679935003074 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 679935003075 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935003076 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 679935003077 DNA binding residues [nucleotide binding] 679935003078 LTXXQ motif family protein; Region: LTXXQ; pfam07813 679935003079 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 679935003080 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 679935003081 2-isopropylmalate synthase; Validated; Region: PRK00915 679935003082 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 679935003083 active site 679935003084 catalytic residues [active] 679935003085 metal binding site [ion binding]; metal-binding site 679935003086 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 679935003087 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 679935003088 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 679935003089 substrate binding site [chemical binding]; other site 679935003090 ligand binding site [chemical binding]; other site 679935003091 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 679935003092 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 679935003093 hypothetical protein; Provisional; Region: PRK14812 679935003094 substrate binding site [chemical binding]; other site 679935003095 (R)-citramalate synthase; Provisional; Region: PRK09389 679935003096 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 679935003097 active site 679935003098 catalytic residues [active] 679935003099 metal binding site [ion binding]; metal-binding site 679935003100 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; pfam08502 679935003101 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 679935003102 tartrate dehydrogenase; Region: TTC; TIGR02089 679935003103 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 679935003104 threonine synthase; Validated; Region: PRK09225 679935003105 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 679935003106 catalytic residue [active] 679935003107 homoserine kinase; Provisional; Region: PRK01212 679935003108 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 679935003109 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 679935003110 acetolactate synthase 2 catalytic subunit; Reviewed; Region: PRK08978 679935003111 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 679935003112 PYR/PP interface [polypeptide binding]; other site 679935003113 dimer interface [polypeptide binding]; other site 679935003114 TPP binding site [chemical binding]; other site 679935003115 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 679935003116 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 679935003117 TPP-binding site [chemical binding]; other site 679935003118 dimer interface [polypeptide binding]; other site 679935003119 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 679935003120 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 679935003121 putative valine binding site [chemical binding]; other site 679935003122 dimer interface [polypeptide binding]; other site 679935003123 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 679935003124 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 679935003125 ketol-acid reductoisomerase; Region: ilvC; TIGR00465 679935003126 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 679935003127 asparagine synthetase B; Provisional; Region: asnB; PRK09431 679935003128 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 679935003129 active site 679935003130 dimer interface [polypeptide binding]; other site 679935003131 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 679935003132 Ligand Binding Site [chemical binding]; other site 679935003133 Molecular Tunnel; other site 679935003134 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 679935003135 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 679935003136 NAD binding site [chemical binding]; other site 679935003137 homodimer interface [polypeptide binding]; other site 679935003138 active site 679935003139 substrate binding site [chemical binding]; other site 679935003140 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 679935003141 Alkaline phosphatase homologues; Region: alkPPc; smart00098 679935003142 active site 679935003143 dimer interface [polypeptide binding]; other site 679935003144 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 679935003145 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935003146 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935003147 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935003148 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 679935003149 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 679935003150 substrate-cofactor binding pocket; other site 679935003151 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935003152 catalytic residue [active] 679935003153 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 679935003154 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 679935003155 putative DNA binding site [nucleotide binding]; other site 679935003156 putative Zn2+ binding site [ion binding]; other site 679935003157 AsnC family; Region: AsnC_trans_reg; pfam01037 679935003158 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 679935003159 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 679935003160 active site 679935003161 phosphorylation site [posttranslational modification] 679935003162 intermolecular recognition site; other site 679935003163 dimerization interface [polypeptide binding]; other site 679935003164 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 679935003165 Walker A motif; other site 679935003166 ATP binding site [chemical binding]; other site 679935003167 Walker B motif; other site 679935003168 arginine finger; other site 679935003169 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 679935003170 DNA-binding interface [nucleotide binding]; DNA binding site 679935003171 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 679935003172 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 679935003173 dimer interface [polypeptide binding]; other site 679935003174 phosphorylation site [posttranslational modification] 679935003175 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 679935003176 ATP binding site [chemical binding]; other site 679935003177 Mg2+ binding site [ion binding]; other site 679935003178 G-X-G motif; other site 679935003179 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 679935003180 Response regulator receiver domain; Region: Response_reg; pfam00072 679935003181 active site 679935003182 phosphorylation site [posttranslational modification] 679935003183 intermolecular recognition site; other site 679935003184 dimerization interface [polypeptide binding]; other site 679935003185 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 679935003186 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4152 679935003187 ATP-binding cassette domain of an uncharacterized transporter; Region: ABC_putative_ATPase; cd03269 679935003188 Walker A/P-loop; other site 679935003189 ATP binding site [chemical binding]; other site 679935003190 Q-loop/lid; other site 679935003191 ABC transporter signature motif; other site 679935003192 Walker B; other site 679935003193 D-loop; other site 679935003194 H-loop/switch region; other site 679935003195 Domain of unknown function (DUF4162); Region: DUF4162; pfam13732 679935003196 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 679935003197 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 679935003198 active site 679935003199 Zn binding site [ion binding]; other site 679935003200 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 679935003201 Phosphoglycerate kinase; Region: PGK; pfam00162 679935003202 substrate binding site [chemical binding]; other site 679935003203 hinge regions; other site 679935003204 ADP binding site [chemical binding]; other site 679935003205 catalytic site [active] 679935003206 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 679935003207 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 679935003208 Int/Topo IB signature motif; other site 679935003209 Phage associated DNA primase [General function prediction only]; Region: COG3378 679935003210 CHC2 zinc finger; Region: zf-CHC2; cl17510 679935003211 Toprim-like; Region: Toprim_2; pfam13155 679935003212 Plasmid recombination enzyme; Region: Mob_Pre; pfam01076 679935003213 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 679935003214 Part of AAA domain; Region: AAA_19; pfam13245 679935003215 Family description; Region: UvrD_C_2; pfam13538 679935003216 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 679935003217 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 679935003218 active site 679935003219 nucleophile elbow; other site 679935003220 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 679935003221 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 679935003222 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 679935003223 dimer interface [polypeptide binding]; other site 679935003224 motif 1; other site 679935003225 active site 679935003226 motif 2; other site 679935003227 motif 3; other site 679935003228 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 679935003229 TPR motif; other site 679935003230 binding surface 679935003231 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 679935003232 TPR motif; other site 679935003233 binding surface 679935003234 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 679935003235 TPR motif; other site 679935003236 Tetratricopeptide repeat; Region: TPR_12; pfam13424 679935003237 binding surface 679935003238 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 679935003239 Septum formation initiator; Region: DivIC; cl17659 679935003240 Peptidase family M23; Region: Peptidase_M23; pfam01551 679935003241 Uncharacterized protein family UPF0054; Region: UPF0054; pfam02130 679935003242 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 679935003243 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 679935003244 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 679935003245 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 679935003246 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 679935003247 homodimer interface [polypeptide binding]; other site 679935003248 substrate-cofactor binding pocket; other site 679935003249 catalytic residue [active] 679935003250 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 679935003251 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 679935003252 active site 679935003253 HIGH motif; other site 679935003254 KMSKS motif; other site 679935003255 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 679935003256 tRNA binding surface [nucleotide binding]; other site 679935003257 anticodon binding site; other site 679935003258 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 679935003259 dimer interface [polypeptide binding]; other site 679935003260 putative tRNA-binding site [nucleotide binding]; other site 679935003261 Peptidase S46; Region: Peptidase_S46; pfam10459 679935003262 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 679935003263 Quinolinate synthetase A protein; Region: NadA; pfam02445 679935003264 Domain of unknown function DUF59; Region: DUF59; cl00941 679935003265 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 679935003266 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 679935003267 Walker A motif; other site 679935003268 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 679935003269 tandem repeat interface [polypeptide binding]; other site 679935003270 oligomer interface [polypeptide binding]; other site 679935003271 active site residues [active] 679935003272 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 679935003273 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 679935003274 tandem repeat interface [polypeptide binding]; other site 679935003275 oligomer interface [polypeptide binding]; other site 679935003276 active site residues [active] 679935003277 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 679935003278 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935003279 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 679935003280 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 679935003281 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 679935003282 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 679935003283 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 679935003284 active site 679935003285 DNA polymerase I; Region: pola; TIGR00593 679935003286 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 679935003287 active site 679935003288 metal binding site 1 [ion binding]; metal-binding site 679935003289 putative 5' ssDNA interaction site; other site 679935003290 metal binding site 3; metal-binding site 679935003291 metal binding site 2 [ion binding]; metal-binding site 679935003292 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 679935003293 putative DNA binding site [nucleotide binding]; other site 679935003294 putative metal binding site [ion binding]; other site 679935003295 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 679935003296 active site 679935003297 catalytic site [active] 679935003298 substrate binding site [chemical binding]; other site 679935003299 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 679935003300 active site 679935003301 DNA binding site [nucleotide binding] 679935003302 catalytic site [active] 679935003303 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 679935003304 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 679935003305 putative transposase OrfB; Reviewed; Region: PHA02517 679935003306 HTH-like domain; Region: HTH_21; pfam13276 679935003307 Integrase core domain; Region: rve; pfam00665 679935003308 Integrase core domain; Region: rve_2; pfam13333 679935003309 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935003310 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935003311 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935003312 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935003313 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 679935003314 homodecamer interface [polypeptide binding]; other site 679935003315 GTP cyclohydrolase I; Provisional; Region: PLN03044 679935003316 active site 679935003317 putative catalytic site residues [active] 679935003318 zinc binding site [ion binding]; other site 679935003319 GTP-CH-I/GFRP interaction surface; other site 679935003320 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 679935003321 active site 679935003322 dimerization interface [polypeptide binding]; other site 679935003323 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 679935003324 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 679935003325 FMN binding site [chemical binding]; other site 679935003326 dimer interface [polypeptide binding]; other site 679935003327 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 679935003328 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935003329 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 679935003330 dimer interface [polypeptide binding]; other site 679935003331 phosphorylation site [posttranslational modification] 679935003332 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 679935003333 ATP binding site [chemical binding]; other site 679935003334 Mg2+ binding site [ion binding]; other site 679935003335 G-X-G motif; other site 679935003336 Response regulator receiver domain; Region: Response_reg; pfam00072 679935003337 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 679935003338 active site 679935003339 phosphorylation site [posttranslational modification] 679935003340 intermolecular recognition site; other site 679935003341 dimerization interface [polypeptide binding]; other site 679935003342 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 679935003343 DHH family; Region: DHH; pfam01368 679935003344 DHHA1 domain; Region: DHHA1; pfam02272 679935003345 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 679935003346 lipoyl synthase; Provisional; Region: PRK05481 679935003347 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 679935003348 FeS/SAM binding site; other site 679935003349 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 679935003350 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 679935003351 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935003352 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 679935003353 RNA/DNA hybrid binding site [nucleotide binding]; other site 679935003354 active site 679935003355 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 679935003356 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 679935003357 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 679935003358 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 679935003359 active site 679935003360 homodimer interface [polypeptide binding]; other site 679935003361 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 679935003362 active site 679935003363 DNA protecting protein DprA; Region: dprA; TIGR00732 679935003364 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 679935003365 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 679935003366 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 679935003367 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 679935003368 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 679935003369 RNA binding site [nucleotide binding]; other site 679935003370 Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only]; Region: COG1453 679935003371 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 679935003372 active site 679935003373 catalytic tetrad [active] 679935003374 Domain of unknown function (DUF362); Region: DUF362; pfam04015 679935003375 Domain of unknown function (DUF1893); Region: TM1506; pfam08973 679935003376 Alpha-galactosidase [Carbohydrate transport and metabolism]; Region: GalA; COG3345 679935003377 Melibiase; Region: Melibiase; pfam02065 679935003378 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 679935003379 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 679935003380 acyl-activating enzyme (AAE) consensus motif; other site 679935003381 AMP binding site [chemical binding]; other site 679935003382 active site 679935003383 CoA binding site [chemical binding]; other site 679935003384 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 679935003385 active site 679935003386 Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase; Region: AAT; pfam03417 679935003387 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 679935003388 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 679935003389 Predicted exporter [General function prediction only]; Region: COG4258 679935003390 Protein export membrane protein; Region: SecD_SecF; cl14618 679935003391 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 679935003392 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 679935003393 putative acyl-acceptor binding pocket; other site 679935003394 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 679935003395 S-adenosylmethionine binding site [chemical binding]; other site 679935003396 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 679935003397 Ligand binding site; other site 679935003398 Putative Catalytic site; other site 679935003399 DXD motif; other site 679935003400 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 679935003401 FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation; Region: FabA_FabZ; cd00493 679935003402 active site 2 [active] 679935003403 dimer interface [polypeptide binding]; other site 679935003404 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 679935003405 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 679935003406 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 679935003407 NodB motif; other site 679935003408 active site 679935003409 catalytic site [active] 679935003410 metal binding site [ion binding]; metal-binding site 679935003411 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 679935003412 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 679935003413 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 679935003414 dimer interface [polypeptide binding]; other site 679935003415 active site 679935003416 Phosphopantetheine attachment site; Region: PP-binding; cl09936 679935003417 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 679935003418 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 679935003419 active site 679935003420 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 679935003421 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 679935003422 active site 679935003423 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 679935003424 active site 2 [active] 679935003425 active site 1 [active] 679935003426 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 679935003427 B12 binding site [chemical binding]; other site 679935003428 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 679935003429 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 679935003430 FeS/SAM binding site; other site 679935003431 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 679935003432 putative acyl-acceptor binding pocket; other site 679935003433 Phosphopantetheine attachment site; Region: PP-binding; cl09936 679935003434 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 679935003435 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 679935003436 dimer interface [polypeptide binding]; other site 679935003437 active site 679935003438 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 679935003439 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 679935003440 NAD(P) binding site [chemical binding]; other site 679935003441 active site 679935003442 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 679935003443 active sites [active] 679935003444 tetramer interface [polypeptide binding]; other site 679935003445 anaerobic sulfatase-maturating enzyme; Region: sulfatase_rSAM; TIGR03942 679935003446 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 679935003447 FeS/SAM binding site; other site 679935003448 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 679935003449 putative transporter; Provisional; Region: PRK10504 679935003450 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 679935003451 putative substrate translocation pore; other site 679935003452 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 679935003453 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935003454 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935003455 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 679935003456 DNA binding residues [nucleotide binding] 679935003457 Secretin and TonB N terminus short domain; Region: STN; pfam07660 679935003458 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935003459 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935003460 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 679935003461 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 679935003462 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935003463 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 679935003464 active site 679935003465 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935003466 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 679935003467 Domain of unknown function (DUF1735); Region: DUF1735; pfam08522 679935003468 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 679935003469 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 679935003470 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 679935003471 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 679935003472 active site 679935003473 Apocytochrome F, C-terminal; Region: Apocytochr_F_C; cl03168 679935003474 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935003475 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 679935003476 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 679935003477 Aerotolerance regulator N-terminal; Region: BatA; pfam07584 679935003478 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 679935003479 metal ion-dependent adhesion site (MIDAS); other site 679935003480 Aerotolerance regulator N-terminal; Region: BatA; pfam07584 679935003481 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 679935003482 metal ion-dependent adhesion site (MIDAS); other site 679935003483 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 679935003484 TPR motif; other site 679935003485 binding surface 679935003486 TPR repeat; Region: TPR_11; pfam13414 679935003487 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 679935003488 Protein of unknown function DUF58; Region: DUF58; pfam01882 679935003489 MoxR-like ATPases [General function prediction only]; Region: COG0714 679935003490 ATPase family associated with various cellular activities (AAA); Region: AAA_3; pfam07726 679935003491 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 679935003492 Part of AAA domain; Region: AAA_19; pfam13245 679935003493 Family description; Region: UvrD_C_2; pfam13538 679935003494 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 679935003495 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 679935003496 active site 679935003497 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 679935003498 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 679935003499 minor groove reading motif; other site 679935003500 helix-hairpin-helix signature motif; other site 679935003501 substrate binding pocket [chemical binding]; other site 679935003502 active site 679935003503 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 679935003504 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 679935003505 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935003506 Walker A/P-loop; other site 679935003507 ATP binding site [chemical binding]; other site 679935003508 Q-loop/lid; other site 679935003509 ABC transporter signature motif; other site 679935003510 Walker B; other site 679935003511 D-loop; other site 679935003512 H-loop/switch region; other site 679935003513 ABC transporter; Region: ABC_tran_2; pfam12848 679935003514 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 679935003515 DHH family; Region: DHH; pfam01368 679935003516 Transcriptional regulator [Transcription]; Region: LysR; COG0583 679935003517 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 679935003518 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 679935003519 putative dimerization interface [polypeptide binding]; other site 679935003520 Predicted membrane protein [Function unknown]; Region: COG2855 679935003521 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 679935003522 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 679935003523 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 679935003524 active site 679935003525 catalytic residues [active] 679935003526 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935003527 Leucine rich repeat; Region: LRR_8; pfam13855 679935003528 Leucine-rich repeats, typical (most populated) subfamily; Region: LRR_TYP; cl15310 679935003529 Leucine rich repeat; Region: LRR_8; pfam13855 679935003530 Leucine rich repeat; Region: LRR_8; pfam13855 679935003531 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935003532 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935003533 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935003534 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935003535 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 679935003536 Domain of unknown function (DUF4091); Region: DUF4091; pfam13320 679935003537 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; pfam00150 679935003538 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 679935003539 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 679935003540 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 679935003541 G3 box; other site 679935003542 Switch II region; other site 679935003543 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 679935003544 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 679935003545 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 679935003546 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 679935003547 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935003548 active site 679935003549 metal binding site [ion binding]; metal-binding site 679935003550 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935003551 Helix-turn-helix domain; Region: HTH_18; pfam12833 679935003552 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935003553 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 679935003554 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 679935003555 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 679935003556 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 679935003557 FeS/SAM binding site; other site 679935003558 CHC2 zinc finger; Region: zf-CHC2; cl17510 679935003559 Toprim-like; Region: Toprim_2; pfam13155 679935003560 active site 679935003561 metal binding site [ion binding]; metal-binding site 679935003562 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935003563 AAA domain; Region: AAA_14; pfam13173 679935003564 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 679935003565 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 679935003566 active site 679935003567 Int/Topo IB signature motif; other site 679935003568 DNA binding site [nucleotide binding] 679935003569 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935003570 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935003571 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 679935003572 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 679935003573 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 679935003574 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935003575 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 679935003576 dimer interface [polypeptide binding]; other site 679935003577 phosphorylation site [posttranslational modification] 679935003578 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 679935003579 ATP binding site [chemical binding]; other site 679935003580 Mg2+ binding site [ion binding]; other site 679935003581 G-X-G motif; other site 679935003582 Response regulator receiver domain; Region: Response_reg; pfam00072 679935003583 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 679935003584 active site 679935003585 phosphorylation site [posttranslational modification] 679935003586 intermolecular recognition site; other site 679935003587 dimerization interface [polypeptide binding]; other site 679935003588 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 679935003589 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 679935003590 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 679935003591 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 679935003592 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 679935003593 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 679935003594 C-terminal processing peptidase-like; serine protease family S41; Region: Peptidase_S41_CPP_like; cd07561 679935003595 Catalytic dyad [active] 679935003596 Peptidase S46; Region: Peptidase_S46; pfam10459 679935003597 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 679935003598 Maf-like protein; Region: Maf; pfam02545 679935003599 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 679935003600 active site 679935003601 dimer interface [polypeptide binding]; other site 679935003602 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 679935003603 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 679935003604 Domain of unknown function (DUF3784); Region: DUF3784; pfam12650 679935003605 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 679935003606 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 679935003607 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 679935003608 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 679935003609 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 679935003610 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 679935003611 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 679935003612 substrate binding pocket [chemical binding]; other site 679935003613 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 679935003614 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 679935003615 S-adenosylmethionine binding site [chemical binding]; other site 679935003616 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 679935003617 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 679935003618 active site 679935003619 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 679935003620 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 679935003621 active site 679935003622 catalytic motif [active] 679935003623 Zn binding site [ion binding]; other site 679935003624 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 679935003625 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 679935003626 active site 679935003627 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 679935003628 putative active site [active] 679935003629 dimerization interface [polypeptide binding]; other site 679935003630 putative tRNAtyr binding site [nucleotide binding]; other site 679935003631 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cl00089 679935003632 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 679935003633 active site 679935003634 substrate binding site [chemical binding]; other site 679935003635 Mg2+ binding site [ion binding]; other site 679935003636 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 679935003637 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 679935003638 FeS/SAM binding site; other site 679935003639 Uncharacterized conserved protein [Function unknown]; Region: COG1284 679935003640 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 679935003641 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 679935003642 Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]; Region: PriA; COG1198 679935003643 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 679935003644 ATP binding site [chemical binding]; other site 679935003645 putative Mg++ binding site [ion binding]; other site 679935003646 helicase superfamily c-terminal domain; Region: HELICc; smart00490 679935003647 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 679935003648 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 679935003649 active site 679935003650 replicative DNA helicase; Region: DnaB; TIGR00665 679935003651 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 679935003652 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 679935003653 Walker A motif; other site 679935003654 ATP binding site [chemical binding]; other site 679935003655 Walker B motif; other site 679935003656 DNA binding loops [nucleotide binding] 679935003657 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 679935003658 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 679935003659 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 679935003660 Walker A motif; other site 679935003661 ATP binding