-- dump date 20140620_071745 -- class Genbank::misc_feature -- table misc_feature_note -- id note 452662000001 Replication initiator protein A; Region: RPA; pfam10134 452662000002 ParA-like protein; Provisional; Region: PHA02518 452662000003 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 452662000004 P-loop; other site 452662000005 Magnesium ion binding site [ion binding]; other site 452662000006 SprT-like family; Region: SprT-like; pfam10263 452662000007 recognition site for restriction enzyme PmeI 452662000008 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 452662000009 Helix-turn-helix domain; Region: HTH_37; pfam13744 452662000010 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 452662000011 catalytic core [active] 452662000012 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 452662000013 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662000014 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662000015 Integrase core domain; Region: rve; pfam00665 452662000016 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 452662000017 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 452662000018 Rv0623-like transcription factor; Region: PSK_trans_fac; pfam07704 452662000019 PIN domain of the VapC-like UPF0110 protein Mb0640 and homologs; Region: PIN_UPF0110; cd09871 452662000020 putative active site [active] 452662000021 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 452662000022 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 452662000023 active site 452662000024 DNA binding site [nucleotide binding] 452662000025 Int/Topo IB signature motif; other site 452662000026 may be target duplication site 452662000027 Homeodomain-like domain; Region: HTH_23; pfam13384 452662000028 Winged helix-turn helix; Region: HTH_29; pfam13551 452662000029 Homeodomain-like domain; Region: HTH_32; pfam13565 452662000030 DDE superfamily endonuclease; Region: DDE_3; pfam13358 452662000031 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 452662000032 may be target duplication site 452662000033 DDE superfamily endonuclease; Region: DDE_5; cl17874 452662000034 transposase; Validated; Region: PRK08181 452662000035 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 452662000036 Walker A motif; other site 452662000037 ATP binding site [chemical binding]; other site 452662000038 Walker B motif; other site 452662000039 Transposase, Mutator family; Region: Transposase_mut; pfam00872 452662000040 MULE transposase domain; Region: MULE; pfam10551 452662000041 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662000042 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662000043 Integrase core domain; Region: rve; pfam00665 452662000044 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 452662000045 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 452662000046 catalytic residues [active] 452662000047 catalytic nucleophile [active] 452662000048 Presynaptic Site I dimer interface [polypeptide binding]; other site 452662000049 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 452662000050 Synaptic Flat tetramer interface [polypeptide binding]; other site 452662000051 Synaptic Site I dimer interface [polypeptide binding]; other site 452662000052 recognition site for restriction enzyme PmeI 452662000053 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 452662000054 non-specific DNA binding site [nucleotide binding]; other site 452662000055 salt bridge; other site 452662000056 sequence-specific DNA binding site [nucleotide binding]; other site 452662000057 conjugal transfer relaxase TraA; Provisional; Region: PRK13889 452662000058 MobA/MobL family; Region: MobA_MobL; pfam03389 452662000059 AAA domain; Region: AAA_30; pfam13604 452662000060 Family description; Region: UvrD_C_2; pfam13538 452662000061 recognition site for restriction enzyme PmeI 452662000062 Conjugal transfer protein TraD; Region: TraD; pfam06412 452662000063 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 452662000064 active site 452662000065 NTP binding site [chemical binding]; other site 452662000066 metal binding triad [ion binding]; metal-binding site 452662000067 antibiotic binding site [chemical binding]; other site 452662000068 Higher Eukarytoes and Prokaryotes Nucleotide-binding domain; Region: HEPN; smart00748 452662000069 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 452662000070 Type IV secretory system Conjugative DNA transfer; Region: T4SS-DNA_transf; pfam02534 452662000071 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 452662000072 Walker A motif; other site 452662000073 ATP binding site [chemical binding]; other site 452662000074 Walker B motif; other site 452662000075 recognition site for restriction enzyme PmeI 452662000076 recognition site for restriction enzyme PmeI 452662000077 PEP synthetase regulatory protein; Provisional; Region: PRK05339 452662000078 Maf-like protein; Provisional; Region: PRK14361 452662000079 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 452662000080 active site 452662000081 dimer interface [polypeptide binding]; other site 452662000082 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 452662000083 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 452662000084 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 452662000085 shikimate binding site; other site 452662000086 NAD(P) binding site [chemical binding]; other site 452662000087 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 452662000088 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 452662000089 CoA-binding site [chemical binding]; other site 452662000090 ATP-binding [chemical binding]; other site 452662000091 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 452662000092 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 452662000093 active site 452662000094 catalytic site [active] 452662000095 substrate binding site [chemical binding]; other site 452662000096 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 452662000097 30S subunit binding site; other site 452662000098 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 452662000099 active site 452662000100 phosphorylation site [posttranslational modification] 452662000101 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 452662000102 CoenzymeA binding site [chemical binding]; other site 452662000103 subunit interaction site [polypeptide binding]; other site 452662000104 PHB binding site; other site 452662000105 Protein of unknown function (DUF1491); Region: DUF1491; pfam07372 452662000106 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 452662000107 Protein of unknown function (DUF1052); Region: DUF1052; cl02197 452662000108 hypothetical protein; Provisional; Region: PRK08999 452662000109 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 452662000110 thiamine phosphate binding site [chemical binding]; other site 452662000111 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 452662000112 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 452662000113 catalytic residue [active] 452662000114 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662000115 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 452662000116 metallophosphoesterase, DNA ligase-associated; Region: P_estr_lig_assc; TIGR04123 452662000117 active site 452662000118 metal binding site [ion binding]; metal-binding site 452662000119 hypothetical protein; Validated; Region: PRK01415 452662000120 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 452662000121 active site residue [active] 452662000122 DEXH box helicase, DNA ligase-associated; Region: DEXH_lig_assoc; TIGR04121 452662000123 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 452662000124 ATP binding site [chemical binding]; other site 452662000125 putative Mg++ binding site [ion binding]; other site 452662000126 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 452662000127 nucleotide binding region [chemical binding]; other site 452662000128 ATP-binding site [chemical binding]; other site 452662000129 DEAD/H associated; Region: DEAD_assoc; pfam08494 452662000130 methionine gamma-lyase; Validated; Region: PRK07049 452662000131 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 452662000132 homodimer interface [polypeptide binding]; other site 452662000133 substrate-cofactor binding pocket; other site 452662000134 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662000135 catalytic residue [active] 452662000136 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 452662000137 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 452662000138 putative ligand binding site [chemical binding]; other site 452662000139 NAD binding site [chemical binding]; other site 452662000140 catalytic site [active] 452662000141 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 452662000142 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 452662000143 motif II; other site 452662000144 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 452662000145 anti sigma factor interaction site; other site 452662000146 regulatory phosphorylation site [posttranslational modification]; other site 452662000147 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 452662000148 Permease; Region: Permease; pfam02405 452662000149 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 452662000150 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662000151 Walker A/P-loop; other site 452662000152 ATP binding site [chemical binding]; other site 452662000153 Q-loop/lid; other site 452662000154 ABC transporter signature motif; other site 452662000155 Walker B; other site 452662000156 D-loop; other site 452662000157 H-loop/switch region; other site 452662000158 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 452662000159 mce related protein; Region: MCE; pfam02470 452662000160 Protein of unknown function (DUF330); Region: DUF330; cl01135 452662000161 aminopeptidase N; Provisional; Region: pepN; PRK14015 452662000162 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 452662000163 active site 452662000164 Zn binding site [ion binding]; other site 452662000165 ParB-like nuclease domain; Region: ParB; smart00470 452662000166 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 452662000167 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 452662000168 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 452662000169 P-loop; other site 452662000170 Magnesium ion binding site [ion binding]; other site 452662000171 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 452662000172 Magnesium ion binding site [ion binding]; other site 452662000173 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 452662000174 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 452662000175 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 452662000176 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 452662000177 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 452662000178 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 452662000179 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 452662000180 trmE is a tRNA modification GTPase; Region: trmE; cd04164 452662000181 G1 box; other site 452662000182 GTP/Mg2+ binding site [chemical binding]; other site 452662000183 Switch I region; other site 452662000184 G2 box; other site 452662000185 Switch II region; other site 452662000186 G3 box; other site 452662000187 G4 box; other site 452662000188 G5 box; other site 452662000189 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 