site [chemical binding]; other site 679935003662 Walker B motif; other site 679935003663 arginine finger; other site 679935003664 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 679935003665 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 679935003666 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 679935003667 active site 679935003668 homodimer interface [polypeptide binding]; other site 679935003669 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 679935003670 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 679935003671 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 679935003672 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 679935003673 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 679935003674 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 679935003675 nucleotide binding site [chemical binding]; other site 679935003676 Cell division protein FtsA; Region: FtsA; cl17206 679935003677 Cell division protein FtsA; Region: FtsA; pfam14450 679935003678 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 679935003679 nucleotide binding site [chemical binding]; other site 679935003680 SulA interaction site; other site 679935003681 Domain of unknown function DUF21; Region: DUF21; pfam01595 679935003682 gliding motility-associated protein GldE; Region: GldE; TIGR03520 679935003683 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 679935003684 Transporter associated domain; Region: CorC_HlyC; smart01091 679935003685 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 679935003686 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 679935003687 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 679935003688 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 679935003689 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 679935003690 active site 679935003691 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 679935003692 active site 679935003693 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 679935003694 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 679935003695 active site 679935003696 interdomain interaction site; other site 679935003697 putative metal-binding site [ion binding]; other site 679935003698 nucleotide binding site [chemical binding]; other site 679935003699 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 679935003700 domain I; other site 679935003701 DNA binding groove [nucleotide binding] 679935003702 phosphate binding site [ion binding]; other site 679935003703 domain II; other site 679935003704 domain III; other site 679935003705 nucleotide binding site [chemical binding]; other site 679935003706 catalytic site [active] 679935003707 domain IV; other site 679935003708 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 679935003709 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 679935003710 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 679935003711 Domain of unknown function (DUF4270); Region: DUF4270; pfam14092 679935003712 Starch synthase catalytic domain; Region: Glyco_transf_5; pfam08323 679935003713 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 679935003714 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 679935003715 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 679935003716 tRNA pseudouridine(55) synthase; Region: TruB; TIGR00431 679935003717 RNA binding site [nucleotide binding]; other site 679935003718 active site 679935003719 Bacitracin resistance protein BacA; Region: BacA; pfam02673 679935003720 Protein of unknown function (DUF3098); Region: DUF3098; pfam11297 679935003721 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 679935003722 Bacterial membrane protein YfhO; Region: YfhO; pfam09586 679935003723 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 679935003724 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 679935003725 substrate binding pocket [chemical binding]; other site 679935003726 chain length determination region; other site 679935003727 substrate-Mg2+ binding site; other site 679935003728 catalytic residues [active] 679935003729 aspartate-rich region 1; other site 679935003730 active site lid residues [active] 679935003731 aspartate-rich region 2; other site 679935003732 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 679935003733 L-fucose transporter; Provisional; Region: PRK10133; cl17665 679935003734 L-fucose transporter; Provisional; Region: PRK10133; cl17665 679935003735 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 679935003736 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 679935003737 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 679935003738 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 679935003739 ATP binding site [chemical binding]; other site 679935003740 Mg2+ binding site [ion binding]; other site 679935003741 G-X-G motif; other site 679935003742 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 679935003743 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 679935003744 active site 679935003745 phosphorylation site [posttranslational modification] 679935003746 intermolecular recognition site; other site 679935003747 dimerization interface [polypeptide binding]; other site 679935003748 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 679935003749 DNA binding residues [nucleotide binding] 679935003750 dimerization interface [polypeptide binding]; other site 679935003751 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 679935003752 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 679935003753 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 679935003754 putative active site [active] 679935003755 catalytic site [active] 679935003756 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 679935003757 putative active site [active] 679935003758 catalytic site [active] 679935003759 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 679935003760 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 679935003761 NodB motif; other site 679935003762 active site 679935003763 catalytic site [active] 679935003764 metal binding site [ion binding]; metal-binding site 679935003765 aromatic acid decarboxylase; Validated; Region: PRK05920 679935003766 Flavoprotein; Region: Flavoprotein; pfam02441 679935003767 elongation factor P; Validated; Region: PRK00529 679935003768 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 679935003769 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 679935003770 RNA binding site [nucleotide binding]; other site 679935003771 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 679935003772 RNA binding site [nucleotide binding]; other site 679935003773 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 679935003774 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935003775 Trehalase; Region: Trehalase; cl17346 679935003776 SusE outer membrane protein; Region: SusE; pfam14292 679935003777 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 679935003778 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 679935003779 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 679935003780 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 679935003781 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935003782 Glycosyl hydrolase family 26; Region: Glyco_hydro_26; pfam02156 679935003783 argininosuccinate lyase; Provisional; Region: PRK00855 679935003784 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 679935003785 active sites [active] 679935003786 tetramer interface [polypeptide binding]; other site 679935003787 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 679935003788 M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases; Region: M20_ArgE_DapE_like5; cd05651 679935003789 metal binding site [ion binding]; metal-binding site 679935003790 dimer interface [polypeptide binding]; other site 679935003791 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 679935003792 nucleotide binding site [chemical binding]; other site 679935003793 N-acetyl-L-glutamate binding site [chemical binding]; other site 679935003794 N-acetylornithine carbamoyltransferase; Reviewed; Region: PRK04523 679935003795 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 679935003796 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 679935003797 acetylornithine aminotransferase; Provisional; Region: PRK02627 679935003798 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 679935003799 inhibitor-cofactor binding pocket; inhibition site 679935003800 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935003801 catalytic residue [active] 679935003802 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 679935003803 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 679935003804 argininosuccinate synthase; Provisional; Region: PRK13820 679935003805 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 679935003806 Ligand Binding Site [chemical binding]; other site 679935003807 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 679935003808 Coenzyme A binding pocket [chemical binding]; other site 679935003809 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 679935003810 HD domain; Region: HD_4; pfam13328 679935003811 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 679935003812 synthetase active site [active] 679935003813 NTP binding site [chemical binding]; other site 679935003814 metal binding site [ion binding]; metal-binding site 679935003815 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 679935003816 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 679935003817 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 679935003818 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 679935003819 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 679935003820 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 679935003821 Coenzyme A binding pocket [chemical binding]; other site 679935003822 Exonuclease VII small subunit; Region: Exonuc_VII_S; pfam02609 679935003823 Core-2/I-Branching enzyme; Region: Branch; pfam02485 679935003824 MAC/Perforin domain; Region: MACPF; cl02616 679935003825 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 679935003826 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 679935003827 generic binding surface II; other site 679935003828 generic binding surface I; other site 679935003829 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 679935003830 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 679935003831 DNA binding site [nucleotide binding] 679935003832 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 679935003833 active site 679935003834 peptide chain release factor 1; Validated; Region: prfA; PRK00591 679935003835 This domain is found in peptide chain release factors; Region: PCRF; smart00937 679935003836 RF-1 domain; Region: RF-1; pfam00472 679935003837 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 679935003838 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 679935003839 aminoacyl-tRNA ligase; Region: PLN02563 679935003840 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 679935003841 HIGH motif; other site 679935003842 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 679935003843 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 679935003844 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 679935003845 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 679935003846 active site 679935003847 KMSKS motif; other site 679935003848 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 679935003849 tRNA binding surface [nucleotide binding]; other site 679935003850 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 679935003851 S17 interaction site [polypeptide binding]; other site 679935003852 S8 interaction site; other site 679935003853 16S rRNA interaction site [nucleotide binding]; other site 679935003854 streptomycin interaction site [chemical binding]; other site 679935003855 23S rRNA interaction site [nucleotide binding]; other site 679935003856 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 679935003857 30S ribosomal protein S7; Validated; Region: PRK05302 679935003858 elongation factor G; Reviewed; Region: PRK12739 679935003859 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 679935003860 G1 box; other site 679935003861 putative GEF interaction site [polypeptide binding]; other site 679935003862 GTP/Mg2+ binding site [chemical binding]; other site 679935003863 Switch I region; other site 679935003864 G2 box; other site 679935003865 G3 box; other site 679935003866 Switch II region; other site 679935003867 G4 box; other site 679935003868 G5 box; other site 679935003869 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 679935003870 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 679935003871 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 679935003872 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 679935003873 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 679935003874 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 679935003875 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 679935003876 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 679935003877 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 679935003878 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 679935003879 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 679935003880 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 679935003881 protein-rRNA interface [nucleotide binding]; other site 679935003882 putative translocon binding site; other site 679935003883 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 679935003884 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 679935003885 G-X-X-G motif; other site 679935003886 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 679935003887 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 679935003888 23S rRNA interface [nucleotide binding]; other site 679935003889 5S rRNA interface [nucleotide binding]; other site 679935003890 putative antibiotic binding site [chemical binding]; other site 679935003891 L25 interface [polypeptide binding]; other site 679935003892 L27 interface [polypeptide binding]; other site 679935003893 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 679935003894 23S rRNA interface [nucleotide binding]; other site 679935003895 putative translocon interaction site; other site 679935003896 signal recognition particle (SRP54) interaction site; other site 679935003897 L23 interface [polypeptide binding]; other site 679935003898 trigger factor interaction site; other site 679935003899 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 679935003900 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 679935003901 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 679935003902 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 679935003903 RNA binding site [nucleotide binding]; other site 679935003904 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 679935003905 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 679935003906 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 679935003907 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 679935003908 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 679935003909 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 679935003910 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 679935003911 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 679935003912 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 679935003913 23S rRNA interface [nucleotide binding]; other site 679935003914 5S rRNA interface [nucleotide binding]; other site 679935003915 L27 interface [polypeptide binding]; other site 679935003916 L5 interface [polypeptide binding]; other site 679935003917 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 679935003918 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 679935003919 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 679935003920 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 679935003921 23S rRNA binding site [nucleotide binding]; other site 679935003922 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 679935003923 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 679935003924 SecY translocase; Region: SecY; pfam00344 679935003925 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 679935003926 active site 679935003927 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 679935003928 rRNA binding site [nucleotide binding]; other site 679935003929 predicted 30S ribosome binding site; other site 679935003930 Ribosomal protein L36; Region: Ribosomal_L36; pfam00444 679935003931 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 679935003932 30S ribosomal protein S13; Region: bact_S13; TIGR03631 679935003933 30S ribosomal protein S11; Validated; Region: PRK05309 679935003934 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 679935003935 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 679935003936 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 679935003937 RNA binding surface [nucleotide binding]; other site 679935003938 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 679935003939 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 679935003940 alphaNTD - beta interaction site [polypeptide binding]; other site 679935003941 alphaNTD homodimer interface [polypeptide binding]; other site 679935003942 alphaNTD - beta' interaction site [polypeptide binding]; other site 679935003943 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 679935003944 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 679935003945 putative transposase OrfB; Reviewed; Region: PHA02517 679935003946 HTH-like domain; Region: HTH_21; pfam13276 679935003947 Integrase core domain; Region: rve; pfam00665 679935003948 Integrase core domain; Region: rve_2; pfam13333 679935003949 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935003950 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935003951 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935003952 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935003953 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 679935003954 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; cl12060 679935003955 Metal-binding active site; metal-binding site 679935003956 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935003957 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 679935003958 active site 679935003959 metal binding site [ion binding]; metal-binding site 679935003960 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935003961 SusD family; Region: SusD; pfam07980 679935003962 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935003963 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935003964 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935003965 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 679935003966 ribulokinase; Provisional; Region: PRK04123 679935003967 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 679935003968 nucleotide binding site [chemical binding]; other site 679935003969 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 679935003970 D-galactonate transporter; Region: 2A0114; TIGR00893 679935003971 putative substrate translocation pore; other site 679935003972 FAD dependent oxidoreductase; Region: FAD_oxidored; pfam12831 679935003973 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 679935003974 putative catalytic site [active] 679935003975 putative metal binding site [ion binding]; other site 679935003976 putative phosphate binding site [ion binding]; other site 679935003977 Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction; Region: HP_HAP_like; cd07061 679935003978 catalytic core [active] 679935003979 triosephosphate isomerase; Provisional; Region: PRK14567 679935003980 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 679935003981 substrate binding site [chemical binding]; other site 679935003982 dimer interface [polypeptide binding]; other site 679935003983 catalytic triad [active] 679935003984 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 679935003985 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 679935003986 dimer interface [polypeptide binding]; other site 679935003987 putative anticodon binding site; other site 679935003988 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 679935003989 motif 1; other site 679935003990 active site 679935003991 motif 2; other site 679935003992 motif 3; other site 679935003993 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 679935003994 active site 679935003995 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 679935003996 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 679935003997 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 679935003998 active site 679935003999 oxyanion hole [active] 679935004000 catalytic triad [active] 679935004001 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; pfam04298 679935004002 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 679935004003 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 679935004004 NAD(P) binding site [chemical binding]; other site 679935004005 active site 679935004006 lipoprotein releasing system, transmembrane protein LolE; Region: lolE_release; TIGR02213 679935004007 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 679935004008 FtsX-like permease family; Region: FtsX; pfam02687 679935004009 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 679935004010 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 679935004011 S-adenosylmethionine binding site [chemical binding]; other site 679935004012 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 679935004013 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 679935004014 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 679935004015 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 679935004016 FeS/SAM binding site; other site 679935004017 probable DNA metabolism protein; Region: SAM_7_link_chp; TIGR03915 679935004018 Surface antigen; Region: Bac_surface_Ag; pfam01103 679935004019 Family of unknown function (DUF490); Region: DUF490; pfam04357 679935004020 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 679935004021 active site 679935004022 DNA polymerase IV; Validated; Region: PRK02406 679935004023 DNA binding site [nucleotide binding] 679935004024 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 679935004025 FMN binding site [chemical binding]; other site 679935004026 dimer interface [polypeptide binding]; other site 679935004027 TspO/MBR family; Region: TspO_MBR; pfam03073 679935004028 cytoplasmic alpha-amylase; Reviewed; Region: PRK09441 679935004029 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 679935004030 active site 679935004031 Na/Ca binding site [ion binding]; other site 679935004032 catalytic site [active] 679935004033 Manganese catalase, ferritin-like diiron-binding domain; Region: Mn_catalase; cd01051 679935004034 dimanganese center [ion binding]; other site 679935004035 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 679935004036 dinuclear metal binding motif [ion binding]; other site 679935004037 CCC1-related domain of ferritin; Region: Ferritin_CCC1_C; cd02431 679935004038 Protein of unknown function (DUF2874); Region: DUF2874; pfam11396 679935004039 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 679935004040 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 679935004041 pullulanase, type I; Region: pulA_typeI; TIGR02104 679935004042 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 679935004043 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 679935004044 Ca binding site [ion binding]; other site 679935004045 active site 679935004046 catalytic site [active] 679935004047 Domain of unknown function (DUF3372); Region: DUF3372; pfam11852 679935004048 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 679935004049 Mechanosensitive ion channel; Region: MS_channel; pfam00924 679935004050 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 679935004051 prolyl-tRNA synthetase; Provisional; Region: PRK08661 679935004052 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 679935004053 dimer interface [polypeptide binding]; other site 679935004054 motif 1; other site 679935004055 active site 679935004056 motif 2; other site 679935004057 motif 3; other site 679935004058 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 679935004059 anticodon binding site; other site 679935004060 zinc-binding site [ion binding]; other site 679935004061 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 679935004062 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 679935004063 RNA polymerase sigma factor; Provisional; Region: PRK12513 679935004064 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935004065 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 679935004066 DNA binding residues [nucleotide binding] 679935004067 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 679935004068 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 679935004069 active site 679935004070 Uncharacterized conserved protein [Function unknown]; Region: COG3189 679935004071 Uncharacterized conserved protein [Function unknown]; Region: HdeD; COG3247 679935004072 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 679935004073 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 679935004074 Linear amide C-N hydrolases, choloylglycine hydrolase family; Region: CBAH; pfam02275 679935004075 Penicillin V acylase (PVA), also known as conjugated bile salt acid hydrolase (CBAH), catalyzes the hydrolysis of penicillin V to yield 6-amino penicillanic acid (6-APA), an important key intermediate of semisynthetic penicillins. PVA has an N-terminal...; Region: Ntn_PVA; cd00542 679935004076 active site 679935004077 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 679935004078 Fic/DOC family; Region: Fic; pfam02661 679935004079 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 679935004080 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935004081 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935004082 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935004083 HsdM N-terminal domain; Region: HsdM_N; pfam12161 679935004084 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 679935004085 Methyltransferase domain; Region: Methyltransf_26; pfam13659 679935004086 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 679935004087 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 679935004088 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 679935004089 Transposase, Mutator family; Region: Transposase_mut; pfam00872 679935004090 MULE transposase domain; Region: MULE; pfam10551 679935004091 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 679935004092 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 679935004093 active site 679935004094 DNA binding site [nucleotide binding] 679935004095 Int/Topo IB signature motif; other site 679935004096 FRG domain; Region: FRG; pfam08867 679935004097 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 679935004098 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 679935004099 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 679935004100 ATP binding site [chemical binding]; other site 679935004101 putative Mg++ binding site [ion binding]; other site 679935004102 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 679935004103 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935004104 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935004105 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935004106 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 679935004107 putative transposase OrfB; Reviewed; Region: PHA02517 679935004108 HTH-like domain; Region: HTH_21; pfam13276 679935004109 Integrase core domain; Region: rve; pfam00665 679935004110 Integrase core domain; Region: rve_3; pfam13683 679935004111 Alpha-L-fucosidase; Region: Alpha_L_fucos; pfam01120 679935004112 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 679935004113 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 679935004114 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 679935004115 Bacterial Ig-like domain (group 1); Region: Big_1; cl17740 679935004116 Uncharacterized protein involved in copper resistance [Inorganic ion transport and metabolism]; Region: CutC; COG3142 679935004117 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935004118 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935004119 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935004120 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 679935004121 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935004122 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 679935004123 active site 679935004124 catalytic residues [active] 679935004125 Lipocalin-like domain; Region: Lipocalin_4; pfam13648 679935004126 RteC protein; Region: RteC; pfam09357 679935004127 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 679935004128 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 679935004129 active site 679935004130 DNA binding site [nucleotide binding] 679935004131 Int/Topo IB signature motif; other site 679935004132 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 679935004133 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 679935004134 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 679935004135 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 679935004136 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 679935004137 active site 679935004138 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 679935004139 N-terminal domain of Chondroitin polymerase functions as a GalNAc transferase; Region: GT2_Chondriotin_Pol_N; cd06420 679935004140 Substrate binding site; other site 679935004141 metal-binding site 679935004142 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 679935004143 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 679935004144 30S subunit binding site; other site 679935004145 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 679935004146 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 679935004147 active site 679935004148 DNA binding site [nucleotide binding] 679935004149 Int/Topo IB signature motif; other site 679935004150 S-formylglutathione hydrolase; Region: PLN02442 679935004151 Putative esterase; Region: Esterase; pfam00756 679935004152 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 679935004153 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 679935004154 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 679935004155 putative substrate translocation pore; other site 679935004156 Bacterial Ig-like domain; Region: Big_5; pfam13205 679935004157 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 679935004158 MG2 domain; Region: A2M_N; pfam01835 679935004159 Alpha-2-macroglobulin family; Region: A2M; pfam00207 679935004160 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 679935004161 surface patch; other site 679935004162 thioester region; other site 679935004163 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 679935004164 Transglycosylase; Region: Transgly; pfam00912 679935004165 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 679935004166 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 679935004167 cryptic beta-D-galactosidase subunit alpha; Reviewed; Region: ebgA; PRK10340 679935004168 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 679935004169 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 679935004170 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 679935004171 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 679935004172 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 679935004173 Sulfatase; Region: Sulfatase; pfam00884 679935004174 Beta-galactosidase/beta-glucuronidase [Carbohydrate transport and metabolism]; Region: LacZ; COG3250 679935004175 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 679935004176 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 679935004177 Sulfatase; Region: Sulfatase; cl17466 679935004178 Beta galactosidase small chain; Region: Bgal_small_N; smart01038 679935004179 Beta-galactosidase; Region: Glyco_hydro_42; pfam02449 679935004180 A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain; Region: A4_beta-galactosidase_middle_domain; cd03143 679935004181 isoleucyl-tRNA synthetase; Region: ileS; TIGR00392 679935004182 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 679935004183 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 679935004184 cofactor binding site; other site 679935004185 DNA binding site [nucleotide binding] 679935004186 substrate interaction site [chemical binding]; other site 679935004187 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 679935004188 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935004189 Fic family protein [Function unknown]; Region: COG3177 679935004190 Fic/DOC family; Region: Fic; pfam02661 679935004191 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 679935004192 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 679935004193 Bacteroides conjugative transposon TraK protein; Region: Bac_Flav_CT_K; TIGR03781 679935004194 Bacteroides conjugation system ATPase, TraG family; Region: Bac_Flav_CT_G; TIGR03783 679935004195 Domain of unknown function, B. Theta Gene description (DUF3875); Region: DUF3875; pfam12991 679935004196 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 679935004197 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 679935004198 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 679935004199 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 679935004200 Domain of unknown function (DUF4406); Region: DUF4406; pfam14359 679935004201 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935004202 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935004203 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935004204 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cd00188 679935004205 active site 679935004206 metal binding site [ion binding]; metal-binding site 679935004207 AAA-like domain; Region: AAA_10; pfam12846 679935004208 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 679935004209 ORF6N domain; Region: ORF6N; pfam10543 679935004210 ORF6N domain; Region: ORF6N; pfam10543 679935004211 Major fimbrial subunit protein (FimA); Region: P_gingi_FimA; pfam06321 679935004212 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 679935004213 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 679935004214 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 679935004215 Peptidase family M23; Region: Peptidase_M23; pfam01551 679935004216 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 679935004217 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 679935004218 P-loop; other site 679935004219 Magnesium ion binding site [ion binding]; other site 679935004220 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 679935004221 Magnesium ion binding site [ion binding]; other site 679935004222 Initiator Replication protein; Region: Rep_3; pfam01051 679935004223 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 679935004224 active site 679935004225 DNA binding site [nucleotide binding] 679935004226 Int/Topo IB signature