452662000190 Predicted ATPase [General function prediction only]; Region: COG2603 452662000191 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 452662000192 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 452662000193 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 452662000194 NADP binding site [chemical binding]; other site 452662000195 dimer interface [polypeptide binding]; other site 452662000196 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 452662000197 Integral membrane protein TerC family; Region: TerC; cl10468 452662000198 transcription termination factor Rho; Provisional; Region: rho; PRK09376 452662000199 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 452662000200 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 452662000201 RNA binding site [nucleotide binding]; other site 452662000202 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 452662000203 multimer interface [polypeptide binding]; other site 452662000204 Walker A motif; other site 452662000205 ATP binding site [chemical binding]; other site 452662000206 Walker B motif; other site 452662000207 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 452662000208 catalytic motif [active] 452662000209 Catalytic residue [active] 452662000210 Aspartyl protease; Region: Asp_protease_2; pfam13650 452662000211 inhibitor binding site; inhibition site 452662000212 catalytic motif [active] 452662000213 Catalytic residue [active] 452662000214 Active site flap [active] 452662000215 Transglycosylase; Region: Transgly; pfam00912 452662000216 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 452662000217 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 452662000218 methionine sulfoxide reductase B; Provisional; Region: PRK00222 452662000219 SelR domain; Region: SelR; pfam01641 452662000220 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 452662000221 Lipopolysaccharide-assembly; Region: LptE; pfam04390 452662000222 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 452662000223 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 452662000224 HIGH motif; other site 452662000225 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 452662000226 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 452662000227 active site 452662000228 KMSKS motif; other site 452662000229 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 452662000230 tRNA binding surface [nucleotide binding]; other site 452662000231 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 452662000232 Predicted membrane protein [Function unknown]; Region: COG3650 452662000233 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 452662000234 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 452662000235 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 452662000236 Mg2+ binding site [ion binding]; other site 452662000237 G-X-G motif; other site 452662000238 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 452662000239 anchoring element; other site 452662000240 dimer interface [polypeptide binding]; other site 452662000241 ATP binding site [chemical binding]; other site 452662000242 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 452662000243 active site 452662000244 putative metal-binding site [ion binding]; other site 452662000245 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 452662000246 Domain of unknown function (DUF1993); Region: DUF1993; pfam09351 452662000247 Predicted membrane protein [Function unknown]; Region: COG2364 452662000248 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 452662000249 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 452662000250 DNA-binding site [nucleotide binding]; DNA binding site 452662000251 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 452662000252 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662000253 homodimer interface [polypeptide binding]; other site 452662000254 catalytic residue [active] 452662000255 Protein of unknown function DUF45; Region: DUF45; pfam01863 452662000256 hypothetical protein; Provisional; Region: PRK05170 452662000257 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 452662000258 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 452662000259 Cu(I) binding site [ion binding]; other site 452662000260 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 452662000261 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 452662000262 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 452662000263 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662000264 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 452662000265 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 452662000266 dimer interface [polypeptide binding]; other site 452662000267 substrate binding site [chemical binding]; other site 452662000268 metal binding sites [ion binding]; metal-binding site 452662000269 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 452662000270 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 452662000271 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 452662000272 protein binding site [polypeptide binding]; other site 452662000273 histidyl-tRNA synthetase; Region: hisS; TIGR00442 452662000274 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 452662000275 dimer interface [polypeptide binding]; other site 452662000276 motif 1; other site 452662000277 active site 452662000278 motif 2; other site 452662000279 motif 3; other site 452662000280 peptide chain release factor 1; Validated; Region: prfA; PRK00591 452662000281 This domain is found in peptide chain release factors; Region: PCRF; smart00937 452662000282 RF-1 domain; Region: RF-1; pfam00472 452662000283 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 452662000284 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 452662000285 Domain of unknown function (DUF4167); Region: DUF4167; pfam13763 452662000286 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 452662000287 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_10; cd04623 452662000288 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 452662000289 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 452662000290 recognition site for restriction enzyme I-CeuI 452662000291 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 452662000292 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 452662000293 amino acid transporter; Region: 2A0306; TIGR00909 452662000294 C-terminus of AA_permease; Region: AA_permease_C; pfam13906 452662000295 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 452662000296 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 452662000297 putative substrate translocation pore; other site 452662000298 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 452662000299 Sel1 repeat; Region: Sel1; cl02723 452662000300 DDE superfamily endonuclease; Region: DDE_3; pfam13358 452662000301 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 452662000302 Winged helix-turn helix; Region: HTH_29; pfam13551 452662000303 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3146 452662000304 Protein of unknown function, DUF482; Region: DUF482; pfam04339 452662000305 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 452662000306 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 452662000307 active site 452662000308 catalytic site [active] 452662000309 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_1; cd02199 452662000310 homotrimer interaction site [polypeptide binding]; other site 452662000311 putative active site [active] 452662000312 Protein of unknown function (DUF3572); Region: DUF3572; pfam12096 452662000313 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 452662000314 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 452662000315 active site 452662000316 phosphorylation site [posttranslational modification] 452662000317 intermolecular recognition site; other site 452662000318 dimerization interface [polypeptide binding]; other site 452662000319 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 452662000320 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 452662000321 active site 452662000322 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 452662000323 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]; Region: NPY1; COG2816 452662000324 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 452662000325 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 452662000326 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 452662000327 putative NADH binding site [chemical binding]; other site 452662000328 putative active site [active] 452662000329 nudix motif; other site 452662000330 putative metal binding site [ion binding]; other site 452662000331 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 452662000332 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 452662000333 minor groove reading motif; other site 452662000334 helix-hairpin-helix signature motif; other site 452662000335 substrate binding pocket [chemical binding]; other site 452662000336 active site 452662000337 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 452662000338 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 452662000339 DNA binding and oxoG recognition site [nucleotide binding] 452662000340 Protein of unknown function (DUF721); Region: DUF721; pfam05258 452662000341 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 452662000342 Thioredoxin; Region: Thioredoxin_4; pfam13462 452662000343 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 452662000344 Thioredoxin; Region: Thioredoxin_4; pfam13462 452662000345 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 452662000346 AAA domain; Region: AAA_23; pfam13476 452662000347 Walker A/P-loop; other site 452662000348 ATP binding site [chemical binding]; other site 452662000349 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 452662000350 ABC transporter signature motif; other site 452662000351 Walker B; other site 452662000352 D-loop; other site 452662000353 H-loop/switch region; other site 452662000354 Catalytic domain, repeat 1, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Region: PLDc_vPLD1_2_like_bac_1; cd09140 452662000355 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 452662000356 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 452662000357 putative active site [active] 452662000358 putative active site [active] 452662000359 catalytic site [active] 452662000360 catalytic site [active] 452662000361 Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Region: PLDc_vPLD1_2_like_bac_2; cd09143 452662000362 putative active site [active] 452662000363 catalytic site [active] 452662000364 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12878 452662000365 UbiA prenyltransferase family; Region: UbiA; pfam01040 452662000366 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 452662000367 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 452662000368 Phospholipid methyltransferase; Region: PEMT; cl17370 452662000369 Protein of unknown function (DUF1345); Region: DUF1345; pfam07077 452662000370 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 452662000371 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 452662000372 RuvA N terminal domain; Region: RuvA_N; pfam01330 452662000373 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 452662000374 GIY-YIG motif/motif A; other site 452662000375 putative active site [active] 452662000376 putative metal binding site [ion binding]; other site 452662000377 