motif; other site 679935004227 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 679935004228 active site 679935004229 Int/Topo IB signature motif; other site 679935004230 DNA binding site [nucleotide binding] 679935004231 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 679935004232 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 679935004233 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 679935004234 DNA binding residues [nucleotide binding] 679935004235 Phage associated DNA primase [General function prediction only]; Region: COG3378 679935004236 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 679935004237 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 679935004238 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 679935004239 Cyclomaltodextrinase, N-terminal; Region: Cyc-maltodext_N; pfam09087 679935004240 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins; Region: AmyAc_bac_CMD_like_3; cd11340 679935004241 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 679935004242 Ca binding site [ion binding]; other site 679935004243 active site 679935004244 homodimer interface [polypeptide binding]; other site 679935004245 catalytic site [active] 679935004246 Cyclo-malto-dextrinase C-terminal domain; Region: Cyc-maltodext_C; pfam10438 679935004247 Alpha amylase catalytic domain found in archaeal and bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_arch_bac_AmyA; cd11313 679935004248 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 679935004249 active site 679935004250 catalytic site [active] 679935004251 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 679935004252 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935004253 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 679935004254 Carbohydrate-binding module 58 from Bacteroides thetaiotaomicron SusG and similar CBMs; Region: CBM58_SusG; cd12961 679935004255 starch binding site [chemical binding]; other site 679935004256 Alpha amylase catalytic domain found in bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_bac2_AmyA; cd11316 679935004257 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 679935004258 active site 679935004259 catalytic site [active] 679935004260 SusE outer membrane protein; Region: SusE; pfam14292 679935004261 carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins; Region: CBM_SusE-F_like; cl17376 679935004262 starch binding site [chemical binding]; other site 679935004263 carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins; Region: CBM_SusE-F_like; cd12956 679935004264 starch binding site [chemical binding]; other site 679935004265 carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins; Region: CBM_SusE-F_like; cl17376 679935004266 starch binding site [chemical binding]; other site 679935004267 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 679935004268 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935004269 SusD family; Region: SusD; pfam07980 679935004270 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935004271 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935004272 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935004273 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 679935004274 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 679935004275 Major Facilitator Superfamily; Region: MFS_1; pfam07690 679935004276 putative substrate translocation pore; other site 679935004277 Histidine kinase; Region: His_kinase; pfam06580 679935004278 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 679935004279 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 679935004280 active site 679935004281 phosphorylation site [posttranslational modification] 679935004282 intermolecular recognition site; other site 679935004283 dimerization interface [polypeptide binding]; other site 679935004284 LytTr DNA-binding domain; Region: LytTR; smart00850 679935004285 4-alpha-glucanotransferase; Region: PLN02950 679935004286 The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is...; Region: CBM20; cl15347 679935004287 starch-binding site 2 [chemical binding]; other site 679935004288 starch-binding site 1 [chemical binding]; other site 679935004289 Starch binding domain; Region: CBM_2; smart01065 679935004290 starch-binding site 2 [chemical binding]; other site 679935004291 starch-binding site 1 [chemical binding]; other site 679935004292 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 679935004293 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 679935004294 Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]; Region: Nei; COG0266 679935004295 N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; Region: FpgNei_N; cl03119 679935004296 DNA binding site [nucleotide binding] 679935004297 catalytic residue [active] 679935004298 H2TH interface [polypeptide binding]; other site 679935004299 putative catalytic residues [active] 679935004300 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 679935004301 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 679935004302 Putative zinc ribbon domain; Region: Zn_ribbon_2; pfam12674 679935004303 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 679935004304 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 679935004305 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 679935004306 methyl indole-3-acetate methyltransferase; Region: PLN02211; cl17657 679935004307 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 679935004308 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 679935004309 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 679935004310 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 679935004311 dimer interface [polypeptide binding]; other site 679935004312 FMN binding site [chemical binding]; other site 679935004313 NADPH bind site [chemical binding]; other site 679935004314 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 679935004315 Surface antigen; Region: Bac_surface_Ag; pfam01103 679935004316 Helix-turn-helix domain; Region: HTH_18; pfam12833 679935004317 periplasmic chaperone; Provisional; Region: PRK10780 679935004318 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 679935004319 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 679935004320 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 679935004321 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 679935004322 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 679935004323 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 679935004324 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 679935004325 Surface antigen; Region: Bac_surface_Ag; pfam01103 679935004326 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 679935004327 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 679935004328 catalytic residue [active] 679935004329 putative FPP diphosphate binding site; other site 679935004330 putative FPP binding hydrophobic cleft; other site 679935004331 dimer interface [polypeptide binding]; other site 679935004332 putative IPP diphosphate binding site; other site 679935004333 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 679935004334 ATP-NAD kinase; Region: NAD_kinase; pfam01513 679935004335 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 679935004336 active site 679935004337 hydrophilic channel; other site 679935004338 dimerization interface [polypeptide binding]; other site 679935004339 catalytic residues [active] 679935004340 active site lid [active] 679935004341 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 679935004342 active site 679935004343 catalytic triad [active] 679935004344 oxyanion hole [active] 679935004345 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 679935004346 tRNA adenylyltransferase; Region: tRNA_CCA_actino; TIGR02692 679935004347 active site 679935004348 NTP binding site [chemical binding]; other site 679935004349 metal binding triad [ion binding]; metal-binding site 679935004350 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 679935004351 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 679935004352 Zn2+ binding site [ion binding]; other site 679935004353 Mg2+ binding site [ion binding]; other site 679935004354 tRNA nucleotidyltransferase domain 2 putative; Region: tRNA_NucTran2_2; pfam13735 679935004355 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 679935004356 EamA-like transporter family; Region: EamA; pfam00892 679935004357 EamA-like transporter family; Region: EamA; pfam00892 679935004358 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 679935004359 EamA-like transporter family; Region: EamA; pfam00892 679935004360 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 679935004361 active site 679935004362 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 679935004363 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 679935004364 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 679935004365 dimer interface [polypeptide binding]; other site 679935004366 active site 679935004367 metal binding site [ion binding]; metal-binding site 679935004368 glutathione binding site [chemical binding]; other site 679935004369 hypothetical protein; Provisional; Region: PRK12378 679935004370 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 679935004371 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 679935004372 active site 679935004373 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 679935004374 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 679935004375 glucose-6-phosphate isomerase; Provisional; Region: pgi; PRK14097 679935004376 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 679935004377 active site 679935004378 dimer interface [polypeptide binding]; other site 679935004379 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 679935004380 dimer interface [polypeptide binding]; other site 679935004381 active site 679935004382 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 679935004383 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 679935004384 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 679935004385 rod shape-determining protein MreB; Provisional; Region: PRK13927 679935004386 MreB and similar proteins; Region: MreB_like; cd10225 679935004387 nucleotide binding site [chemical binding]; other site 679935004388 Mg binding site [ion binding]; other site 679935004389 putative protofilament interaction site [polypeptide binding]; other site 679935004390 RodZ interaction site [polypeptide binding]; other site 679935004391 rod shape-determining protein MreC; Provisional; Region: PRK13922 679935004392 rod shape-determining protein MreC; Region: MreC; pfam04085 679935004393 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 679935004394 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 679935004395 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 679935004396 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 679935004397 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 679935004398 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 679935004399 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 679935004400 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 679935004401 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 679935004402 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 679935004403 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 679935004404 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 679935004405 active site 679935004406 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 679935004407 glutamate dehydrogenase; Provisional; Region: PRK14030 679935004408 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 679935004409 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 679935004410 NAD(P) binding site [chemical binding]; other site 679935004411 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 679935004412 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 679935004413 phosphorylation site [posttranslational modification] 679935004414 intermolecular recognition site; other site 679935004415 Response regulator receiver domain; Region: Response_reg; pfam00072 679935004416 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 679935004417 active site 679935004418 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 679935004419 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 679935004420 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 679935004421 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK07565 679935004422 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 679935004423 phosphate binding site [ion binding]; other site 679935004424 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 679935004425 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935004426 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 679935004427 Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins; Region: GDPD_AtGDE_like; cd08566 679935004428 putative active site [active] 679935004429 catalytic site [active] 679935004430 putative metal binding site [ion binding]; other site 679935004431 oligomer interface [polypeptide binding]; other site 679935004432 S1/P1 nucleases and related enzymes; Region: S1-P1_nuclease; cd11010 679935004433 active site 679935004434 Zn binding site [ion binding]; other site 679935004435 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935004436 SusD family; Region: SusD; pfam07980 679935004437 Secretin and TonB N terminus short domain; Region: STN; pfam07660 679935004438 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935004439 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935004440 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935004441 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 679935004442 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935004443 FecR protein; Region: FecR; pfam04773 679935004444 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935004445 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935004446 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 679935004447 DNA binding residues [nucleotide binding] 679935004448 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 679935004449 Uncharacterized conserved protein [Function unknown]; Region: COG2966 679935004450 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 679935004451 Protein of unknown function (DUF3815); Region: DUF3815; pfam12821 679935004452 phosphodiesterase; Provisional; Region: PRK12704 679935004453 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 679935004454 Zn2+ binding site [ion binding]; other site 679935004455 Mg2+ binding site [ion binding]; other site 679935004456 Cell division protein ZapA; Region: ZapA; pfam05164 679935004457 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 679935004458 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 679935004459 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 679935004460 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 679935004461 FeS/SAM binding site; other site 679935004462 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 679935004463 putative catalytic site [active] 679935004464 putative metal binding site [ion binding]; other site 679935004465 putative phosphate binding site [ion binding]; other site 679935004466 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935004467 SusD family; Region: SusD; pfam07980 679935004468 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935004469 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935004470 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 679935004471 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 679935004472 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 679935004473 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 679935004474 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 679935004475 P loop; other site 679935004476 GTP binding site [chemical binding]; other site 679935004477 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 679935004478 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 679935004479 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935004480 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935004481 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 679935004482 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 679935004483 Domain of unknown function (DUF4295); Region: DUF4295; pfam14128 679935004484 ribosomal protein L33; Region: rpl33; CHL00104 679935004485 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 679935004486 Tetratricopeptide repeat; Region: TPR_12; pfam13424 679935004487 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935004488 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 679935004489 dimer interface [polypeptide binding]; other site 679935004490 phosphorylation site [posttranslational modification] 679935004491 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 679935004492 ATP binding site [chemical binding]; other site 679935004493 Mg2+ binding site [ion binding]; other site 679935004494 G-X-G motif; other site 679935004495 Competence-damaged protein; Region: CinA; pfam02464 679935004496 competence damage-inducible protein A; Provisional; Region: PRK00549 679935004497 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 679935004498 putative MPT binding site; other site 679935004499 Competence-damaged protein; Region: CinA; pfam02464 679935004500 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 679935004501 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 679935004502 quinone interaction residues [chemical binding]; other site 679935004503 active site 679935004504 catalytic residues [active] 679935004505 FMN binding site [chemical binding]; other site 679935004506 substrate binding site [chemical binding]; other site 679935004507 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 679935004508 D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains; Region: ErythrP_dh; cd12158 679935004509 ligand binding site [chemical binding]; other site 679935004510 NAD binding site [chemical binding]; other site 679935004511 catalytic site [active] 679935004512 homodimer interface [polypeptide binding]; other site 679935004513 agmatinase; Region: agmatinase; TIGR01230 679935004514 Agmatinase and related proteins; Region: Agmatinase-like_2; cd11593 679935004515 putative active site [active] 679935004516 Mn binding site [ion binding]; other site 679935004517 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 679935004518 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 679935004519 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 679935004520 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 679935004521 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 679935004522 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 679935004523 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 679935004524 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 679935004525 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 679935004526 Coenzyme A binding pocket [chemical binding]; other site 679935004527 Domain of unknown function (DUF3127); Region: DUF3127; pfam11325 679935004528 S1/P1 nucleases and related enzymes; Region: S1-P1_nuclease; cd11010 679935004529 active site 679935004530 Zn binding site [ion binding]; other site 679935004531 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 679935004532 AAA domain; Region: AAA_13; pfam13166 679935004533 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 679935004534 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 679935004535 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 679935004536 elongation factor Tu; Reviewed; Region: PRK12735 679935004537 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 679935004538 G1 box; other site 679935004539 GEF interaction site [polypeptide binding]; other site 679935004540 GTP/Mg2+ binding site [chemical binding]; other site 679935004541 Switch I region; other site 679935004542 G2 box; other site 679935004543 G3 box; other site 679935004544 Switch II region; other site 679935004545 G4 box; other site 679935004546 G5 box; other site 679935004547 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 679935004548 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 679935004549 Antibiotic Binding Site [chemical binding]; other site 679935004550 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 679935004551 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 679935004552 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 679935004553 putative homodimer interface [polypeptide binding]; other site 679935004554 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 679935004555 heterodimer interface [polypeptide binding]; other site 679935004556 homodimer interface [polypeptide binding]; other site 679935004557 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 679935004558 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 679935004559 23S rRNA interface [nucleotide binding]; other site 679935004560 L7/L12 interface [polypeptide binding]; other site 679935004561 putative thiostrepton binding site; other site 679935004562 L25 interface [polypeptide binding]; other site 679935004563 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 679935004564 mRNA/rRNA interface [nucleotide binding]; other site 679935004565 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 679935004566 23S rRNA interface [nucleotide binding]; other site 679935004567 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 679935004568 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 679935004569 core dimer interface [polypeptide binding]; other site 679935004570 peripheral dimer interface [polypeptide binding]; other site 679935004571 L10 interface [polypeptide binding]; other site 679935004572 L11 interface [polypeptide binding]; other site 679935004573 putative EF-Tu interaction site [polypeptide binding]; other site 679935004574 putative EF-G interaction site [polypeptide binding]; other site 679935004575 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 679935004576 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 679935004577 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 679935004578 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 679935004579 RNA polymerase beta subunit external 1 domain; Region: RNA_pol_Rpb2_45; pfam10385 679935004580 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 679935004581 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 679935004582 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 679935004583 RPB3 interaction site [polypeptide binding]; other site 679935004584 RPB1 interaction site [polypeptide binding]; other site 679935004585 RPB11 interaction site [polypeptide binding]; other site 679935004586 RPB10 interaction site [polypeptide binding]; other site 679935004587 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 679935004588 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 679935004589 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 679935004590 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 679935004591 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 679935004592 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 679935004593 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 679935004594 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 679935004595 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 679935004596 DNA binding site [nucleotide binding] 679935004597 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 679935004598 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 679935004599 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 679935004600 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 679935004601 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 679935004602 aspartate aminotransferase; Provisional; Region: PRK07568 679935004603 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 679935004604 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935004605 homodimer interface [polypeptide binding]; other site 679935004606 catalytic residue [active] 679935004607 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 679935004608 IHF - DNA interface [nucleotide binding]; other site 679935004609 IHF dimer interface [polypeptide binding]; other site 679935004610 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 679935004611 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 679935004612 ATP binding site [chemical binding]; other site 679935004613 Mg++ binding site [ion binding]; other site 679935004614 motif III; other site 679935004615 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 679935004616 nucleotide binding region [chemical binding]; other site 679935004617 ATP-binding site [chemical binding]; other site 679935004618 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 679935004619 RNA binding site [nucleotide binding]; other site 679935004620 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 679935004621 Enoyl-(Acyl carrier protein) reductase; Region: adh_short_C2; pfam13561 679935004622 NAD binding site [chemical binding]; other site 679935004623 homotetramer interface [polypeptide binding]; other site 679935004624 homodimer interface [polypeptide binding]; other site 679935004625 substrate binding site [chemical binding]; other site 679935004626 active site 679935004627 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 679935004628 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 679935004629 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 679935004630 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 679935004631 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 679935004632 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 679935004633 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 679935004634 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 679935004635 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935004636 SusD family; Region: SusD; pfam07980 679935004637 Putative glycoside hydrolase xylanase; Region: Xylanase; pfam13201 679935004638 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 679935004639 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 679935004640 active site 679935004641 catalytic triad [active] 679935004642 oxyanion hole [active] 679935004643 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4299 679935004644 D-xylose transporter XylE; Provisional; Region: xylE; PRK10077 679935004645 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 679935004646 putative substrate translocation pore; other site 679935004647 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 679935004648 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; cd00249 679935004649 dimerization interface [polypeptide binding]; other site 679935004650 putative active cleft [active] 679935004651 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935004652 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 679935004653 active site 679935004654 metal binding site [ion binding]; metal-binding site 679935004655 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 679935004656 FAD dependent oxidoreductase; Region: FAD_oxidored; pfam12831 679935004657 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 679935004658 Endoglucanase E-like members of the SGNH hydrolase family; Endoglucanase E catalyzes the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans; Region: Endoglucanase_E_like; cd01831 679935004659 active site 679935004660 catalytic triad [active] 679935004661 oxyanion hole [active] 679935004662 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 679935004663 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 679935004664 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 679935004665 motif II; other site 679935004666 Response regulator receiver domain; Region: Response_reg; pfam00072 679935004667 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 679935004668 active site 679935004669 phosphorylation site [posttranslational modification] 679935004670 dimerization interface [polypeptide binding]; other site 679935004671 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 679935004672 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 679935004673 Walker A motif; other site 679935004674 ATP binding site [chemical binding]; other site 679935004675 Walker B motif; other site 679935004676 arginine finger; other site 679935004677 Domain of unknown function (DUF4290); Region: DUF4290; pfam14123 679935004678 Domain of unknown function (DUF4369); Region: DUF4369; pfam14289 679935004679 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 679935004680 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 679935004681 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 679935004682 putative active site [active] 679935004683 putative metal binding site [ion binding]; other site 679935004684 thymidylate synthase; Reviewed; Region: thyA; PRK01827 679935004685 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 679935004686 dimerization interface [polypeptide binding]; other site 679935004687 active site 679935004688 Right handed beta helix region; Region: Beta_helix; pfam13229 679935004689 Starch-binding associating with outer membrane; Region: SusD-like_3; pfam14322 679935004690 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935004691 SusD family; Region: SusD; pfam07980 679935004692 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935004693 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935004694 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 679935004695 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 679935004696 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 679935004697 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 679935004698 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 679935004699 Transcriptional regulators [Transcription]; Region: PurR; COG1609 679935004700 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 679935004701 DNA binding site [nucleotide binding] 679935004702 domain linker motif; other site 679935004703 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 679935004704 dimerization interface [polypeptide binding]; other site 679935004705 ligand binding site [chemical binding]; other site 679935004706 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 679935004707 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u1; cd11477 679935004708 Na binding site [ion binding]; other site 679935004709 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 679935004710 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 679935004711 folate binding site [chemical binding]; other site 679935004712 NADP+ binding site [chemical binding]; other site 679935004713 4Fe-4S dicluster domain; Region: Fer4_17; pfam13534 679935004714 CoB--CoM heterodisulfide reductase, subunit B; Region: CoB_CoM_SS_B; TIGR03288 679935004715 Cysteine-rich domain; Region: CCG; pfam02754 679935004716 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 679935004717 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 679935004718 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 679935004719 4Fe-4S dicluster domain; Region: Fer4_17; pfam13534 679935004720 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 679935004721 Cysteine-rich domain; Region: CCG; pfam02754 679935004722 Cysteine-rich domain; Region: CCG; pfam02754 679935004723 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 679935004724 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 679935004725 dimer interface [polypeptide binding]; other site 679935004726 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935004727 catalytic residue [active] 679935004728 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 679935004729 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 679935004730 putative active site [active] 679935004731 putative NTP binding site [chemical binding]; other site 679935004732 putative nucleic acid binding site [nucleotide binding]; other site 679935004733 Type II intron maturase; Region: Intron_maturas2; pfam01348 679935004734 DEAD-like helicases superfamily; Region: DEXDc; smart00487 679935004735 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 679935004736 putative Mg++ binding site [ion binding]; other site 679935004737 putative transposase OrfB; Reviewed; Region: PHA02517 679935004738 HTH-like domain; Region: HTH_21; pfam13276 679935004739 Integrase core domain; Region: rve; pfam00665 679935004740 Integrase core domain; Region: rve_3; pfam13683 679935004741 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935004742 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 679935004743 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 679935004744 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 679935004745 Int/Topo IB signature motif; other site 679935004746 ParB-like nuclease domain; Region: ParB; smart00470 679935004747 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935004748 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935004749 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935004750 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935004751 putative transposase OrfB; Reviewed; Region: PHA02517 679935004752 HTH-like domain; Region: HTH_21; pfam13276 679935004753 Integrase core domain; Region: rve; pfam00665 679935004754 Integrase core domain; Region: rve_2; pfam13333 679935004755 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 679935004756 Ligand Binding Site [chemical binding]; other site 679935004757 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935004758 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935004759 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 679935004760 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 679935004761 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 679935004762 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 679935004763 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 679935004764 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 679935004765 active site 679935004766 DNA binding site [nucleotide binding] 679935004767 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 679935004768 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 679935004769 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 679935004770 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 679935004771 Catalytic site [active] 679935004772 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 679935004773 TPR motif; other site 679935004774 binding surface 679935004775 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 679935004776 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 679935004777 Domain of unknown function (DUF4249); Region: DUF4249; pfam14054 679935004778 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 679935004779 Domain of unknown function, B. Theta Gene description (DUF3872); Region: DUF3872; pfam12988 679935004780 Conjugative transposon protein TraO; Region: TraO; pfam10626 679935004781 Bacteroides conjugative transposon TraN protein; Region: Bac_Flav_CT_N; TIGR03780 679935004782 