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 452662000378 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 452662000379 Walker A motif; other site 452662000380 ATP binding site [chemical binding]; other site 452662000381 Walker B motif; other site 452662000382 arginine finger; other site 452662000383 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 452662000384 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 452662000385 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 452662000386 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 452662000387 dimerization interface [polypeptide binding]; other site 452662000388 DPS ferroxidase diiron center [ion binding]; other site 452662000389 ion pore; other site 452662000390 transcription elongation factor regulatory protein; Validated; Region: PRK06342 452662000391 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 452662000392 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 452662000393 cobaltochelatase, CobT subunit; Region: CobT; TIGR01651 452662000394 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 452662000395 metal ion-dependent adhesion site (MIDAS); other site 452662000396 Tyrosine phosphatase family; Region: Y_phosphatase3; pfam13350 452662000397 Tyrosine phosphatase family C-terminal region; Region: Y_phosphatase3C; pfam13348 452662000398 OsmC-like protein; Region: OsmC; pfam02566 452662000399 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 452662000400 Cobaltochelatase CobS subunit N terminal; Region: CobS_N; pfam12556 452662000401 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 452662000402 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 452662000403 HSP70 interaction site [polypeptide binding]; other site 452662000404 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 452662000405 GST_N family, Class Sigma_like; composed of GSTs belonging to class Sigma and similar proteins, including GSTs from class Mu, Pi and Alpha. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of...; Region: GST_N_Sigma_like; cd03039 452662000406 glutathione s-transferase; Provisional; Region: PTZ00057 452662000407 GSH binding site (G-site) [chemical binding]; other site 452662000408 C-terminal domain interface [polypeptide binding]; other site 452662000409 dimer interface [polypeptide binding]; other site 452662000410 C-terminal, alpha helical domain of Class Sigma-like Glutathione S-transferases; Region: GST_C_Sigma_like; cd03192 452662000411 dimer interface [polypeptide binding]; other site 452662000412 N-terminal domain interface [polypeptide binding]; other site 452662000413 substrate binding pocket (H-site) [chemical binding]; other site 452662000414 Pirin-related protein [General function prediction only]; Region: COG1741 452662000415 Pirin; Region: Pirin; pfam02678 452662000416 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 452662000417 zinc-ribbon domain; Region: zinc_ribbon_5; pfam13719 452662000418 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 452662000419 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 452662000420 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 452662000421 Walker A/P-loop; other site 452662000422 ATP binding site [chemical binding]; other site 452662000423 Q-loop/lid; other site 452662000424 ABC transporter signature motif; other site 452662000425 Walker B; other site 452662000426 D-loop; other site 452662000427 H-loop/switch region; other site 452662000428 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 452662000429 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 452662000430 putative active site [active] 452662000431 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 452662000432 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 452662000433 putative acyl-acceptor binding pocket; other site 452662000434 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 452662000435 prephenate dehydrogenase; Validated; Region: PRK08507 452662000436 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 452662000437 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 452662000438 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662000439 homodimer interface [polypeptide binding]; other site 452662000440 catalytic residue [active] 452662000441 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 452662000442 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 452662000443 putative ligand binding site [chemical binding]; other site 452662000444 NAD binding site [chemical binding]; other site 452662000445 catalytic site [active] 452662000446 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 452662000447 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 452662000448 Methyltransferase domain; Region: Methyltransf_23; pfam13489 452662000449 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 452662000450 S-adenosylmethionine binding site [chemical binding]; other site 452662000451 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; pfam12951 452662000452 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 452662000453 Autotransporter beta-domain; Region: Autotransporter; pfam03797 452662000454 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 452662000455 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662000456 NAD(P) binding site [chemical binding]; other site 452662000457 active site 452662000458 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 452662000459 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 452662000460 active site 452662000461 hypothetical protein; Provisional; Region: PRK06208 452662000462 intersubunit interface [polypeptide binding]; other site 452662000463 active site 452662000464 Zn2+ binding site [ion binding]; other site 452662000465 