Domain of unknown function (DUF4138); Region: DUF4138; pfam13595 679935004783 Bacteroides conjugative transposon TraM protein; Region: Bac_Flav_CT_M; TIGR03779 679935004784 Protein of unknown function (DUF3714); Region: DUF3714; pfam12508 679935004785 Protein of unknown function (DUF3989); Region: DUF3989; pfam13150 679935004786 Bacteroides conjugative transposon TraK protein; Region: Bac_Flav_CT_K; TIGR03781 679935004787 Bacteroides conjugative transposon TraJ protein; Region: Bac_Flav_CT_J; TIGR03782 679935004788 Domain of unknown function (DUF4141); Region: DUF4141; pfam13605 679935004789 Domain of unknown function, B. Theta Gene description (DUF3876); Region: DUF3876; pfam12992 679935004790 Retron-type reverse transcriptase [DNA replication, recombination, and repair]; Region: COG3344 679935004791 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 679935004792 putative active site [active] 679935004793 putative NTP binding site [chemical binding]; other site 679935004794 putative nucleic acid binding site [nucleotide binding]; other site 679935004795 Type II intron maturase; Region: Intron_maturas2; pfam01348 679935004796 Domain of unknown function (DUF4133); Region: DUF4133; pfam13571 679935004797 Domain of unknown function (DUF4134); Region: DUF4134; pfam13572 679935004798 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 679935004799 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 679935004800 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 679935004801 P-loop; other site 679935004802 Magnesium ion binding site [ion binding]; other site 679935004803 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 679935004804 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 679935004805 active site 679935004806 catalytic residues [active] 679935004807 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 679935004808 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 679935004809 active site 679935004810 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935004811 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935004812 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 679935004813 IgA Peptidase M64; Region: Peptidase_M64; pfam09471 679935004814 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 679935004815 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 679935004816 sequence-specific DNA binding site [nucleotide binding]; other site 679935004817 salt bridge; other site 679935004818 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 679935004819 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 679935004820 non-specific DNA binding site [nucleotide binding]; other site 679935004821 salt bridge; other site 679935004822 sequence-specific DNA binding site [nucleotide binding]; other site 679935004823 Protein of unknown function (DUF3945); Region: DUF3945; pfam13101 679935004824 Domain of unknown function (DUF1896); Region: DUF1896; pfam08989 679935004825 Major fimbrial subunit protein (FimA); Region: P_gingi_FimA; pfam06321 679935004826 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 679935004827 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 679935004828 S-adenosylmethionine binding site [chemical binding]; other site 679935004829 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 679935004830 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 679935004831 ATP binding site [chemical binding]; other site 679935004832 putative Mg++ binding site [ion binding]; other site 679935004833 nucleotide binding region [chemical binding]; other site 679935004834 Helicase conserved C-terminal domain; Region: Helicase_C; pfam00271 679935004835 Domain of unknown function (DUF3560); Region: DUF3560; pfam12083 679935004836 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 679935004837 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 679935004838 Domain of unknown function, B. Theta Gene description (DUF3871); Region: DUF3871; pfam12987 679935004839 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 679935004840 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 679935004841 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 679935004842 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 679935004843 Thioredoxin-like domain; Region: Thioredoxin_2; pfam13098 679935004844 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 679935004845 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 679935004846 active site 679935004847 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 679935004848 substrate binding site [chemical binding]; other site 679935004849 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 679935004850 ATP binding site [chemical binding]; other site 679935004851 6-phosphofructokinase; Provisional; Region: PRK03202 679935004852 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 679935004853 active site 679935004854 ADP/pyrophosphate binding site [chemical binding]; other site 679935004855 dimerization interface [polypeptide binding]; other site 679935004856 allosteric effector site; other site 679935004857 fructose-1,6-bisphosphate binding site; other site 679935004858 PspC domain; Region: PspC; pfam04024 679935004859 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 679935004860 Predicted transcriptional regulators [Transcription]; Region: COG1695 679935004861 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 679935004862 PspC domain; Region: PspC; pfam04024 679935004863 PspC domain; Region: PspC; pfam04024 679935004864 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 679935004865 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 679935004866 DNA binding residues [nucleotide binding] 679935004867 Domain of unknown function (DUF4252); Region: DUF4252; pfam14060 679935004868 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated; Region: PRK07570 679935004869 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 679935004870 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07573 679935004871 L-aspartate oxidase; Provisional; Region: PRK06175 679935004872 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 679935004873 succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family; Region: sdhC_b558_fam; TIGR02046 679935004874 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 679935004875 putative Iron-sulfur protein interface [polypeptide binding]; other site 679935004876 proximal heme binding site [chemical binding]; other site 679935004877 distal heme binding site [chemical binding]; other site 679935004878 putative dimer interface [polypeptide binding]; other site 679935004879 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 679935004880 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 679935004881 Uncharacterized ArCR, COG2043; Region: DUF169; cl00894 679935004882 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 679935004883 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 679935004884 nucleophile elbow; other site 679935004885 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 679935004886 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 679935004887 GIY-YIG motif/motif A; other site 679935004888 active site 679935004889 catalytic site [active] 679935004890 putative DNA binding site [nucleotide binding]; other site 679935004891 metal binding site [ion binding]; metal-binding site 679935004892 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 679935004893 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 679935004894 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 679935004895 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 679935004896 N-terminal plug; other site 679935004897 ligand-binding site [chemical binding]; other site 679935004898 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_IV; cd01994 679935004899 Ligand Binding Site [chemical binding]; other site 679935004900 Syd protein (SUKH-2); Region: Syd; cl06405 679935004901 Predicted metal-binding protein (DUF2284); Region: DUF2284; cl02248 679935004902 putative transporter; Validated; Region: PRK03818 679935004903 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 679935004904 TrkA-C domain; Region: TrkA_C; pfam02080 679935004905 TrkA-C domain; Region: TrkA_C; pfam02080 679935004906 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 679935004907 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 679935004908 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 679935004909 homodimer interface [polypeptide binding]; other site 679935004910 Walker A motif; other site 679935004911 ATP binding site [chemical binding]; other site 679935004912 hydroxycobalamin binding site [chemical binding]; other site 679935004913 Walker B motif; other site 679935004914 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 679935004915 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 679935004916 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935004917 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 679935004918 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 679935004919 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 679935004920 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 679935004921 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 679935004922 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 679935004923 active site 679935004924 metal binding site [ion binding]; metal-binding site 679935004925 interdomain interaction site; other site 679935004926 Virulence-associated protein E; Region: VirE; pfam05272 679935004927 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935004928 HipA-like N-terminal domain; Region: HipA_N; pfam07805 679935004929 HipA-like C-terminal domain; Region: HipA_C; pfam07804 679935004930 HipA N-terminal domain; Region: couple_hipA; TIGR03071 679935004931 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935004932 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935004933 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935004934 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 679935004935 non-specific DNA binding site [nucleotide binding]; other site 679935004936 salt bridge; other site 679935004937 sequence-specific DNA binding site [nucleotide binding]; other site 679935004938 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 679935004939 active site 679935004940 Int/Topo IB signature motif; other site 679935004941 DNA binding site [nucleotide binding] 679935004942 Helix-turn-helix domain; Region: HTH_18; pfam12833 679935004943 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935004944 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG; TIGR02491 679935004945 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 679935004946 FeS/SAM binding site; other site 679935004947 ATP cone domain; Region: ATP-cone; pfam03477 679935004948 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08271 679935004949 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 679935004950 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 679935004951 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 679935004952 Predicted membrane protein [Function unknown]; Region: COG2246 679935004953 GtrA-like protein; Region: GtrA; pfam04138 679935004954 DPM1_like represents putative enzymes similar to eukaryotic DPM1; Region: DPM1_like; cd06442 679935004955 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 679935004956 Ligand binding site; other site 679935004957 Putative Catalytic site; other site 679935004958 DXD motif; other site 679935004959 A new structural DNA glycosylase; Region: AlkD_like; cd06561 679935004960 active site 679935004961 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 679935004962 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 679935004963 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 679935004964 putative acetyltransferase; Provisional; Region: PRK03624 679935004965 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 679935004966 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 679935004967 Membrane protein of unknown function (DUF340); Region: DUF340; pfam03956 679935004968 Transcriptional regulators [Transcription]; Region: MarR; COG1846 679935004969 Winged helix DNA-binding domain; Region: HTH_34; pfam13601 679935004970 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; cl01930 679935004971 2TM domain; Region: 2TM; pfam13239 679935004972 Domain of unknown function (DUF303); Region: DUF303; pfam03629 679935004973 Predicted acetyltransferase [General function prediction only]; Region: COG2388 679935004974 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 679935004975 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 679935004976 minor groove reading motif; other site 679935004977 helix-hairpin-helix signature motif; other site 679935004978 substrate binding pocket [chemical binding]; other site 679935004979 active site 679935004980 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 679935004981 DNA binding and oxoG recognition site [nucleotide binding] 679935004982 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 679935004983 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 679935004984 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 679935004985 zinc transporter ZupT; Provisional; Region: PRK04201 679935004986 Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]; Region: NagD; COG0647 679935004987 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 679935004988 active site 679935004989 motif I; other site 679935004990 motif II; other site 679935004991 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 679935004992 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 679935004993 Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins; Region: GDPD_AtGDE_like; cd08566 679935004994 putative active site [active] 679935004995 catalytic site [active] 679935004996 putative metal binding site [ion binding]; other site 679935004997 oligomer interface [polypeptide binding]; other site 679935004998 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 679935004999 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935005000 active site 679935005001 metal binding site [ion binding]; metal-binding site 679935005002 Glycerol-1-phosphate dehydrogenase (G1PDH) catalyzes the reversible reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in an NADH-dependent manner; Region: G1PDH; cd08175 679935005003 active site 679935005004 metal binding site [ion binding]; metal-binding site 679935005005 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 679935005006 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 679935005007 putative substrate translocation pore; other site 679935005008 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 679935005009 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 679935005010 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 679935005011 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935005012 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 679935005013 dihydroorotase; Validated; Region: pyrC; PRK09357 679935005014 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 679935005015 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 679935005016 active site 679935005017 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 679935005018 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 679935005019 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 679935005020 catalytic site [active] 679935005021 subunit interface [polypeptide binding]; other site 679935005022 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 679935005023 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 679935005024 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 679935005025 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 679935005026 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 679935005027 ATP-grasp domain; Region: ATP-grasp_4; cl17255 679935005028 Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways...; Region: MGS_CPS_II; cd01424 679935005029 IMP binding site; other site 679935005030 dimer interface [polypeptide binding]; other site 679935005031 interdomain contacts; other site 679935005032 partial ornithine binding site; other site 679935005033 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 679935005034 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 679935005035 FAD binding pocket [chemical binding]; other site 679935005036 FAD binding motif [chemical binding]; other site 679935005037 phosphate binding motif [ion binding]; other site 679935005038 beta-alpha-beta structure motif; other site 679935005039 NAD binding pocket [chemical binding]; other site 679935005040 Iron coordination center [ion binding]; other site 679935005041 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 679935005042 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 679935005043 heterodimer interface [polypeptide binding]; other site 679935005044 active site 679935005045 FMN binding site [chemical binding]; other site 679935005046 homodimer interface [polypeptide binding]; other site 679935005047 substrate binding site [chemical binding]; other site 679935005048 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 679935005049 active site 679935005050 dimer interface [polypeptide binding]; other site 679935005051 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 679935005052 catalytic residues [active] 679935005053 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 679935005054 active site 679935005055 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 679935005056 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 679935005057 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 679935005058 siderophore transporter, RhtX/FptX family; Region: sider_RhtX_FptX; TIGR02718 679935005059 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 679935005060 Domain of unknown function (DUF377); Region: DUF377; pfam04041 679935005061 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 679935005062 active site 679935005063 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 679935005064 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 679935005065 Glycosyl hydrolase family 67 N-terminus; Region: Glyco_hydro_67N; pfam03648 679935005066 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 679935005067 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 679935005068 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 679935005069 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 679935005070 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 679935005071 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 679935005072 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 679935005073 ATP-grasp domain; Region: ATP-grasp; pfam02222 679935005074 phosphoribosylformylglycinamidine synthase, clade II; Region: FGAM-synthase; TIGR01857 679935005075 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 679935005076 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 679935005077 dimerization interface [polypeptide binding]; other site 679935005078 ATP binding site [chemical binding]; other site 679935005079 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 679935005080 dimerization interface [polypeptide binding]; other site 679935005081 ATP binding site [chemical binding]; other site 679935005082 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 679935005083 putative active site [active] 679935005084 catalytic triad [active] 679935005085 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 679935005086 putative catalytic site [active] 679935005087 putative metal binding site [ion binding]; other site 679935005088 putative phosphate binding site [ion binding]; other site 679935005089 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 679935005090 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 679935005091 ATP binding site [chemical binding]; other site 679935005092 active site 679935005093 substrate binding site [chemical binding]; other site 679935005094 amidophosphoribosyltransferase; Provisional; Region: PRK07272 679935005095 Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the...; Region: GPATase_N; cd00715 679935005096 active site 679935005097 tetramer interface [polypeptide binding]; other site 679935005098 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 679935005099 active site 679935005100 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 679935005101 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 679935005102 dimerization interface [polypeptide binding]; other site 679935005103 putative ATP binding site [chemical binding]; other site 679935005104 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 679935005105 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 679935005106 active site 679935005107 substrate binding site [chemical binding]; other site 679935005108 cosubstrate binding site; other site 679935005109 catalytic site [active] 679935005110 Uncharacterized stress protein (general stress protein 26) [General function prediction only]; Region: COG3871 679935005111 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 679935005112 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 679935005113 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 679935005114 purine monophosphate binding site [chemical binding]; other site 679935005115 dimer interface [polypeptide binding]; other site 679935005116 putative catalytic residues [active] 679935005117 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 679935005118 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 679935005119 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 679935005120 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 679935005121 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 679935005122 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 679935005123 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]; Region: FolD; COG0190 679935005124 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 679935005125 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 679935005126 homodimer interface [polypeptide binding]; other site 679935005127 NADP binding site [chemical binding]; other site 679935005128 substrate binding site [chemical binding]; other site 679935005129 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 679935005130 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 679935005131 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 679935005132 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 679935005133 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 679935005134 Coenzyme A binding pocket [chemical binding]; other site 679935005135 Sulfatase; Region: Sulfatase; cl17466 679935005136 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 679935005137 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 679935005138 dimerization interface [polypeptide binding]; other site 679935005139 active site 679935005140 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 679935005141 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 679935005142 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 679935005143 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 679935005144 DNA binding residues [nucleotide binding] 679935005145 dimerization interface [polypeptide binding]; other site 679935005146 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 679935005147 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 679935005148 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 679935005149 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 679935005150 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 679935005151 putative dimer interface [polypeptide binding]; other site 679935005152 putative anticodon binding site; other site 679935005153 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 679935005154 motif 1; other site 679935005155 dimer interface [polypeptide binding]; other site 679935005156 active site 679935005157 motif 2; other site 679935005158 motif 3; other site 679935005159 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 679935005160 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 679935005161 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 679935005162 glutamate dehydrogenase; Provisional; Region: PRK09414 679935005163 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 679935005164 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 679935005165 NAD(P) binding site [chemical binding]; other site 679935005166 NAD synthetase; Reviewed; Region: nadE; PRK02628 679935005167 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 679935005168 multimer interface [polypeptide binding]; other site 679935005169 active site 679935005170 catalytic triad [active] 679935005171 protein interface 1 [polypeptide binding]; other site 679935005172 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 679935005173 homodimer interface [polypeptide binding]; other site 679935005174 NAD binding pocket [chemical binding]; other site 679935005175 ATP binding pocket [chemical binding]; other site 679935005176 Mg binding site [ion binding]; other site 679935005177 active-site loop [active] 679935005178 peptidase T; Region: peptidase-T; TIGR01882 679935005179 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 679935005180 metal binding site [ion binding]; metal-binding site 679935005181 dimer interface [polypeptide binding]; other site 679935005182 OPT oligopeptide transporter protein; Region: OPT; pfam03169 679935005183 putative oligopeptide transporter, OPT family; Region: TIGR00733 679935005184 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea; Region: NTP-PPase_u4; cd11541 679935005185 putative metal binding site [ion binding]; other site 679935005186 4-alpha-glucanotransferase; Region: PLN02950 679935005187 The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is...; Region: CBM20; cl15347 679935005188 starch-binding site 2 [chemical binding]; other site 679935005189 starch-binding site 1 [chemical binding]; other site 679935005190 The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is...; Region: CBM20; cl15347 679935005191 starch-binding site 2 [chemical binding]; other site 679935005192 starch-binding site 1 [chemical binding]; other site 679935005193 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 679935005194 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 679935005195 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 679935005196 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 679935005197 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 679935005198 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 679935005199 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 679935005200 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 679935005201 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 679935005202 Substrate binding site; other site 679935005203 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 679935005204 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 679935005205 Domain of unknown function (DUF4289); Region: DUF4289; pfam14121 679935005206 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 679935005207 N-acetyl-D-glucosamine binding site [chemical binding]; other site 679935005208 catalytic residue [active] 679935005209 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 679935005210 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 679935005211 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 679935005212 Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the Nudix hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most...; Region: Ap6A_hydrolase; cd03673 679935005213 active site 679935005214 Ap6A binding site [chemical binding]; other site 679935005215 nudix motif; other site 679935005216 metal binding site [ion binding]; metal-binding site 679935005217 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935005218 Walker A/P-loop; other site 679935005219 ATP binding site [chemical binding]; other site 679935005220 Q-loop/lid; other site 679935005221 ABC transporter signature motif; other site 679935005222 Walker B; other site 679935005223 D-loop; other site 679935005224 H-loop/switch region; other site 679935005225 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 679935005226 hydrophobic ligand binding site; other site 679935005227 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 679935005228 Response regulator receiver domain; Region: Response_reg; pfam00072 679935005229 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 679935005230 active site 679935005231 phosphorylation site [posttranslational modification] 679935005232 intermolecular recognition site; other site 679935005233 dimerization interface [polypeptide binding]; other site 679935005234 PglZ domain; Region: PglZ; pfam08665 679935005235 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 679935005236 IHF dimer interface [polypeptide binding]; other site 679935005237 IHF - DNA interface [nucleotide binding]; other site 679935005238 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 679935005239 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 679935005240 homodimer interface [polypeptide binding]; other site 679935005241 oligonucleotide binding site [chemical binding]; other site 679935005242 Predicted HD phosphohydrolase [General function prediction only]; Region: COG4341; cl17564 679935005243 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; pfam02559 679935005244 DEAD-like helicases superfamily; Region: DEXDc; smart00487 679935005245 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 679935005246 ATP binding site [chemical binding]; other site 679935005247 putative Mg++ binding site [ion binding]; other site 679935005248 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 679935005249 nucleotide binding region [chemical binding]; other site 679935005250 ATP-binding site [chemical binding]; other site 679935005251 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 679935005252 pantothenate kinase; Reviewed; Region: PRK13320 679935005253 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 679935005254 Tetratricopeptide repeat; Region: TPR_16; pfam13432 679935005255 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 679935005256 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 679935005257 Domain of unknown function DUF21; Region: DUF21; pfam01595 679935005258 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 679935005259 Transporter associated domain; Region: CorC_HlyC; smart01091 679935005260 SurA N-terminal domain; Region: SurA_N_3; cl07813 679935005261 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 679935005262 PPIC-type PPIASE domain; Region: Rotamase_3; pfam13616 679935005263 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 679935005264 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 679935005265 dimer interface [polypeptide binding]; other site 679935005266 active site 679935005267 metal binding site [ion binding]; metal-binding site 679935005268 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 679935005269 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 679935005270 active site 679935005271 substrate binding site [chemical binding]; other site 679935005272 coenzyme B12 binding site [chemical binding]; other site 679935005273 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 679935005274 B12 binding site [chemical binding]; other site 679935005275 cobalt ligand [ion binding]; other site 679935005276 methylmalonyl-CoA mutase, heterodimeric type, beta chain; Region: mmCoA_mut_beta; TIGR00642 679935005277 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 679935005278 heterodimer interface [polypeptide binding]; other site 679935005279 substrate interaction site [chemical binding]; other site 679935005280 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 679935005281 B12 binding site [chemical binding]; other site 679935005282 Glutamine synthetase type III N terminal; Region: GSIII_N; pfam12437 679935005283 Uncharacterized protein related to glutamine synthetase [General function prediction only]; Region: COG3968 679935005284 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 679935005285 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 679935005286 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: murQ; PRK05441 679935005287 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 679935005288 putative active site [active] 679935005289 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 679935005290 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 679935005291 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 679935005292 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935005293 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935005294 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935005295 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 679935005296 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 679935005297 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 679935005298 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935005299 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 679935005300 dimer interface [polypeptide binding]; other site 679935005301 phosphorylation site [posttranslational modification] 679935005302 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 679935005303 ATP binding site [chemical binding]; other site 679935005304 Mg2+ binding site [ion binding]; other site 679935005305 G-X-G motif; other site 679935005306 Response regulator receiver domain; Region: Response_reg; pfam00072 679935005307 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 679935005308 active site 679935005309 phosphorylation site [posttranslational modification] 679935005310 intermolecular recognition site; other site 679935005311 dimerization interface [polypeptide binding]; other site 679935005312 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 679935005313 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935005314 Domain of unknown function (DUF4185); Region: DUF4185; pfam13810 679935005315 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935005316 SusD family; Region: SusD; pfam07980 679935005317 Protein of unknown function (DUF2961); Region: DUF2961; pfam11175 679935005318 Protein of unknown function (DUF2961); Region: DUF2961; pfam11175 679935005319 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 679935005320 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 679935005321 putative substrate binding site [chemical binding]; other site 679935005322 putative ATP binding site [chemical binding]; other site 679935005323 D-xylose transporter XylE; Provisional; Region: xylE; PRK10077 679935005324 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 679935005325 putative substrate translocation pore; other site 679935005326 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 679935005327 putative transposase OrfB; Reviewed; Region: PHA02517 679935005328 HTH-like domain; Region: HTH_21; pfam13276 679935005329 Integrase core domain; Region: rve; pfam00665 679935005330 Integrase core domain; Region: rve_3; pfam13683 679935005331 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935005332 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935005333 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935005334 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 679935005335 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 679935005336 putative substrate translocation pore; other site 679935005337 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935005338 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935005339 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 679935005340 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935005341 FecR protein; Region: FecR; pfam04773 679935005342 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935005343 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935005344 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 679935005345 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 679935005346 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935005347 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 679935005348 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 679935005349 active site 679935005350 catalytic site [active] 679935005351 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 679935005352 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 679935005353 active site 679935005354 catalytic site [active] 679935005355 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GpsA; COG0240 679935005356 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 679935005357 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 679935005358 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 679935005359 putative catalytic site [active] 679935005360 putative metal binding site [ion binding]; other site 679935005361 putative phosphate binding site [ion binding]; other site 679935005362 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 679935005363 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 679935005364 TPP-binding site [chemical binding]; other site 679935005365 dimer interface [polypeptide binding]; other site 679935005366 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 679935005367 PYR/PP interface [polypeptide binding]; other site 679935005368 dimer interface [polypeptide binding]; other site 679935005369 TPP binding site [chemical binding]; other site 679935005370 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 679935005371 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 679935005372 Int/Topo IB signature motif; other site 679935005373 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 679935005374 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 679935005375 Int/Topo IB signature motif; other site 679935005376 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935005377 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935005378 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; cl10029 679935005379 Predicted metal-binding protein (DUF2284); Region: DUF2284; pfam10050 679935005380 ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CeuD; COG4604 679935005381 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 679935005382 Walker A/P-loop; other site 679935005383 ATP binding site [chemical binding]; other site 679935005384 Q-loop/lid; other site 679935005385 ABC transporter signature motif; other site 679935005386 Walker B; other site 679935005387 D-loop; other site 679935005388 H-loop/switch region; other site 679935005389 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 679935005390 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 679935005391 ABC-ATPase subunit interface; other site 679935005392 dimer interface [polypeptide binding]; other site 679935005393 putative PBP binding regions; other site 679935005394 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 679935005395 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 679935005396 putative ligand binding site [chemical binding]; other site 679935005397 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 679935005398 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 679935005399 Uncharacterized conserved protein [Function unknown]; Region: COG3391 679935005400 Putative glycoside hydrolase xylanase; Region: Xylanase; pfam13201 679935005401 Receptor L domain; Region: Recep_L_domain; pfam01030 679935005402 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 679935005403 active site 679935005404 Int/Topo IB signature motif; other site 679935005405 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 679935005406 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 679935005407 active site 679935005408 Int/Topo IB signature motif; other site 679935005409 DNA binding site [nucleotide binding] 679935005410 Penicillinase repressor; Region: Pencillinase_R; pfam03965 679935005411 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 679935005412 KWG Leptospira; Region: KWG; pfam07656 679935005413 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 679935005414 early DNA-binding protein E2A; Provisional; Region: PHA03384 679935005415 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 679935005416 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 679935005417 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 679935005418 active site 679935005419 HIGH motif; other site 679935005420 nucleotide binding site [chemical binding]; other site 679935005421 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 679935005422 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 679935005423 active site 679935005424 KMSKS motif; other site 679935005425 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 679935005426 tRNA binding surface [nucleotide binding]; other site 679935005427 anticodon binding site; other site 679935005428 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 679935005429 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935005430 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 679935005431 dimer interface [polypeptide binding]; other site 679935005432 phosphorylation site [posttranslational modification] 679935005433 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 679935005434 ATP binding site [chemical binding]; other site 679935005435 Mg2+ binding site [ion binding]; other site 679935005436 G-X-G motif; other site 679935005437 maltose O-acetyltransferase; Provisional; Region: PRK10092 679935005438 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 679935005439 active site 679935005440 substrate binding site [chemical binding]; other site 679935005441 trimer interface [polypeptide binding]; other site 679935005442 CoA binding site [chemical binding]; other site 679935005443 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 679935005444 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 679935005445 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 679935005446 Walker A/P-loop; other site 679935005447 ATP binding site [chemical binding]; other site 679935005448 Q-loop/lid; other site 679935005449 ABC transporter signature motif; other site 679935005450 Walker B; other site 679935005451 D-loop; other site 679935005452 H-loop/switch region; other site 679935005453 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 679935005454 RNA/DNA hybrid binding site [nucleotide binding]; other site 679935005455 active site 679935005456 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 679935005457 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 679935005458 active site 679935005459 HIGH motif; other site 679935005460 nucleotide binding site [chemical binding]; other site 679935005461 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 679935005462 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 679935005463 active site 679935005464 KMSKS motif; other site 679935005465 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 679935005466 tRNA binding surface [nucleotide binding]; other site 679935005467 anticodon binding site; other site 679935005468 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 679935005469 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 679935005470 Found in ATP-dependent protease La (LON); Region: LON; smart00464 679935005471 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 679935005472 Walker A motif; other site 679935005473 ATP binding site [chemical binding]; other site 679935005474 Walker B motif; other site 679935005475 arginine finger; other site 679935005476 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 679935005477 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 679935005478 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 679935005479 Ligand binding site; other site 679935005480 oligomer interface; other site 679935005481 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 679935005482 KpsF/GutQ family protein; Region: kpsF; TIGR00393 679935005483 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 679935005484 putative active site [active] 679935005485 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 679935005486 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2350 679935005487 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 679935005488 PAS fold; Region: PAS_4; pfam08448 679935005489 putative voltage-gated ClC-type chloride channel ClcB; Provisional; Region: PRK01862 679935005490 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 679935005491 Cl- selectivity filter; other site 679935005492 Cl- binding residues [ion binding]; other site 679935005493 pore gating glutamate residue; other site 679935005494 dimer interface [polypeptide binding]; other site 679935005495 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 679935005496 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 679935005497 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 679935005498 active site 679935005499 HIGH motif; other site 679935005500 dimer interface [polypeptide binding]; other site 679935005501 KMSKS motif; other site 679935005502 Transcriptional regulator [Transcription]; Region: LysR; COG0583 679935005503 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 679935005504 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 679935005505 dimerization interface [polypeptide binding]; other site 679935005506 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 679935005507 FtsH Extracellular; Region: FtsH_ext; pfam06480 679935005508 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 679935005509 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 679935005510 Walker A motif; other site 679935005511 ATP binding site [chemical binding]; other site 679935005512 Walker B motif; other site 679935005513 arginine finger; other site 679935005514 Peptidase family M41; Region: Peptidase_M41; pfam01434 679935005515 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 679935005516 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 679935005517 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 679935005518 Adenosylhomocysteinase; Provisional; Region: PTZ00075 679935005519 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 679935005520 homotetramer interface [polypeptide binding]; other site 679935005521 ligand binding site [chemical binding]; other site 679935005522 catalytic site [active] 679935005523 NAD binding site [chemical binding]; other site 679935005524 putative transposase OrfB; Reviewed; Region: PHA02517 679935005525 HTH-like domain; Region: HTH_21; pfam13276 679935005526 Integrase core domain; Region: rve; pfam00665 679935005527 Integrase core domain; Region: rve_2; pfam13333 679935005528 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935005529 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935005530 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935005531 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935005532 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 679935005533 Interdomain contacts; other site 679935005534 Cytokine receptor motif; other site 679935005535 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 679935005536 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 679935005537 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 679935005538 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 679935005539 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 679935005540 Protein of unknown function (DUF456); Region: DUF456; pfam04306 679935005541 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 679935005542 tetramerization interface [polypeptide binding]; other site 679935005543 active site 679935005544 pantoate--beta-alanine ligase; Region: panC; TIGR00018 679935005545 Pantoate-beta-alanine ligase; Region: PanC; cd00560 679935005546 active site 679935005547 ATP-binding site [chemical binding]; other site 679935005548 pantoate-binding site; other site 679935005549 HXXH motif; other site 679935005550 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 679935005551 Peptidase family M49; Region: Peptidase_M49; pfam03571 679935005552 Rubredoxin [Energy production and conversion]; Region: COG1773 679935005553 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 679935005554 iron binding site [ion binding]; other site 679935005555 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 679935005556 substrate binding site; other site 679935005557 dimer interface; other site 679935005558 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3787; cl17897 679935005559 putative peptidase; Provisional; Region: PRK11649 679935005560 Peptidase family M23; Region: Peptidase_M23; pfam01551 679935005561 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 679935005562 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 679935005563 purine nucleoside phosphorylase; Provisional; Region: PRK08202 679935005564 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 679935005565 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 679935005566 dimer interface [polypeptide binding]; other site 679935005567 ssDNA binding site [nucleotide binding]; other site 679935005568 tetramer (dimer of dimers) interface [polypeptide binding]; other site 679935005569 short chain dehydrogenase; Provisional; Region: PRK07024 679935005570 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 679935005571 NAD(P) binding site [chemical binding]; other site 679935005572 active site 679935005573 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 679935005574 catalytic motif [active] 679935005575 Zn binding site [ion binding]; other site 679935005576 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK12901 679935005577 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 679935005578 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 679935005579 nucleotide binding region [chemical binding]; other site 679935005580 ATP-binding site [chemical binding]; other site 679935005581 SEC-C motif; Region: SEC-C; pfam02810 679935005582 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 679935005583 active site 679935005584 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 679935005585 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 679935005586 active site 679935005587 Protein of unknown function (DUF2851); Region: DUF2851; pfam11013 679935005588 Domain of unknown function DUF59; Region: DUF59; cl00941 679935005589 Fe-S metabolism associated domain; Region: SufE; cl00951 679935005590 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 679935005591 GSCFA family; Region: GSCFA; pfam08885 679935005592 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14609 679935005593 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 679935005594 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 679935005595 Protein of unknown function (DUF454); Region: DUF454; cl01063 679935005596 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935005597 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935005598 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935005599 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935005600 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935005601 putative transposase OrfB; Reviewed; Region: PHA02517 679935005602 HTH-like domain; Region: HTH_21; pfam13276 679935005603 Integrase core domain; Region: rve; pfam00665 679935005604 Integrase core domain; Region: rve_2; pfam13333 679935005605 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 679935005606 Int/Topo IB signature motif; other site 679935005607 Domain of unknown function (DUF4377); Region: DUF4377; pfam14302 679935005608 Domain of unknown function (DUF4377); Region: DUF4377; pfam14302 679935005609 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 679935005610 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 679935005611 G1 box; other site 679935005612 putative GEF interaction site [polypeptide binding]; other site 679935005613 GTP/Mg2+ binding site [chemical binding]; other site 679935005614 Switch I region; other site 679935005615 G2 box; other site 679935005616 G3 box; other site 679935005617 Switch II region; other site 679935005618 G4 box; other site 679935005619 G5 box; other site 679935005620 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 679935005621 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 679935005622 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 679935005623 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 679935005624 active site 679935005625 dimer interface [polypeptide binding]; other site 679935005626 metal binding site [ion binding]; metal-binding site 679935005627 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 679935005628 Malic enzyme, N-terminal domain; Region: malic; pfam00390 679935005629 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 679935005630 putative NAD(P) binding site [chemical binding]; other site 679935005631 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 679935005632 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 679935005633 Walker A motif; other site 679935005634 ATP binding site [chemical binding]; other site 679935005635 Walker B motif; other site 679935005636 arginine finger; other site 679935005637 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 679935005638 NigD-like protein; Region: NigD; pfam12667 679935005639 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; Region: Sig-70_plancto1; TIGR02984 679935005640 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935005641 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 679935005642 DNA binding residues [nucleotide binding] 679935005643 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 679935005644 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 679935005645 Catalytic site [active] 679935005646 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 679935005647 Lumazine binding domain; Region: Lum_binding; pfam00677 679935005648 Lumazine binding domain; Region: Lum_binding; pfam00677 679935005649 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 679935005650 dimer interface [polypeptide binding]; other site 679935005651 phosphorylation site [posttranslational modification] 679935005652 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 679935005653 ATP binding site [chemical binding]; other site 679935005654 Mg2+ binding site [ion binding]; other site 679935005655 G-X-G motif; other site 679935005656 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 679935005657 GtrA-like protein; Region: GtrA; pfam04138 679935005658 TIGR04076 family protein; Region: TIGR04076 679935005659 excinuclease ABC subunit B; Provisional; Region: PRK05298 679935005660 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 679935005661 ATP binding site [chemical binding]; other site 679935005662 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 679935005663 nucleotide binding region [chemical binding]; other site 679935005664 ATP-binding site [chemical binding]; other site 679935005665 Ultra-violet resistance protein B; Region: UvrB; pfam12344 679935005666 UvrB/uvrC motif; Region: UVR; pfam02151 679935005667 DNA primase; Validated; Region: dnaG; PRK05667 679935005668 CHC2 zinc finger; Region: zf-CHC2; pfam01807 679935005669 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 679935005670 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 679935005671 active site 679935005672 metal binding site [ion binding]; metal-binding site 679935005673 interdomain interaction site; other site 679935005674 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 679935005675 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 679935005676 SmpB-tmRNA interface; other site 679935005677 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 679935005678 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 679935005679 active site 679935005680 motif I; other site 679935005681 motif II; other site 679935005682 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 679935005683 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 679935005684 Glycoprotease family; Region: Peptidase_M22; pfam00814 679935005685 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 679935005686 The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase; Region: GH31; cl11402 679935005687 active site 679935005688 catalytic site [active] 679935005689 RmuC family; Region: RmuC; pfam02646 679935005690 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935005691 Walker A/P-loop; other site 679935005692 ATP binding site [chemical binding]; other site 679935005693 ABC transporter; Region: ABC_tran; pfam00005 679935005694 Q-loop/lid; other site 679935005695 ABC transporter signature motif; other site 679935005696 Walker B; other site 679935005697 D-loop; other site 679935005698 H-loop/switch region; other site 679935005699 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 679935005700 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 679935005701 substrate binding site [chemical binding]; other site 679935005702 hexamer interface [polypeptide binding]; other site 679935005703 metal binding site [ion binding]; metal-binding site 679935005704 HD domain; Region: HD_3; pfam13023 679935005705 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 679935005706 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935005707 Walker A/P-loop; other site 679935005708 ATP binding site [chemical binding]; other site 679935005709 Q-loop/lid; other site 679935005710 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 679935005711 ABC transporter signature motif; other site 679935005712 Walker B; other site 679935005713 D-loop; other site 679935005714 ABC transporter; Region: ABC_tran_2; pfam12848 679935005715 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 679935005716 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 679935005717 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 679935005718 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 679935005719 Domain of unknown function (DUF4153); Region: DUF4153; pfam13687 679935005720 Protein of unknown function DUF45; Region: DUF45; pfam01863 679935005721 sn-glycerol-3-phosphate transporter; Provisional; Region: glpT; PRK11273 679935005722 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 679935005723 putative substrate translocation pore; other site 679935005724 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 679935005725 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 679935005726 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; pfam08220 679935005727 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 679935005728 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 679935005729 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 679935005730 DNA binding residues [nucleotide binding] 679935005731 dimerization interface [polypeptide binding]; other site 679935005732 Protein of unknown function (DUF1349); Region: DUF1349; pfam07081 679935005733 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 679935005734 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 679935005735 active site 679935005736 catalytic site [active] 679935005737 Galactokinase [Carbohydrate transport and metabolism]; Region: GalK; COG0153 679935005738 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 679935005739 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 679935005740 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 679935005741 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 679935005742 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 679935005743 Coenzyme A binding pocket [chemical binding]; other site 679935005744 MarR family; Region: MarR_2; pfam12802 679935005745 Transcriptional regulators [Transcription]; Region: MarR; COG1846 679935005746 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 679935005747 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 679935005748 nucleotide binding site [chemical binding]; other site 679935005749 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 679935005750 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 679935005751 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 679935005752 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 679935005753 active site 679935005754 trimer interface [polypeptide binding]; other site 679935005755 allosteric site; other site 679935005756 active site lid [active] 679935005757 hexamer (dimer of trimers) interface [polypeptide binding]; other site 679935005758 glucosamine-6-phosphate deaminase-like protein; Validated; Region: PRK02122 679935005759 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 679935005760 active site 679935005761 trimer interface [polypeptide binding]; other site 679935005762 allosteric site; other site 679935005763 active site lid [active] 679935005764 hexamer (dimer of trimers) interface [polypeptide binding]; other site 679935005765 GlcNAc-PI de-N-acetylase; Region: PIG-L; pfam02585 679935005766 DOMON-like type 9 carbohydrate binding module; Region: CBM9_like_3; cd09620 679935005767 putative ligand binding site [chemical binding]; other site 679935005768 Phosphotransferase enzyme family; Region: APH; pfam01636 679935005769 Phosphomannose isomerase [Carbohydrate transport and metabolism]; Region: ManA; COG1482 679935005770 Alpha-Mannosidase Binding Domain of Atg19/34; Region: ABD; cl15429 679935005771 ligand binding site [chemical binding]; other site 679935005772 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 679935005773 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 679935005774 nucleotide binding site [chemical binding]; other site 679935005775 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 679935005776 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 679935005777 putative substrate translocation pore; other site 679935005778 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 679935005779 putative catalytic site [active] 679935005780 putative metal binding site [ion binding]; other site 679935005781 putative phosphate binding site [ion binding]; other site 679935005782 putative transposase OrfB; Reviewed; Region: PHA02517 679935005783 HTH-like domain; Region: HTH_21; pfam13276 679935005784 Integrase core domain; Region: rve; pfam00665 679935005785 Integrase core domain; Region: rve_3; pfam13683 679935005786 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 679935005787 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 679935005788 Domain of unknown function (DUF4249); Region: DUF4249; pfam14054 679935005789 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 679935005790 binding surface 679935005791 TPR motif; other site 679935005792 Tetratricopeptide repeat; Region: TPR_12; pfam13424 679935005793 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 679935005794 binding surface 679935005795 TPR motif; other site 679935005796 JmjC domain, hydroxylase; Region: JmjC; pfam02373 679935005797 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 679935005798 active site 679935005799 NTP binding site [chemical binding]; other site 679935005800 metal binding triad [ion binding]; metal-binding site 679935005801 HEPN domain; Region: HEPN; pfam05168 679935005802 BRO family, N-terminal domain; Region: Bro-N; smart01040 679935005803 Methyltransferase domain; Region: Methyltransf_31; pfam13847 679935005804 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 679935005805 S-adenosylmethionine binding site [chemical binding]; other site 679935005806 Peptidase S8 family domain, uncharacterized subfamily 15; Region: Peptidases_S8_15; cd07498 679935005807 active site 679935005808 catalytic triad [active] 679935005809 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 679935005810 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 679935005811 binding surface 679935005812 TPR motif; other site 679935005813 Protein of unknown function (DUF4099); Region: DUF4099; pfam13351 679935005814 Protein of unknown function (DUF3945); Region: DUF3945; pfam13101 679935005815 Protein of unknown function (DUF4099); Region: DUF4099; pfam13351 679935005816 Major fimbrial subunit protein (FimA); Region: P_gingi_FimA; pfam06321 679935005817 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 679935005818 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 679935005819 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 679935005820 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 679935005821 active site 679935005822 DNA binding site [nucleotide binding] 679935005823 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 679935005824 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 679935005825 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 679935005826 Catalytic site [active] 679935005827 ORF6N domain; Region: ORF6N; pfam10543 679935005828 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 679935005829 Int/Topo IB signature motif; other site 679935005830 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 679935005831 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 679935005832 TPR motif; other site 679935005833 binding surface 679935005834 TPR repeat; Region: TPR_11; pfam13414 679935005835 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 679935005836 binding surface 679935005837 TPR motif; other site 679935005838 TPR repeat; Region: TPR_11; pfam13414 679935005839 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 679935005840 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 679935005841 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 679935005842 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 679935005843 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 679935005844 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 679935005845 active site 679935005846 DNA binding site [nucleotide binding] 679935005847 Int/Topo IB signature motif; other site 679935005848 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 679935005849 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 679935005850 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 679935005851 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N_2; pfam13588 679935005852 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 679935005853 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 679935005854 active site 679935005855 phosphorylation site [posttranslational modification] 679935005856 intermolecular recognition site; other site 679935005857 dimerization interface [polypeptide binding]; other site 679935005858 LytTr DNA-binding domain; Region: LytTR; smart00850 679935005859 Histidine kinase; Region: His_kinase; pfam06580 679935005860 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 679935005861 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 679935005862 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 679935005863 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 679935005864 acyl-activating enzyme (AAE) consensus motif; other site 679935005865 AMP binding site [chemical binding]; other site 679935005866 active site 679935005867 CoA binding site [chemical binding]; other site 679935005868 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 679935005869 Uncharacterized conserved protein [Function unknown]; Region: COG1284 679935005870 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 679935005871 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 679935005872 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 679935005873 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14329 679935005874 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 679935005875 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 679935005876 FeS/SAM binding site; other site 679935005877 TRAM domain; Region: TRAM; pfam01938 679935005878 DEAD-like helicases superfamily; Region: DEXDc; smart00487 679935005879 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 679935005880 ATP binding site [chemical binding]; other site 679935005881 Mg++ binding site [ion binding]; other site 679935005882 motif III; other site 679935005883 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 679935005884 nucleotide binding region [chemical binding]; other site 679935005885 ATP-binding site [chemical binding]; other site 679935005886 GTP-binding protein Der; Reviewed; Region: PRK00093 679935005887 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 679935005888 G1 box; other site 679935005889 GTP/Mg2+ binding site [chemical binding]; other site 679935005890 Switch I region; other site 679935005891 G2 box; other site 679935005892 Switch II region; other site 679935005893 G3 box; other site 679935005894 G4 box; other site 679935005895 G5 box; other site 679935005896 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 679935005897 G1 box; other site 679935005898 GTP/Mg2+ binding site [chemical binding]; other site 679935005899 Switch I region; other site 679935005900 G2 box; other site 679935005901 G3 box; other site 679935005902 Switch II region; other site 679935005903 G4 box; other site 679935005904 G5 box; other site 679935005905 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 679935005906 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 679935005907 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 679935005908 Ligand Binding Site [chemical binding]; other site 679935005909 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 679935005910 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 679935005911 putative substrate translocation pore; other site 679935005912 Outer membrane protein beta-barrel domain; Region: OMP_b-brl_2; pfam13568 679935005913 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 679935005914 PhoH-like protein; Region: PhoH; pfam02562 679935005915 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 679935005916 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 679935005917 metal binding site [ion binding]; metal-binding site 679935005918 dimer interface [polypeptide binding]; other site 679935005919 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 679935005920 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 679935005921 PEGA domain; Region: PEGA; pfam08308 679935005922 SnoaL-like domain; Region: SnoaL_2; pfam12680 679935005923 Protein of unknown