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662000466 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 452662000467 N-terminal plug; other site 452662000468 ligand-binding site [chemical binding]; other site 452662000469 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 452662000470 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 452662000471 substrate binding pocket [chemical binding]; other site 452662000472 membrane-bound complex binding site; other site 452662000473 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 452662000474 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 452662000475 active site 452662000476 non-prolyl cis peptide bond; other site 452662000477 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662000478 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 452662000479 N-terminal plug; other site 452662000480 ligand-binding site [chemical binding]; other site 452662000481 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 452662000482 Sulfatase; Region: Sulfatase; pfam00884 452662000483 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 452662000484 Uncharacterized conserved protein [Function unknown]; Region: COG1262 452662000485 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662000486 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 452662000487 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 452662000488 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662000489 NAD(P) binding site [chemical binding]; other site 452662000490 active site 452662000491 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 452662000492 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 452662000493 dimer interface [polypeptide binding]; other site 452662000494 active site 452662000495 Transcriptional regulators [Transcription]; Region: MarR; COG1846 452662000496 MarR family; Region: MarR_2; pfam12802 452662000497 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 452662000498 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662000499 substrate binding site [chemical binding]; other site 452662000500 oxyanion hole (OAH) forming residues; other site 452662000501 trimer interface [polypeptide binding]; other site 452662000502 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 452662000503 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662000504 substrate binding site [chemical binding]; other site 452662000505 oxyanion hole (OAH) forming residues; other site 452662000506 trimer interface [polypeptide binding]; other site 452662000507 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 452662000508 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662000509 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662000510 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 452662000511 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 452662000512 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662000513 active site 452662000514 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 452662000515 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 452662000516 Prostaglandin dehydrogenases; Region: PGDH; cd05288 452662000517 NAD(P) binding site [chemical binding]; other site 452662000518 substrate binding site [chemical binding]; other site 452662000519 dimer interface [polypeptide binding]; other site 452662000520 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 452662000521 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 452662000522 acyl-activating enzyme (AAE) consensus motif; other site 452662000523 AMP binding site [chemical binding]; other site 452662000524 active site 452662000525 CoA binding site [chemical binding]; other site 452662000526 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662000527 NAD(P) binding site [chemical binding]; other site 452662000528 active site 452662000529 Fic family protein [Function unknown]; Region: COG3177 452662000530 Fic/DOC family; Region: Fic; pfam02661 452662000531 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 452662000532 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 452662000533 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 452662000534 active site 452662000535 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 452662000536 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 452662000537 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 452662000538 active site 452662000539 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 452662000540 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 452662000541 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 452662000542 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662000543 Walker A/P-loop; other site 452662000544 ATP binding site [chemical binding]; other site 452662000545 Q-loop/lid; other site 452662000546 ABC transporter signature motif; other site 452662000547 Walker B; other site 452662000548 D-loop; other site 452662000549 H-loop/switch region; other site 452662000550 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 452662000551 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 452662000552 trimer interface [polypeptide binding]; other site 452662000553 active site 452662000554 substrate binding site [chemical binding]; other site 452662000555 CoA binding site [chemical binding]; other site 452662000556 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 452662000557 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 452662000558 motif II; other site 452662000559 Possible lysine decarboxylase; Region: Lysine_decarbox; pfam03641 452662000560 phytoene desaturase; Region: crtI_fam; TIGR02734 452662000561 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 452662000562 Lycopene