function (DUF419); Region: DUF419; pfam04237 679935005924 Nicotinamide mononucleotide transporter; Region: NMN_transporter; cl01256 679935005925 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 679935005926 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 679935005927 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 679935005928 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 679935005929 D-xylose transporter XylE; Provisional; Region: xylE; PRK10077 679935005930 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 679935005931 putative substrate translocation pore; other site 679935005932 xylose isomerase; Provisional; Region: PRK05474 679935005933 xylose isomerase; Region: xylose_isom_A; TIGR02630 679935005934 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 679935005935 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 679935005936 nucleotide binding site [chemical binding]; other site 679935005937 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 679935005938 nudix motif; other site 679935005939 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 679935005940 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 679935005941 active site 679935005942 catalytic residues [active] 679935005943 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 679935005944 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 679935005945 HIGH motif; other site 679935005946 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 679935005947 active site 679935005948 KMSKS motif; other site 679935005949 GTP-binding protein YchF; Reviewed; Region: PRK09601 679935005950 YchF GTPase; Region: YchF; cd01900 679935005951 G1 box; other site 679935005952 GTP/Mg2+ binding site [chemical binding]; other site 679935005953 Switch I region; other site 679935005954 G2 box; other site 679935005955 Switch II region; other site 679935005956 G3 box; other site 679935005957 G4 box; other site 679935005958 G5 box; other site 679935005959 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 679935005960 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 679935005961 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 679935005962 domain in bacterial beta-glucosidases other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins; Region: PA14; smart00758 679935005963 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 679935005964 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 679935005965 Transcriptional regulators [Transcription]; Region: PurR; COG1609 679935005966 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 679935005967 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935005968 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 679935005969 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 679935005970 Fn3 associated; Region: Fn3_assoc; pfam13287 679935005971 domain in bacterial beta-glucosidases other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins; Region: PA14; smart00758 679935005972 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 679935005973 putative catalytic site [active] 679935005974 putative metal binding site [ion binding]; other site 679935005975 putative phosphate binding site [ion binding]; other site 679935005976 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases; Region: PI-PLCc_GDPD_SF_unchar3; cd08577 679935005977 putative active site [active] 679935005978 catalytic site [active] 679935005979 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 679935005980 Alkaline phosphatase homologues; Region: alkPPc; smart00098 679935005981 active site 679935005982 dimer interface [polypeptide binding]; other site 679935005983 Glycogen debranching enzyme [Carbohydrate transport and metabolism]; Region: GDB1; COG3408 679935005984 Trehalase; Region: Trehalase; cl17346 679935005985 Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain; Region: MPP_Dcr2; cd07383 679935005986 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 679935005987 putative active site [active] 679935005988 putative metal binding site [ion binding]; other site 679935005989 Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain; Region: MPP_Dcr2; cd07383 679935005990 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 679935005991 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 679935005992 nucleotide binding site [chemical binding]; other site 679935005993 Glycosyl hydrolase family 20, domain 2; Region: Glyco_hydro_20b; pfam02838 679935005994 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 679935005995 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 679935005996 active site 679935005997 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK13108 679935005998 Predicted methyltransferases [General function prediction only]; Region: COG0313 679935005999 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 679935006000 putative SAM binding site [chemical binding]; other site 679935006001 putative homodimer interface [polypeptide binding]; other site 679935006002 Domain of unknown function (DUF389); Region: DUF389; pfam04087 679935006003 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 679935006004 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 679935006005 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 679935006006 putative acyl-acceptor binding pocket; other site 679935006007 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 679935006008 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 679935006009 Probable Catalytic site; other site 679935006010 metal-binding site 679935006011 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 679935006012 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935006013 GyrI-like small molecule binding domain; Region: GyrI-like; pfam06445 679935006014 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 679935006015 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 679935006016 active site 679935006017 HIGH motif; other site 679935006018 nucleotide binding site [chemical binding]; other site 679935006019 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 679935006020 KMSKS motif; other site 679935006021 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 679935006022 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 679935006023 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 679935006024 active site 679935006025 oligomerization interface [polypeptide binding]; other site 679935006026 metal binding site [ion binding]; metal-binding site 679935006027 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 679935006028 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 679935006029 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 679935006030 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 679935006031 active site 679935006032 Protein of unknown function (DUF3795); Region: DUF3795; pfam12675 679935006033 GMP synthase; Reviewed; Region: guaA; PRK00074 679935006034 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 679935006035 AMP/PPi binding site [chemical binding]; other site 679935006036 candidate oxyanion hole; other site 679935006037 catalytic triad [active] 679935006038 potential glutamine specificity residues [chemical binding]; other site 679935006039 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 679935006040 ATP Binding subdomain [chemical binding]; other site 679935006041 Ligand Binding sites [chemical binding]; other site 679935006042 Dimerization subdomain; other site 679935006043 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 679935006044 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 679935006045 putative substrate translocation pore; other site 679935006046 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 679935006047 active site 679935006048 catalytic triad [active] 679935006049 oxyanion hole [active] 679935006050 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 679935006051 active site 679935006052 catalytic site [active] 679935006053 substrate binding site [chemical binding]; other site 679935006054 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 679935006055 dimer interface [polypeptide binding]; other site 679935006056 catalytic triad [active] 679935006057 peroxidatic and resolving cysteines [active] 679935006058 Uncharacterized conserved protein [Function unknown]; Region: COG1359 679935006059 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 679935006060 active site 679935006061 Int/Topo IB signature motif; other site 679935006062 DNA binding site [nucleotide binding] 679935006063 Domain of unknown function (DUF4373); Region: DUF4373; pfam14297 679935006064 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 679935006065 IHF - DNA interface [nucleotide binding]; other site 679935006066 IHF dimer interface [polypeptide binding]; other site 679935006067 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 679935006068 Active Sites [active] 679935006069 Radical SAM superfamily; Region: Radical_SAM; pfam04055 679935006070 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 679935006071 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; cl17257 679935006072 DNA binding residues [nucleotide binding] 679935006073 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 679935006074 S-adenosylmethionine binding site [chemical binding]; other site 679935006075 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 679935006076 DEAD-like helicases superfamily; Region: DEXDc; smart00487 679935006077 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 679935006078 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 679935006079 nucleotide binding region [chemical binding]; other site 679935006080 ATP-binding site [chemical binding]; other site 679935006081 KilA-N domain; Region: KilA-N; pfam04383 679935006082 salt bridge; other site 679935006083 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 679935006084 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 679935006085 non-specific DNA binding site [nucleotide binding]; other site 679935006086 salt bridge; other site 679935006087 sequence-specific DNA binding site [nucleotide binding]; other site 679935006088 large terminase protein; Provisional; Region: 17; PHA02533 679935006089 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 679935006090 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 679935006091 active site 679935006092 metal binding site [ion binding]; metal-binding site 679935006093 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 679935006094 putative ABC transporter; Region: ycf24; CHL00085 679935006095 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 679935006096 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 679935006097 FeS assembly ATPase SufC; Region: sufC; TIGR01978 679935006098 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 679935006099 Walker A/P-loop; other site 679935006100 ATP binding site [chemical binding]; other site 679935006101 Q-loop/lid; other site 679935006102 ABC transporter signature motif; other site 679935006103 Walker B; other site 679935006104 D-loop; other site 679935006105 H-loop/switch region; other site 679935006106 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 679935006107 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 679935006108 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 679935006109 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 679935006110 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 679935006111 catalytic residue [active] 679935006112 Thymidylate kinase [Nucleotide transport and metabolism]; Region: Tmk; COG0125 679935006113 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 679935006114 TMP-binding site; other site 679935006115 ATP-binding site [chemical binding]; other site 679935006116 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 679935006117 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 679935006118 HlyD family secretion protein; Region: HlyD_3; pfam13437 679935006119 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 679935006120 Outer membrane efflux protein; Region: OEP; pfam02321 679935006121 Outer membrane efflux protein; Region: OEP; pfam02321 679935006122 OsmC-like protein; Region: OsmC; pfam02566 679935006123 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 679935006124 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 679935006125 binding surface 679935006126 TPR motif; other site 679935006127 Bladder cancer-related protein BC10; Region: BC10; cl17570 679935006128 Protein of unknown function (DUF2089); Region: DUF2089; pfam09862 679935006129 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 679935006130 YceG-like family; Region: YceG; pfam02618 679935006131 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 679935006132 dimerization interface [polypeptide binding]; other site 679935006133 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 679935006134 Protein of unknown function (DUF4199); Region: DUF4199; pfam13858 679935006135 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 679935006136 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 679935006137 Ligand binding site; other site 679935006138 Putative Catalytic site; other site 679935006139 DXD motif; other site 679935006140 Domain of unknown function (DUF4293); Region: DUF4293; pfam14126 679935006141 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935006142 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935006143 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cl00089 679935006144 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 679935006145 active site 679935006146 substrate binding site [chemical binding]; other site 679935006147 Mg2+ binding site [ion binding]; other site 679935006148 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 679935006149 putative catalytic site [active] 679935006150 putative metal binding site [ion binding]; other site 679935006151 putative phosphate binding site [ion binding]; other site 679935006152 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 679935006153 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 679935006154 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 679935006155 Sulfatase; Region: Sulfatase; pfam00884 679935006156 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 679935006157 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 679935006158 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 679935006159 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 679935006160 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 679935006161 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 679935006162 salt bridge; other site 679935006163 non-specific DNA binding site [nucleotide binding]; other site 679935006164 sequence-specific DNA binding site [nucleotide binding]; other site 679935006165 Protein of unknown function (DUF975); Region: DUF975; cl10504 679935006166 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 679935006167 Acyl-ACP thioesterase; Region: Acyl-ACP_TE; pfam01643 679935006168 active site 679935006169 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 679935006170 active site 679935006171 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 679935006172 Ferritin-like domain; Region: Ferritin; pfam00210 679935006173 heme binding site [chemical binding]; other site 679935006174 ferroxidase pore; other site 679935006175 ferroxidase diiron center [ion binding]; other site 679935006176 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935006177 This family is most closely related to the GT1 family of glycosyltransferases. ORF704 in E. coli has been shown to be involved in the biosynthesis of O-specific mannose homopolysaccharides; Region: GT1_ecORF704_like; cd03822 679935006178 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 679935006179 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 679935006180 non-specific DNA binding site [nucleotide binding]; other site 679935006181 salt bridge; other site 679935006182 sequence-specific DNA binding site [nucleotide binding]; other site 679935006183 Cupin domain; Region: Cupin_2; pfam07883 679935006184 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 679935006185 Major Facilitator Superfamily; Region: MFS_1; pfam07690 679935006186 putative substrate translocation pore; other site 679935006187 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 679935006188 TPR motif; other site 679935006189 binding surface 679935006190 TPR repeat; Region: TPR_11; pfam13414 679935006191 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 679935006192 binding surface 679935006193 TPR repeat; Region: TPR_11; pfam13414 679935006194 TPR motif; other site 679935006195 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 679935006196 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 679935006197 binding surface 679935006198 TPR motif; other site 679935006199 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 679935006200 binding surface 679935006201 TPR motif; other site 679935006202 TPR repeat; Region: TPR_11; pfam13414 679935006203 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 679935006204 TPR motif; other site 679935006205 TPR repeat; Region: TPR_11; pfam13414 679935006206 binding surface 679935006207 GTPase Era; Reviewed; Region: era; PRK00089 679935006208 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 679935006209 G1 box; other site 679935006210 GTP/Mg2+ binding site [chemical binding]; other site 679935006211 Switch I region; other site 679935006212 G2 box; other site 679935006213 Switch II region; other site 679935006214 G3 box; other site 679935006215 G4 box; other site 679935006216 G5 box; other site 679935006217 KH domain; Region: KH_2; pfam07650 679935006218 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 679935006219 putative FMN binding site [chemical binding]; other site 679935006220 signal recognition particle protein; Provisional; Region: PRK10867 679935006221 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 679935006222 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 679935006223 P loop; other site 679935006224 GTP binding site [chemical binding]; other site 679935006225 Signal peptide binding domain; Region: SRP_SPB; pfam02978 679935006226 Domain of unknown function (DUF4294); Region: DUF4294; pfam14127 679935006227 Predicted thioesterase [General function prediction only]; Region: COG5496 679935006228 NHAD transporter family protein; Provisional; Region: PLN00137 679935006229 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 679935006230 TSCPD domain; Region: TSCPD; cl14834 679935006231 Preprotein translocase subunit; Region: YajC; pfam02699 679935006232 Protein of unknown function (DUF1573); Region: DUF1573; pfam07610 679935006233 transcription antitermination factor NusB; Region: nusB; TIGR01951 679935006234 flavoprotein, HI0933 family; Region: TIGR00275 679935006235 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 679935006236 Protein of unknown function (DUF2795); Region: DUF2795; pfam11387 679935006237 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 679935006238 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935006239 active site 679935006240 metal binding site [ion binding]; metal-binding site 679935006241 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935006242 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935006243 Susd and RagB outer membrane lipoprotein; Region: SusD-like; pfam12741 679935006244 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935006245 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935006246 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935006247 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 679935006248 Methyltransferase domain; Region: Methyltransf_23; pfam13489 679935006249 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 679935006250 S-adenosylmethionine binding site [chemical binding]; other site 679935006251 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4627 679935006252 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 679935006253 S1 domain; Region: S1_2; pfam13509 679935006254 S1 domain; Region: S1_2; pfam13509 679935006255 Predicted acyl esterases [General function prediction only]; Region: COG2936 679935006256 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 679935006257 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; smart00939 679935006258 C-N hydrolase family amidase; Provisional; Region: PRK10438 679935006259 Xanthomonas campestris XC1258 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases); Region: Xc-1258_like; cd07575 679935006260 putative active site [active] 679935006261 catalytic triad [active] 679935006262 dimer interface [polypeptide binding]; other site 679935006263 multimer interface [polypeptide binding]; other site 679935006264 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 679935006265 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 679935006266 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 679935006267 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 679935006268 Domain of unknown function (DUF4251); Region: DUF4251; pfam14059 679935006269 Domain of unknown function (DUF4251); Region: DUF4251; pfam14059 679935006270 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 679935006271 homotrimer interaction site [polypeptide binding]; other site 679935006272 zinc binding site [ion binding]; other site 679935006273 CDP-binding sites; other site 679935006274 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 679935006275 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 679935006276 metal binding site [ion binding]; metal-binding site 679935006277 dimer interface [polypeptide binding]; other site 679935006278 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 679935006279 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 679935006280 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 679935006281 hexamer interface [polypeptide binding]; other site 679935006282 ligand binding site [chemical binding]; other site 679935006283 putative active site [active] 679935006284 NAD(P) binding site [chemical binding]; other site 679935006285 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 679935006286 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935006287 Walker A/P-loop; other site 679935006288 ATP binding site [chemical binding]; other site 679935006289 Q-loop/lid; other site 679935006290 ABC transporter signature motif; other site 679935006291 Walker B; other site 679935006292 D-loop; other site 679935006293 H-loop/switch region; other site 679935006294 GTPase CgtA; Reviewed; Region: obgE; PRK12299 679935006295 GTP1/OBG; Region: GTP1_OBG; pfam01018 679935006296 Obg GTPase; Region: Obg; cd01898 679935006297 G1 box; other site 679935006298 GTP/Mg2+ binding site [chemical binding]; other site 679935006299 Switch I region; other site 679935006300 G2 box; other site 679935006301 G3 box; other site 679935006302 Switch II region; other site 679935006303 G4 box; other site 679935006304 G5 box; other site 679935006305 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_1; cd04870 679935006306 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_2; cd04871 679935006307 phosphoserine phosphatase SerB; Region: serB; TIGR00338 679935006308 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 679935006309 motif II; other site 679935006310 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 679935006311 Mechanosensitive ion channel; Region: MS_channel; pfam00924 679935006312 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 679935006313 active site 679935006314 dimer interfaces [polypeptide binding]; other site 679935006315 catalytic residues [active] 679935006316 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 679935006317 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 679935006318 FMN binding site [chemical binding]; other site 679935006319 active site 679935006320 catalytic residues [active] 679935006321 substrate binding site [chemical binding]; other site 679935006322 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 679935006323 Domain of unknown function DUF21; Region: DUF21; pfam01595 679935006324 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 679935006325 Transporter associated domain; Region: CorC_HlyC; smart01091 679935006326 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 679935006327 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 679935006328 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 679935006329 active site 679935006330 HIGH motif; other site 679935006331 nucleotide binding site [chemical binding]; other site 679935006332 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 679935006333 KMSK motif region; other site 679935006334 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 679935006335 tRNA binding surface [nucleotide binding]; other site 679935006336 anticodon binding site; other site 679935006337 putative transposase OrfB; Reviewed; Region: PHA02517 679935006338 HTH-like domain; Region: HTH_21; pfam13276 679935006339 Integrase core domain; Region: rve; pfam00665 679935006340 Integrase core domain; Region: rve_2; pfam13333 679935006341 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935006342 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935006343 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 679935006344 Helix-turn-helix domain; Region: HTH_28; pfam13518 679935006345 putative hydrolase; Provisional; Region: PRK02113 679935006346 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 679935006347 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 679935006348 short chain dehydrogenase; Provisional; Region: PRK06181 679935006349 NAD(P) binding site [chemical binding]; other site 679935006350 active site 679935006351 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 679935006352 Sec-independent protein secretion pathway components [Intracellular trafficking and secretion]; Region: TatA; COG1826 679935006353 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 679935006354 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 679935006355 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 679935006356 active site 679935006357 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 679935006358 G1 box; other site 679935006359 GTP/Mg2+ binding site [chemical binding]; other site 679935006360 Switch I region; other site 679935006361 G2 box; other site 679935006362 G3 box; other site 679935006363 Switch II region; other site 679935006364 G4 box; other site 679935006365 G5 box; other site 679935006366 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 679935006367 putative catalytic site [active] 679935006368 putative metal binding site [ion binding]; other site 679935006369 putative phosphate binding site [ion binding]; other site 679935006370 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 679935006371 Linear amide C-N hydrolases, choloylglycine hydrolase family; Region: CBAH; pfam02275 679935006372 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 679935006373 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 679935006374 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935006375 Walker A/P-loop; other site 679935006376 ATP binding site [chemical binding]; other site 679935006377 ABC transporter signature motif; other site 679935006378 Walker B; other site 679935006379 D-loop; other site 679935006380 H-loop/switch region; other site 679935006381 ABC transporter; Region: ABC_tran_2; pfam12848 679935006382 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 679935006383 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 679935006384 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 679935006385 dimer interface [polypeptide binding]; other site 679935006386 active site 679935006387 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 679935006388 catalytic residues [active] 679935006389 substrate binding site [chemical binding]; other site 679935006390 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 679935006391 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 679935006392 Walker A motif; other site 679935006393 ATP binding site [chemical binding]; other site 679935006394 Walker B motif; other site 679935006395 arginine finger; other site 679935006396 Lipopolysaccharide-assembly; Region: LptE; pfam04390 679935006397 Preprotein translocase SecG subunit; Region: SecG; pfam03840 679935006398 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 679935006399 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 679935006400 Uncharacterized conserved protein [Function unknown]; Region: COG1624 679935006401 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 679935006402 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 679935006403 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 679935006404 RuvA N terminal domain; Region: RuvA_N; pfam01330 679935006405 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 679935006406 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 679935006407 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 679935006408 nucleotide binding site [chemical binding]; other site 679935006409 NEF interaction site [polypeptide binding]; other site 679935006410 SBD interface [polypeptide binding]; other site 679935006411 Alpha-L-fucosidase; Region: Alpha_L_fucos; pfam01120 679935006412 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 679935006413 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 679935006414 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 679935006415 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 679935006416 Protein export membrane protein; Region: SecD_SecF; pfam02355 679935006417 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 679935006418 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 679935006419 CoA-binding site [chemical binding]; other site 679935006420 ATP-binding [chemical binding]; other site 679935006421 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 679935006422 dihydropteroate synthase; Region: DHPS; TIGR01496 679935006423 substrate binding pocket [chemical binding]; other site 679935006424 dimer interface [polypeptide binding]; other site 679935006425 inhibitor binding site; inhibition site 679935006426 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 679935006427 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 679935006428 Walker A/P-loop; other site 679935006429 ATP binding site [chemical binding]; other site 679935006430 Q-loop/lid; other site 679935006431 ABC transporter signature motif; other site 679935006432 Walker B; other site 679935006433 D-loop; other site 679935006434 H-loop/switch region; other site 679935006435 Protein of unknown function (DUF2400); Region: DUF2400; pfam09674 679935006436 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 679935006437 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 679935006438 S-adenosylmethionine binding site [chemical binding]; other site 679935006439 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 679935006440 A new structural DNA glycosylase; Region: AlkD_like; cl11434 679935006441 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 679935006442 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 679935006443 catalytic residues [active] 679935006444 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 679935006445 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 679935006446 NAD(P) binding site [chemical binding]; other site 679935006447 active site 679935006448 DNA repair protein RadA; Provisional; Region: PRK11823 679935006449 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 679935006450 Walker A motif/ATP binding site; other site 679935006451 ATP binding site [chemical binding]; other site 679935006452 Walker B motif; other site 679935006453 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 679935006454 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 679935006455 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 679935006456 RIP metalloprotease RseP; Region: TIGR00054 679935006457 active site 679935006458 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 679935006459 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 679935006460 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 679935006461 putative substrate binding region [chemical binding]; other site 679935006462 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 679935006463 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 679935006464 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 679935006465 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 679935006466 Peptidase family M23; Region: Peptidase_M23; pfam01551 679935006467 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 679935006468 active site 679935006469 Chain length determinant protein; Region: Wzz; cl15801 679935006470 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 679935006471 capsular exopolysaccharide family; Region: eps_fam; TIGR01007 679935006472 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 679935006473 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 679935006474 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 679935006475 SLBB domain; Region: SLBB; pfam10531 679935006476 Alpha amylase catalytic domain found in archaeal and bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_arch_bac_AmyA; cd11313 679935006477 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 679935006478 active site 679935006479 catalytic site [active] 679935006480 Repair protein; Region: Repair_PSII; pfam04536 679935006481 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 679935006482 EamA-like transporter family; Region: EamA; pfam00892 679935006483 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935006484 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 679935006485 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 679935006486 Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Region: HTH_BmrR; cd01107 679935006487 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 679935006488 DNA binding residues [nucleotide binding] 679935006489 drug binding residues [chemical binding]; other site 679935006490 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 679935006491 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 679935006492 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 679935006493 putative acyl-acceptor binding pocket; other site 679935006494 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 679935006495 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 679935006496 ATP binding site [chemical binding]; other site 679935006497 Mg2+ binding site [ion binding]; other site 679935006498 G-X-G motif; other site 679935006499 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 679935006500 anchoring element; other site 679935006501 dimer interface [polypeptide binding]; other site 679935006502 ATP binding site [chemical binding]; other site 679935006503 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 679935006504 active site 679935006505 putative metal-binding site [ion binding]; other site 679935006506 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 679935006507 DNA topoisomerase IV subunit A; Provisional; Region: PRK12758 679935006508 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 679935006509 CAP-like domain; other site 679935006510 active site 679935006511 shikimate kinase; Reviewed; Region: aroK; PRK00131 679935006512 shikimate kinase II; Reviewed; Region: aroL; cl17327 679935006513 glutamate racemase; Provisional; Region: PRK00865 679935006514 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 679935006515 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 679935006516 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 679935006517 This domain directs oriented DNA translocation and forms a winged helix structure; Region: Ftsk_gamma; smart00843 679935006518 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 679935006519 DNA gyrase subunit A; Validated; Region: PRK05560 679935006520 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 679935006521 CAP-like domain; other site 679935006522 active site 679935006523 primary dimer interface [polypeptide binding]; other site 679935006524 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 679935006525 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 679935006526 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 679935006527 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 679935006528 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 679935006529 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 679935006530 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 679935006531 binding surface 679935006532 TPR motif; other site 679935006533 Predicted ATPase [General function prediction only]; Region: COG3910 679935006534 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935006535 Walker A/P-loop; other site 679935006536 ATP binding site [chemical binding]; other site 679935006537 Q-loop/lid; other site 679935006538 ABC transporter signature motif; other site 679935006539 Walker B; other site 679935006540 D-loop; other site 679935006541 H-loop/switch region; other site 679935006542 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 679935006543 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 679935006544 Invertebrate innate immunity transcript family; Region: Innate_immun; pfam12782 679935006545 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 679935006546 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 679935006547 RNA binding surface [nucleotide binding]; other site 679935006548 Pseudouridine synthases, RsuA subfamily; Region: PseudoU_synth_RsuA_like; cd02870 679935006549 active site 679935006550 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935006551 Clostripain family; Region: Peptidase_C11; pfam03415 679935006552 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 679935006553 dihydrodipicolinate synthase; Region: dapA; TIGR00674 679935006554 dimer interface [polypeptide binding]; other site 679935006555 active site 679935006556 catalytic residue [active] 679935006557 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 679935006558 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 679935006559 nucleotide binding pocket [chemical binding]; other site 679935006560 K-X-D-G motif; other site 679935006561 catalytic site [active] 679935006562 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 679935006563 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 679935006564 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 679935006565 Dimer interface [polypeptide binding]; other site 679935006566 BRCT sequence motif; other site 679935006567 Leucine Rich repeats (2 copies); Region: LRR_4; pfam12799 679935006568 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 679935006569 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 679935006570 GDP-binding site [chemical binding]; other site 679935006571 ACT binding site; other site 679935006572 IMP binding site; other site 679935006573 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 679935006574 Ligand binding site [chemical binding]; other site 679935006575 Electron transfer flavoprotein domain; Region: ETF; pfam01012 679935006576 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 679935006577 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 679935006578 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 679935006579 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 679935006580 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 679935006581 active site 679935006582 Acyl-CoA dehydrogenase C terminal; Region: AcylCoA_dehyd_C; pfam12186 679935006583 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 679935006584 non-specific DNA binding site [nucleotide binding]; other site 679935006585 salt bridge; other site 679935006586 sequence-specific DNA binding site [nucleotide binding]; other site 679935006587 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 679935006588 non-specific DNA binding site [nucleotide binding]; other site 679935006589 salt bridge; other site 679935006590 sequence-specific DNA binding site [nucleotide binding]; other site 679935006591 glutaminase; Reviewed; Region: PRK12356 679935006592 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 679935006593 putative glutamate/gamma-aminobutyrate antiporter; Region: put_Glu_GABA_T; TIGR03813 679935006594 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 679935006595 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 679935006596 Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either...; Region: rubredoxin_like; cl00202 679935006597 iron binding site [ion binding]; other site 679935006598 Rubrerythrin [Energy production and conversion]; Region: COG1592 679935006599 rubrerythrin-like, diiron-binding domain; Region: Rubrerythrin_like; cd01046 679935006600 diiron binding motif [ion binding]; other site 679935006601 Protein of unknown function (DUF1273); Region: DUF1273; cl01859 679935006602 Protein of unknown function (DUF1273); Region: DUF1273; cl01859 679935006603 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases; Region: PFK; cl00204 679935006604 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 679935006605 active site 679935006606 ADP/pyrophosphate binding site [chemical binding]; other site 679935006607 dimerization interface [polypeptide binding]; other site 679935006608 allosteric effector site; other site 679935006609 fructose-1,6-bisphosphate binding site; other site 679935006610 Domain of unknown function (DUF4377); Region: DUF4377; pfam14302 679935006611 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 679935006612 DNA-binding site [nucleotide binding]; DNA binding site 679935006613 RNA-binding motif; other site 679935006614 radical SAM enzyme, rSAM/lipoprotein system; Region: rSAM_w_lipo; TIGR04133 679935006615 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 679935006616 FeS/SAM binding site; other site 679935006617 Domain of unknown function (DUF4008); Region: DUF4008; cl14869 679935006618 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 679935006619 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 679935006620 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 679935006621 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 679935006622 motif II; other site 679935006623 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 679935006624 classical (c) SDRs; Region: SDR_c; cd05233 679935006625 NAD(P) binding site [chemical binding]; other site 679935006626 active site 679935006627 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 679935006628 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 679935006629 active site 679935006630 FMN binding site [chemical binding]; other site 679935006631 substrate binding site [chemical binding]; other site 679935006632 putative catalytic residue [active] 679935006633 3-oxo-5-alpha-steroid 4-dehydrogenase; Region: Steroid_dh; cl17474 679935006634 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 679935006635 tyrosine decarboxylase MnfA; Region: tyr_de_CO2_Arch; TIGR03812 679935006636 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935006637 catalytic residue [active] 679935006638 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 679935006639 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. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_2; cd03402 679935006640 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4877 679935006641 NAD-dependent deacetylase; Provisional; Region: PRK00481 679935006642 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 679935006643 NAD+ binding site [chemical binding]; other site 679935006644 substrate binding site [chemical binding]; other site 679935006645 Zn binding site [ion binding]; other site 679935006646 membrane ATPase/protein kinase; Provisional; Region: PRK09435 679935006647 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 679935006648 Walker A; other site 679935006649 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 679935006650 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 679935006651 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935006652 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 679935006653 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 679935006654 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 679935006655 dimer interface [polypeptide binding]; other site 679935006656 substrate binding site [chemical binding]; other site 679935006657 metal binding site [ion binding]; metal-binding site 679935006658 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 679935006659 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 679935006660 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 679935006661 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK05641 679935006662 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 679935006663 carboxyltransferase (CT) interaction site; other site 679935006664 biotinylation site [posttranslational modification]; other site 679935006665 Na+-transporting oxaloacetate decarboxylase beta subunit; Region: OAD_beta; cl00816 679935006666 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 679935006667 23S rRNA interface [nucleotide binding]; other site 679935006668 L3 interface [polypeptide binding]; other site 679935006669 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 679935006670 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 679935006671 rRNA interaction site [nucleotide binding]; other site 679935006672 S8 interaction site; other site 679935006673 putative laminin-1 binding site; other site 679935006674 elongation factor Ts; Provisional; Region: tsf; PRK09377 679935006675 UBA/TS-N domain; Region: UBA; pfam00627 679935006676 Elongation factor TS; Region: EF_TS; pfam00889 679935006677 Elongation factor TS; Region: EF_TS; pfam00889 679935006678 HprK-related kinase A; Region: HprK_rel_A; TIGR04352 679935006679 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 679935006680 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 679935006681 Walker A/P-loop; other site 679935006682 ATP binding site [chemical binding]; other site 679935006683 Q-loop/lid; other site 679935006684 ABC transporter signature motif; other site 679935006685 Walker B; other site 679935006686 D-loop; other site 679935006687 H-loop/switch region; other site 679935006688 Part of AAA domain; Region: AAA_19; pfam13245 679935006689 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 679935006690 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 679935006691 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 679935006692 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 679935006693 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 679935006694 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 679935006695 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 679935006696 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 679935006697 Peptidase family M23; Region: Peptidase_M23; pfam01551 679935006698 Peptidase family M23; Region: Peptidase_M23; pfam01551 679935006699 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 679935006700 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 679935006701 motif 1; other site 679935006702 active site 679935006703 motif 2; other site 679935006704 motif 3; other site 679935006705 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 679935006706 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 679935006707 phosphoglyceromutase; Provisional; Region: PRK05434 679935006708 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 679935006709 putative deacylase active site [active] 679935006710 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 679935006711 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 679935006712 putative ligand binding site [chemical binding]; other site 679935006713 putative NAD binding site [chemical binding]; other site 679935006714 catalytic site [active] 679935006715 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 679935006716 putative ATP binding site [chemical binding]; other site 679935006717 putative substrate interface [chemical binding]; other site 679935006718 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 679935006719 active site 679935006720 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 679935006721 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 679935006722 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 679935006723 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 679935006724 Rubredoxin; Region: Rubredoxin; pfam00301 679935006725 iron binding site [ion binding]; other site 679935006726 FMN-binding domain; Region: FMN_bind; cl01081 679935006727 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 679935006728 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 679935006729 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 679935006730 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 679935006731 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 679935006732 catalytic loop [active] 679935006733 iron binding site [ion binding]; other site 679935006734 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 679935006735 FAD binding pocket [chemical binding]; other site 679935006736 FAD binding motif [chemical binding]; other site 679935006737 phosphate binding motif [ion binding]; other site 679935006738 beta-alpha-beta structure motif; other site 679935006739 NAD binding pocket [chemical binding]; other site 679935006740 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 679935006741 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 679935006742 Protein of unknown function (DUF2776); Region: DUF2776; pfam10951 679935006743 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 679935006744 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 679935006745 motif II; other site 679935006746 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 679935006747 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 679935006748 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 679935006749 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 679935006750 Domain of unknown function DUF20; Region: UPF0118; pfam01594 679935006751 pyruvate carboxylase subunit B; Validated; Region: PRK09282 679935006752 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 679935006753 active site 679935006754 catalytic residues [active] 679935006755 metal binding site [ion binding]; metal-binding site 679935006756 homodimer binding site [polypeptide binding]; other site 679935006757 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 679935006758 carboxyltransferase (CT) interaction site; other site 679935006759 biotinylation site [posttranslational modification]; other site 679935006760 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 679935006761 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 679935006762 Ion channel; Region: Ion_trans_2; pfam07885 679935006763 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]; Region: HisI; COG0139 679935006764 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 679935006765 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 679935006766 metal binding site [ion binding]; metal-binding site 679935006767 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 679935006768 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 679935006769 substrate binding site [chemical binding]; other site 679935006770 glutamase interaction surface [polypeptide binding]; other site 679935006771 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 679935006772 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 679935006773 catalytic residues [active] 679935006774 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13181 679935006775 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 679935006776 putative active site [active] 679935006777 oxyanion strand; other site 679935006778 catalytic triad [active] 679935006779 histidinol-phosphatase; Region: hisB_Nterm; TIGR01261 679935006780 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 679935006781 active site 679935006782 motif I; other site 679935006783 motif II; other site 679935006784 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 679935006785 4-fold oligomerization interface [polypeptide binding]; other site 679935006786 putative active site pocket [active] 679935006787 metal binding residues [ion binding]; metal-binding site 679935006788 3-fold/trimer interface [polypeptide binding]; other site 679935006789 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 679935006790 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 679935006791 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935006792 homodimer interface [polypeptide binding]; other site 679935006793 catalytic residue [active] 679935006794 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 679935006795 histidinol dehydrogenase; Region: hisD; TIGR00069 679935006796 NAD binding site [chemical binding]; other site 679935006797 dimerization interface [polypeptide binding]; other site 679935006798 product binding site; other site 679935006799 substrate binding site [chemical binding]; other site 679935006800 zinc binding site [ion binding]; other site 679935006801 catalytic residues [active] 679935006802 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 679935006803 ATP phosphoribosyltransferase; Region: hisG; TIGR00070 679935006804 ATP phosphoribosyltransferase, C-terminal domain; Region: HisG_C-term; TIGR03455 679935006805 Protein of unknown function (DUF1271); Region: DUF1271; pfam06902 679935006806 Na(+)/iodide (NIS) and Na(+)/multivitamin (SMVT) cotransporters, and related proteins; solute binding domain; Region: SLC5sbd_NIS-like; cd10326 679935006807 Na binding site [ion binding]; other site 679935006808 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 679935006809 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 679935006810 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 679935006811 Interdomain contacts; other site 679935006812 Cytokine receptor motif; other site 679935006813 Yqey-like protein; Region: YqeY; pfam09424 679935006814 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 679935006815 catalytic motif [active] 679935006816 Catalytic residue [active] 679935006817 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 679935006818 Protein of unknown function, DUF486; Region: DUF486; cl01236 679935006819 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 679935006820 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 679935006821 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 679935006822 motif II; other site 679935006823 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 679935006824 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935006825 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 679935006826 putative deacylase active site [active] 679935006827 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935006828 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_6; cd04955 679935006829 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG0535 679935006830 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 679935006831 FeS/SAM binding site; other site 679935006832 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 679935006833 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935006834 This family is most closely related to the GT1 family of glycosyltransferases. ExpE7 in Sinorhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucans (exopolysaccharide II); Region: GT1_ExpE7_like; cd03823 679935006835 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 679935006836 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 679935006837 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935006838 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935006839 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 679935006840 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 679935006841 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 679935006842 putative ADP-binding pocket [chemical binding]; other site 679935006843 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 679935006844 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 679935006845 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 679935006846 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term; Region: FrhB_FdhB_N; pfam04422 679935006847 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus; Region: FrhB_FdhB_C; pfam04432 679935006848 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 679935006849 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 679935006850 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 679935006851 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 679935006852 NAD binding site [chemical binding]; other site 679935006853 substrate binding site [chemical binding]; other site 679935006854 homodimer interface [polypeptide binding]; other site 679935006855 active site 679935006856 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 679935006857 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 679935006858 NADP binding site [chemical binding]; other site 679935006859 active site 679935006860 putative substrate binding site [chemical binding]; other site 679935006861 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 679935006862 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 679935006863 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 679935006864 substrate binding site; other site 679935006865 tetramer interface; other site 679935006866 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 679935006867 Bacterial sugar transferase; Region: Bac_transf; pfam02397 679935006868 Transcription antiterminator [Transcription]; Region: NusG; COG0250 679935006869 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; Region: NGN_SP_UpxY; cd09895 679935006870 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 679935006871 homodimer interface [polypeptide binding]; other site 679935006872 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 679935006873 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 679935006874 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 679935006875 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 679935006876 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 679935006877 ligand binding site [chemical binding]; other site 679935006878 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 679935006879 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 679935006880 dimer interface [polypeptide binding]; other site 679935006881 active site 679935006882 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 679935006883 catalytic residues [active] 679935006884 substrate binding site [chemical binding]; other site 679935006885 cysteate synthase; Region: cysteate_syn; TIGR03844 679935006886 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 679935006887 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 679935006888 catalytic residue [active] 679935006889 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 679935006890 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 679935006891 glutamate formiminotransferase; Region: FtcD; TIGR02024 679935006892 Formiminotransferase domain, N-terminal subdomain; Region: FTCD_N; pfam07837 679935006893 Formiminotransferase domain; Region: FTCD; pfam02971 679935006894 Formiminotransferase-cyclodeaminase; Region: FTCD_C; pfam04961 679935006895 urocanate hydratase; Provisional; Region: PRK05414 679935006896 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 679935006897 active sites [active] 679935006898 tetramer interface [polypeptide binding]; other site 679935006899 imidazolonepropionase; Validated; Region: PRK09356 679935006900 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 679935006901 active site 679935006902 bifunctional methionine sulfoxide reductase B/A protein; Provisional; Region: PRK05550 679935006903 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229; cl15841 679935006904 methionine sulfoxide reductase A; Provisional; Region: PRK14054 679935006905 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 679935006906 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 679935006907 trimer interface [polypeptide binding]; other site 679935006908 active site 679935006909 substrate binding site [chemical binding]; other site 679935006910 CoA binding site [chemical binding]; other site 679935006911 Domain of unknown function (DUF1848); Region: DUF1848; pfam08902 679935006912 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 679935006913 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 679935006914 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935006915 homodimer interface [polypeptide binding]; other site 679935006916 catalytic residue [active] 679935006917 Cysteine dioxygenase type I; Region: CDO_I; pfam05995 679935006918 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 679935006919 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 679935006920 S-adenosylmethionine binding site [chemical binding]; other site 679935006921 AAA domain; Region: AAA_30; pfam13604 679935006922 AAA domain; Region: AAA_22; pfam13401 679935006923 Family description; Region: UvrD_C_2; pfam13538 679935006924 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 679935006925 putative active site [active] 679935006926 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 679935006927 MutS domain I; Region: MutS_I; pfam01624 679935006928 MutS domain II; Region: MutS_II; pfam05188 679935006929 MutS domain III; Region: MutS_III; pfam05192 679935006930 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 679935006931 Walker A/P-loop; other site 679935006932 ATP binding site [chemical binding]; other site 679935006933 Q-loop/lid; other site 679935006934 ABC transporter signature motif; other site 679935006935 Walker B; other site 679935006936 D-loop; other site 679935006937 H-loop/switch region; other site 679935006938 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 679935006939 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 679935006940 ATP-binding site [chemical binding]; other site 679935006941 Sugar specificity; other site 679935006942 Pyrimidine base specificity; other site 679935006943 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 679935006944 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 679935006945 ATP binding site [chemical binding]; other site 679935006946 Mg2+ binding site [ion binding]; other site 679935006947 G-X-G motif; other site 679935006948 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 679935006949 anchoring element; other site 679935006950 dimer interface [polypeptide binding]; other site 679935006951 ATP binding site [chemical binding]; other site 679935006952 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 679935006953 active site 679935006954 putative metal-binding site [ion binding]; other site 679935006955 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 679935006956 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 679935006957 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935006958 Walker A/P-loop; other site 679935006959 ATP binding site [chemical binding]; other site 679935006960 Q-loop/lid; other site 679935006961 ABC transporter signature motif; other site 679935006962 Walker B; other site 679935006963 D-loop; other site 679935006964 H-loop/switch region; other site 679935006965 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 679935006966 GAF domain; Region: GAF; pfam01590 679935006967 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 679935006968 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 679935006969 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 679935006970 dimer interface [polypeptide binding]; other site 679935006971 phosphorylation site [posttranslational modification] 679935006972 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 679935006973 ATP binding site [chemical binding]; other site 679935006974 Mg2+ binding site [ion binding]; other site 679935006975 G-X-G motif; other site 679935006976 Response regulator receiver domain; Region: Response_reg; pfam00072 679935006977 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 679935006978 active site 679935006979 phosphorylation site [posttranslational modification] 679935006980 intermolecular recognition site; other site 679935006981 dimerization interface [polypeptide binding]; other site 679935006982 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 679935006983 active site 679935006984 DNA binding site [nucleotide binding] 679935006985 Int/Topo IB signature motif; other site 679935006986 Domain of unknown function (DUF4114); Region: DUF4114; pfam13448 679935006987 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 679935006988 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935006989 active site 679935006990 metal binding site [ion binding]; metal-binding site 679935006991 PQQ-like domain; Region: PQQ_2; pfam13360 679935006992 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 679935006993 active site 679935006994 Trp docking motif [polypeptide binding]; other site 679935006995 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 679935006996 ATP-grasp domain; Region: ATP-grasp; pfam02222 679935006997 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 679935006998 active site 679935006999 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 679935007000 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 679935007001 LL-diaminopimelate aminotransferase; Provisional; Region: PRK09276 679935007002 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 679935007003 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935007004 homodimer interface [polypeptide binding]; other site 679935007005 catalytic residue [active] 679935007006 putative transporter; Validated; Region: PRK03818 679935007007 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 679935007008 TrkA-C domain; Region: TrkA_C; pfam02080 679935007009 TrkA-C domain; Region: TrkA_C; pfam02080 679935007010 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 679935007011 LrgB-like family; Region: LrgB; pfam04172 679935007012 LrgA family; Region: LrgA; pfam03788 679935007013 FeoA domain; Region: FeoA; pfam04023 679935007014 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 679935007015 ferrous iron transporter FeoB; Region: feoB; TIGR00437 679935007016 G1 box; other site 679935007017 GTP/Mg2+ binding site [chemical binding]; other site 679935007018 Switch I region; other site 679935007019 G2 box; other site 679935007020 G3 box; other site 679935007021 Switch II region; other site 679935007022 G4 box; other site 679935007023 G5 box; other site 679935007024 Nucleoside recognition; Region: Gate; pfam07670 679935007025 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 679935007026 Nucleoside recognition; Region: Gate; pfam07670 679935007027 Nucleoside recognition; Region: Gate; pfam07670 679935007028 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 679935007029 Sulfatase; Region: Sulfatase; pfam00884 679935007030 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 679935007031 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 679935007032 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 679935007033 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 679935007034 HlyD family secretion protein; Region: HlyD_3; pfam13437 679935007035 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 679935007036 Sulfatase; Region: Sulfatase; cl17466 679935007037 Surface antigen; Region: Bac_surface_Ag; pfam01103 679935007038 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 679935007039 Low molecular weight phosphatase family; Region: LMWPc; cd00115 679935007040 active site 679935007041 Chloramphenicol O-acetyltransferase [Defense mechanisms]; Region: COG4845 679935007042 Chloramphenicol acetyltransferase; Region: CAT; smart01059 679935007043 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 679935007044 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 679935007045 NAD(P) binding site [chemical binding]; other site 679935007046 homotetramer interface [polypeptide binding]; other site 679935007047 homodimer interface [polypeptide binding]; other site 679935007048 active site 679935007049 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 679935007050 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 679935007051 dimer interface [polypeptide binding]; other site 679935007052 active site 679935007053 glycine-pyridoxal phosphate binding site [chemical binding]; other site 679935007054 folate binding site [chemical binding]; other site 679935007055 Conserved hypothetical protein (DUF2461); Region: DUF2461; pfam09365 679935007056 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 679935007057 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 679935007058 Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]; Region: MtlA; COG2213 679935007059 PTS system, mannitol-specific IIC component; Region: mtlA; TIGR00851 679935007060 PTS_IIB_mannitol: subunit IIB of enzyme II (EII) of the mannitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a mannitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane...; Region: PTS_IIB_mannitol; cd05567 679935007061 active site 679935007062 P-loop; other site 679935007063 phosphorylation site [posttranslational modification] 679935007064 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 679935007065 active site 679935007066 phosphorylation site [posttranslational modification] 679935007067 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 679935007068 dimerization domain swap beta strand [polypeptide binding]; other site 679935007069 regulatory protein interface [polypeptide binding]; other site 679935007070 active site 679935007071 regulatory phosphorylation site [posttranslational modification]; other site 679935007072 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 679935007073 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 679935007074 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 679935007075 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 679935007076 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 679935007077 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 679935007078 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 679935007079 FecR protein; Region: FecR; pfam04773 679935007080 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935007081 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935007082 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 679935007083 DNA binding residues [nucleotide binding] 679935007084 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 679935007085 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935007086 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935007087 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935007088 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 679935007089 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 679935007090 starch binding outer membrane protein SusD; Region: SusD; cl17845 679935007091 SusD family; Region: SusD; pfam07980 679935007092 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 679935007093 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 679935007094 active site 679935007095 metal binding site [ion binding]; metal-binding site 679935007096 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 679935007097 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 679935007098 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 679935007099 active site 679935007100 catalytic site [active] 679935007101 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935007102 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935007103 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 679935007104 starch binding outer membrane protein SusD; Region: SusD; cd08977 679935007105 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935007106 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 679935007107 TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region; Region: SusC_RagA_signa; TIGR04057 679935007108 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 679935007109 FecR protein; Region: FecR; pfam04773 679935007110 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 679935007111 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 679935007112 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 679935007113 DNA binding residues [nucleotide binding] 679935007114 mannitol-1-phosphate 5-dehydrogenase; Provisional; Region: PRK02318 679935007115 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 679935007116 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 679935007117 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 679935007118 Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins; Region: GDPD_AtGDE_like; cd08566 679935007119 putative active site [active] 679935007120 catalytic site [active] 679935007121 putative metal binding site [ion binding]; other site 679935007122 oligomer interface [polypeptide binding]; other site 679935007123 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 679935007124 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 679935007125 putative substrate translocation pore; other site 679935007126 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 679935007127 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 679935007128 glutaminase active site [active] 679935007129 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 679935007130 dimer interface [polypeptide binding]; other site 679935007131 active site 679935007132 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 679935007133 dimer interface [polypeptide binding]; other site 679935007134 active site 679935007135 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935007136 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935007137 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935007138 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 679935007139 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 679935007140 active site 679935007141 dimerization interface [polypeptide binding]; other site 679935007142 hypothetical protein; Validated; Region: PRK09104 679935007143 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_3; cd05680 679935007144 metal binding site [ion binding]; metal-binding site 679935007145 putative dimer interface [polypeptide binding]; other site 679935007146 NlpE N-terminal domain; Region: NlpE; pfam04170 679935007147 phosphoglucosamine mutase; Region: Arch_GlmM; TIGR03990 679935007148 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 679935007149 active site 679935007150 substrate binding site [chemical binding]; other site 679935007151 metal binding site [ion binding]; metal-binding site 679935007152 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 679935007153 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 679935007154 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 679935007155 DNA polymerase III subunit beta; Validated; Region: PRK05643 679935007156 putative DNA binding surface [nucleotide binding]; other site 679935007157 dimer interface [polypeptide binding]; other site 679935007158 beta-clamp/translesion DNA polymerase binding surface; other site 679935007159 beta-clamp/clamp loader binding surface; other site 679935007160 DNA polymerase III subunit epsilon; Validated; Region: PRK06310 679935007161 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 679935007162 active site 679935007163 catalytic site [active] 679935007164 substrate binding site [chemical binding]; other site 679935007165 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 679935007166 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 679935007167 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 679935007168 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 679935007169 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 679935007170 ligand binding site [chemical binding]; other site 679935007171 redox-sensing transcriptional repressor Rex; Provisional; Region: PRK05472 679935007172 Putative DNA-binding protein N-terminus; Region: Put_DNA-bind_N; pfam06971 679935007173 CoA binding domain; Region: CoA_binding; pfam02629 679935007174 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 679935007175 active site 679935007176 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 679935007177 active site 679935007178 heat shock protein 90; Provisional; Region: PRK05218 679935007179 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 679935007180 ATP binding site [chemical binding]; other site 679935007181 Mg2+ binding site [ion binding]; other site 679935007182 G-X-G motif; other site 679935007183 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 679935007184 putative FMN binding site [chemical binding]; other site 679935007185 TIGR03503 family protein; Region: TIGR03503 679935007186 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 679935007187 Domain of unknown function (DUF4377); Region: DUF4377; pfam14302 679935007188 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 679935007189 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 679935007190 Int/Topo IB signature motif; other site 679935007191 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 679935007192 Transposase; Region: DEDD_Tnp_IS110; pfam01548 679935007193 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 679935007194 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 679935007195 putative transposase OrfB; Reviewed; Region: PHA02517 679935007196 HTH-like domain; Region: HTH_21; pfam13276 679935007197 Integrase core domain; Region: rve; pfam00665 679935007198 Integrase core domain; Region: rve_3; pfam13683 679935007199 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 679935007200 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 679935007201 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 679935007202 Uncharacterized protein conserved in Bacteroidetes; Region: DUF4425; cd11379 679935007203 dimer interface [polypeptide binding]; other site 679935007204 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 679935007205 DNA binding residues [nucleotide binding] 679935007206 OmpA family; Region: OmpA; pfam00691 679935007207 Protein of unknown function (DUF3575); Region: DUF3575; pfam12099 679935007208 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 679935007209 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 679935007210 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 679935007211 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 679935007212 Helix-turn-helix domain; Region: HTH_17; cl17695 679935007213 Helix-turn-helix domain; Region: HTH_17; pfam12728 679935007214 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 679935007215 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 679935007216 Int/Topo IB signature motif; other site 679935007217 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 679935007218 Transposase DDE domain; Region: DDE_Tnp_1_3; pfam13612 679935007219 aldose 1-epimerase superfamily; Region: Aldose_epim; cd01081 679935007220 active site 679935007221 catalytic residues [active] 679935007222 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 679935007223 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 679935007224 catalytic residues [active] 679935007225 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 679935007226 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 679935007227 active site 679935007228 PHP Thumb interface [polypeptide binding]; other site 679935007229 metal binding site [ion binding]; metal-binding site 679935007230 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 679935007231 generic binding surface I; other site 679935007232 generic binding surface II; other site 679935007233 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 679935007234 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 679935007235 Shikimate 5-dehydrogenase [Amino acid transport and metabolism]; Region: AroE; COG0169 679935007236 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 679935007237 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 679935007238 shikimate binding site; other site 679935007239 NAD(P) binding site [chemical binding]; other site 679935007240 Domain of unknown function (DUF368); Region: DUF368; pfam04018 679935007241 Protein of unknown function (DUF3276); Region: DUF3276; pfam11680 679935007242 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 679935007243 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 679935007244 protein binding site [polypeptide binding]; other site 679935007245 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 679935007246 Catalytic dyad [active] 679935007247 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 679935007248 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 679935007249 dimer interface [polypeptide binding]; other site 679935007250 motif 1; other site 679935007251 active site 679935007252 motif 2; other site 679935007253 motif 3; other site 679935007254 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 679935007255 anticodon binding site; other site 679935007256 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 679935007257 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 679935007258 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 679935007259 ABC transporter; Region: ABC_tran_2; pfam12848 679935007260 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 679935007261 Rubrerythrin [Energy production and conversion]; Region: COG1592 679935007262 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 679935007263 binuclear metal center [ion binding]; other site 679935007264 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 679935007265 iron binding site [ion binding]; other site 679935007266 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 679935007267 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 679935007268 putative active site [active] 679935007269 putative metal binding site [ion binding]; other site 679935007270 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 679935007271 EamA-like transporter family; Region: EamA; pfam00892 679935007272 EamA-like transporter family; Region: EamA; pfam00892 679935007273 methylaspartate ammonia-lyase; Region: B_methylAsp_ase; TIGR01502 679935007274 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 679935007275 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 679935007276 putative active site [active] 679935007277 putative metal binding site [ion binding]; other site 679935007278 RibD C-terminal domain; Region: RibD_C; cl17279 679935007279 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 679935007280 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 679935007281 catalytic motif [active] 679935007282 Zn binding site [ion binding]; other site 679935007283 Outer membrane efflux protein; Region: OEP; pfam02321 679935007284 Outer membrane efflux protein; Region: OEP; pfam02321 679935007285 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 679935007286 HlyD family secretion protein; Region: HlyD_3; pfam13437 679935007287 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 679935007288 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 679935007289 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 679935007290 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 679935007291 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 679935007292 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 679935007293 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 679935007294 active site 679935007295 phosphorylation site [posttranslational modification] 679935007296 intermolecular recognition site; other site 679935007297 dimerization interface [polypeptide binding]; other site 679935007298 LytTr DNA-binding domain; Region: LytTR; smart00850 679935007299 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 679935007300 RNA binding site [nucleotide binding]; other site 679935007301 Histidine kinase; Region: His_kinase; pfam06580 679935007302 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 679935007303 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 679935007304 trimer interface [polypeptide binding]; other site 679935007305 putative metal binding site [ion binding]; other site 679935007306 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 679935007307 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 679935007308 homodimer interface [polypeptide binding]; other site 679935007309 metal binding site [ion binding]; metal-binding site 679935007310 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 679935007311 homodimer interface [polypeptide binding]; other site 679935007312 active site 679935007313 putative chemical substrate binding site [chemical binding]; other site 679935007314 metal binding site [ion binding]; metal-binding site 679935007315 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 679935007316 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 679935007317 active site 679935007318 Restriction endonuclease BglII; Region: Endonuc-BglII; pfam09195 679935007319 YhhN-like protein; Region: YhhN; pfam07947 679935007320 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 679935007321 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 679935007322 putative tRNA-binding site [nucleotide binding]; other site 679935007323 B3/4 domain; Region: B3_4; pfam03483 679935007324 tRNA synthetase B5 domain; Region: B5; pfam03484 679935007325 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 679935007326 dimer interface [polypeptide binding]; other site 679935007327 motif 1; other site 679935007328 motif 3; other site 679935007329 motif 2; other site 679935007330 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 679935007331 tryptophan synthase subunit beta; Reviewed; Region: PRK12391 679935007332 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 679935007333 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 679935007334 catalytic residue [active] 679935007335 EamA-like transporter family; Region: EamA; cl17759 679935007336 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 679935007337 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 679935007338 active site 679935007339 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 679935007340 substrate binding site [chemical binding]; other site 679935007341 catalytic residues [active] 679935007342 dimer interface [polypeptide binding]; other site 679935007343 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]; Region: UbiA; cl00337 679935007344 UbiA prenyltransferase family; Region: UbiA; pfam01040 679935007345 GTP-binding protein LepA; Provisional; Region: PRK05433 679935007346 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 679935007347 G1 box; other site 679935007348 putative GEF interaction site [polypeptide binding]; other site 679935007349 GTP/Mg2+ binding site [chemical binding]; other site 679935007350 Switch I region; other site 679935007351 G2 box; other site 679935007352 G3 box; other site 679935007353 Switch II region; other site 679935007354 G4 box; other site 679935007355 G5 box; other site 679935007356 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 679935007357 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 679935007358 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 679935007359 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 679935007360 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 679935007361 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 679935007362 acyl-activating enzyme (AAE) consensus motif; other site 679935007363 acyl-activating enzyme (AAE) consensus motif; other site 679935007364 putative AMP binding site [chemical binding]; other site 679935007365 putative active site [active] 679935007366 putative CoA binding site [chemical binding]; other site 679935007367 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 679935007368 active site 679935007369 DNA binding site [nucleotide binding] 679935007370 Int/Topo IB signature motif; other site 679935007371 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 679935007372 ligand binding site [chemical binding]; other site 679935007373 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 679935007374 Tandemly repeated domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like; cl17916 679935007375 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 679935007376 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 679935007377 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 679935007378 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 679935007379 active site 679935007380 catalytic site [active] 679935007381 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 679935007382 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 679935007383 transcription termination factor Rho; Provisional; Region: PRK12608 679935007384 RNA binding site [nucleotide binding]; other site 679935007385 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 679935007386 multimer interface [polypeptide binding]; other site 679935007387 Walker A motif; other site 679935007388 ATP binding site [chemical binding]; other site 679935007389 Walker B motif; other site 679935007390 S1/P1 nucleases and related enzymes; Region: S1-P1_nuclease; cd11010 679935007391 active site 679935007392 Zn binding site [ion binding]; other site 679935007393 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 679935007394 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 679935007395 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 679935007396 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 679935007397 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935007398 Walker A/P-loop; other site 679935007399 ATP binding site [chemical binding]; other site 679935007400 Q-loop/lid; other site 679935007401 ABC transporter signature motif; other site 679935007402 Walker B; other site 679935007403 D-loop; other site 679935007404 H-loop/switch region; other site 679935007405 Bacteroidetes-Associated Carbohydrate-binding Often N-terminal; Region: BACON; pfam13004 679935007406 Cna protein B-type domain; Region: Cna_B_2; pfam13715 679935007407 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 679935007408 flavodoxin FldA; Validated; Region: PRK09267 679935007409 Protein of unknown function (DUF2023); Region: DUF2023; pfam09633 679935007410 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 679935007411 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 679935007412 putative active site [active] 679935007413 putative NTP binding site [chemical binding]; other site 679935007414 putative nucleic acid binding site [nucleotide binding]; other site 679935007415 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 679935007416 Type II intron maturase; Region: Intron_maturas2; pfam01348 679935007417 putative transposase OrfB; Reviewed; Region: PHA02517 679935007418 HTH-like domain; Region: HTH_21; pfam13276 679935007419 Integrase core domain; Region: rve; pfam00665 679935007420 Integrase core domain; Region: rve_3; pfam13683 679935007421 Protein of unknown function (DUF3408); Region: DUF3408; pfam11888 679935007422 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 679935007423 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 679935007424 Int/Topo IB signature motif; other site 679935007425 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 679935007426 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 679935007427 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 679935007428 NAD(P) binding site [chemical binding]; other site 679935007429 catalytic residues [active] 679935007430 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 679935007431 dimer interface [polypeptide binding]; other site 679935007432 FMN binding site [chemical binding]; other site 679935007433 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 679935007434 non-specific DNA binding site [nucleotide binding]; other site 679935007435 salt bridge; other site 679935007436 sequence-specific DNA binding site [nucleotide binding]; other site 679935007437 Acyltransferase family; Region: Acyl_transf_3; pfam01757 679935007438 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 679935007439 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 679935007440 4Fe-4S binding domain; Region: Fer4_5; pfam12801 679935007441 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 679935007442 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 679935007443 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 679935007444 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 679935007445 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 679935007446 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 679935007447 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 679935007448 active site 679935007449 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 679935007450 catalytic tetrad [active] 679935007451 Helix-turn-helix domain; Region: HTH_18; pfam12833 679935007452 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935007453 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 679935007454 catalytic core [active] 679935007455 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 679935007456 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 679935007457 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; Region: LDH_like_2; cd12183 679935007458 putative ligand binding site [chemical binding]; other site 679935007459 putative NAD binding site [chemical binding]; other site 679935007460 catalytic site [active] 679935007461 fructose-bisphosphate aldolase; Provisional; Region: PRK09250 679935007462 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs); Region: DhnA; cd00958 679935007463 putative active site; other site 679935007464 catalytic residue [active] 679935007465 Helix-turn-helix domain; Region: HTH_18; pfam12833 679935007466 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 679935007467 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 679935007468 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 679935007469 HlyD family secretion protein; Region: HlyD_3; pfam13437 679935007470 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 679935007471 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 679935007472 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 679935007473 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 679935007474 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 679935007475 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 679935007476 homodimer interface [polypeptide binding]; other site 679935007477 substrate-cofactor binding pocket; other site 679935007478 pyridoxal 5'-phosphate binding site [chemical binding]; other site 679935007479 catalytic residue [active] 679935007480 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 679935007481 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 679935007482 Homoserine dehydrogenase [Amino acid transport and metabolism]; Region: ThrA; COG0460 679935007483 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 679935007484 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 679935007485 Protein of unknown function (DUF3988); Region: DUF3988; pfam13149 679935007486 N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins; Region: BF2867_like_N; cd13120 679935007487 C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins; Region: BF2867_like_C; cd13121 679935007488 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 679935007489 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 679935007490 Major Facilitator Superfamily; Region: MFS_1; pfam07690 679935007491 putative substrate translocation pore; other site 679935007492 Zinc finger domain containing protein (CDGSH-type) [Function unknown]; Region: COG3369 679935007493 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; pfam09360 679935007494 Protein of unknown function (DUF1271); Region: DUF1271; cl01443 679935007495 CDGSH-type zinc finger. Function unknown; Region: ZnF_CDGSH; smart00704 679935007496 IgA Peptidase M64; Region: Peptidase_M64; pfam09471 679935007497 hypothetical protein; Provisional; Region: PRK13665 679935007498 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 679935007499 Cation transport protein; Region: TrkH; cl17365 679935007500 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 679935007501 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 679935007502 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 679935007503 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 679935007504 FeS/SAM binding site; other site 679935007505 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 679935007506 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 679935007507 ABC-ATPase subunit interface; other site 679935007508 dimer interface [polypeptide binding]; other site 679935007509 putative PBP binding regions; other site 679935007510 Predicted permeases [General function prediction only]; Region: COG0795 679935007511 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 679935007512 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 679935007513 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 679935007514 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 679935007515 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 679935007516 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 679935007517 dimerization interface [polypeptide binding]; other site 679935007518 active site 679935007519 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 679935007520 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 679935007521 putative active site [active] 679935007522 substrate binding site [chemical binding]; other site 679935007523 putative cosubstrate binding site; other site 679935007524 catalytic site [active] 679935007525 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 679935007526 substrate binding site [chemical binding]; other site 679935007527 peroxiredoxin; Provisional; Region: PRK13189 679935007528 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 679935007529 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 679935007530 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; pfam01558 679935007531 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit [Energy production and conversion]; Region: PorB; COG1013 679935007532 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 679935007533 TPP-binding site [chemical binding]; other site 679935007534 2-ketoisovalerate ferredoxin reductase; Validated; Region: PRK07119 679935007535 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 679935007536 dimer interface [polypeptide binding]; other site 679935007537 PYR/PP interface [polypeptide binding]; other site 679935007538 TPP binding site [chemical binding]; other site 679935007539 substrate binding site [chemical binding]; other site 679935007540 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 679935007541 Ferredoxin [Energy production and conversion]; Region: COG1146 679935007542 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 679935007543 Uncharacterized conserved protein [Function unknown]; Region: COG4198 679935007544 Protein of unknown function (DUF1015); Region: DUF1015; pfam06245 679935007545 Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_like_3; cd12174 679935007546 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain; Region: 2-Hacid_dh; pfam00389 679935007547 putative ligand binding site [chemical binding]; other site 679935007548 putative NAD binding site [chemical binding]; other site 679935007549 putative catalytic site [active] 679935007550 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 679935007551 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 679935007552 catalytic residue [active] 679935007553 hypothetical protein; Provisional; Region: PRK11820 679935007554 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 679935007555 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 679935007556 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 679935007557 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 679935007558 catalytic site [active] 679935007559 G-X2-G-X-G-K; other site 679935007560 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 679935007561 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 679935007562 active site 679935007563 (T/H)XGH motif; other site 679935007564 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 679935007565 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 679935007566 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 679935007567 ATP-grasp domain; Region: ATP-grasp_4; cl17255 679935007568 Protein of unknown function (DUF3109); Region: DUF3109; pfam11307 679935007569 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 679935007570 Peptidase family M23; Region: Peptidase_M23; pfam01551 679935007571 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 679935007572 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 679935007573 nuc_hydro: Nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. This group contains eukaryotic, bacterial and archeal...; Region: nuc_hydro; cl00226 679935007574 active site 679935007575 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 679935007576 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 679935007577 substrate binding site [chemical binding]; other site 679935007578 dimer interface [polypeptide binding]; other site 679935007579 ATP binding site [chemical binding]; other site 679935007580 Transcriptional regulators [Transcription]; Region: PurR; COG1609 679935007581 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 679935007582 DNA binding site [nucleotide binding] 679935007583 domain linker motif; other site 679935007584 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 679935007585 dimerization interface [polypeptide binding]; other site 679935007586 ligand binding site [chemical binding]; other site 679935007587 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 679935007588 Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]; Region: ProC; COG0345 679935007589 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 679935007590 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 679935007591 catalytic residue [active] 679935007592 Peptidase family C69; Region: Peptidase_C69; cl17793 679935007593 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 679935007594 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 679935007595 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 679935007596 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 679935007597 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 679935007598 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 679935007599 dimerization interface 3.5A [polypeptide binding]; other site 679935007600 active site 679935007601 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 679935007602 Aspartase; Region: Aspartase; cd01357 679935007603 active sites [active] 679935007604 tetramer interface [polypeptide binding]; other site 679935007605 dihydrodipicolinate reductase; Provisional; Region: PRK00048 679935007606 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 679935007607 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 679935007608 Signal peptidase I [Intracellular trafficking and secretion]; Region: LepB; COG0681 679935007609 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 679935007610 Catalytic site [active] 679935007611 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 679935007612 Uncharacterized conserved protein [Function unknown]; Region: COG1739 679935007613 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 679935007614 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 679935007615 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 679935007616 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 679935007617 ABC transporter signature motif; other site 679935007618 Walker B; other site 679935007619 D-loop; other site 679935007620 H-loop/switch region; other site 679935007621 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 679935007622 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 679935007623 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 679935007624 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 679935007625 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_3; cd03140 679935007626 conserved cys residue [active] 679935007627 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 679935007628 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 679935007629 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 679935007630 homodimer interface [polypeptide binding]; other site 679935007631 metal binding site [ion binding]; metal-binding site 679935007632 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 679935007633 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 679935007634 active site 679935007635 substrate binding site [chemical binding]; other site 679935007636 metal binding site [ion binding]; metal-binding site