cyclase protein; Region: Lycopene_cycl; pfam05834 452662000563 lycopene cyclase; Region: lycopene_cycl; TIGR01789 452662000564 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 452662000565 putative metal binding site [ion binding]; other site 452662000566 putative homodimer interface [polypeptide binding]; other site 452662000567 putative homotetramer interface [polypeptide binding]; other site 452662000568 putative homodimer-homodimer interface [polypeptide binding]; other site 452662000569 putative allosteric switch controlling residues; other site 452662000570 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 452662000571 HI0933-like protein; Region: HI0933_like; pfam03486 452662000572 Putative phosphatase (DUF442); Region: DUF442; cl17385 452662000573 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 452662000574 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 452662000575 ATP binding site [chemical binding]; other site 452662000576 putative Mg++ binding site [ion binding]; other site 452662000577 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 452662000578 nucleotide binding region [chemical binding]; other site 452662000579 ATP-binding site [chemical binding]; other site 452662000580 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 452662000581 HRDC domain; Region: HRDC; pfam00570 452662000582 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 452662000583 Beta-lactamase; Region: Beta-lactamase; pfam00144 452662000584 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 452662000585 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 452662000586 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 452662000587 TrkA-C domain; Region: TrkA_C; pfam02080 452662000588 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 452662000589 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 452662000590 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 452662000591 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 452662000592 Tetramer interface [polypeptide binding]; other site 452662000593 active site 452662000594 FMN-binding site [chemical binding]; other site 452662000595 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08159 452662000596 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 452662000597 NAD binding site [chemical binding]; other site 452662000598 homotetramer interface [polypeptide binding]; other site 452662000599 homodimer interface [polypeptide binding]; other site 452662000600 substrate binding site [chemical binding]; other site 452662000601 active site 452662000602 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 452662000603 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 452662000604 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 452662000605 HSP70 interaction site [polypeptide binding]; other site 452662000606 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 452662000607 substrate binding site [polypeptide binding]; other site 452662000608 dimer interface [polypeptide binding]; other site 452662000609 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 452662000610 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 452662000611 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 452662000612 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 452662000613 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 452662000614 Predicted flavoprotein [General function prediction only]; Region: COG0431 452662000615 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 452662000616 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 452662000617 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 452662000618 GDP-binding site [chemical binding]; other site 452662000619 ACT binding site; other site 452662000620 IMP binding site; other site 452662000621 Histidyl-tRNA synthetase; Region: tRNA-synt_His; pfam13393 452662000622 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 452662000623 motif 1; other site 452662000624 dimer interface [polypeptide binding]; other site 452662000625 active site 452662000626 motif 2; other site 452662000627 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 452662000628 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 452662000629 ligand binding site [chemical binding]; other site 452662000630 NAD binding site [chemical binding]; other site 452662000631 dimerization interface [polypeptide binding]; other site 452662000632 catalytic site [active] 452662000633 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 452662000634 putative L-serine binding site [chemical binding]; other site 452662000635 phosphoserine aminotransferase; Provisional; Region: PRK03080 452662000636 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 452662000637 catalytic residue [active] 452662000638 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 452662000639 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 452662000640 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 452662000641 active site lid residues [active] 452662000642 substrate binding pocket [chemical binding]; other site 452662000643 catalytic residues [active] 452662000644 substrate-Mg2+ binding site; other site 452662000645 aspartate-rich region 1; other site 452662000646 aspartate-rich region 2; other site 452662000647 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 452662000648 Nitrogen regulatory protein P-II; Region: P-II; pfam00543 452662000649 Nitrogen regulatory protein P-II; Region: P-II; smart00938 452662000650 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 452662000651 protease TldD; Provisional; Region: tldD; PRK10735 452662000652 Zinc-finger domain; Region: zf-CHCC; pfam10276 452662000653 MarR family; Region: MarR_2; cl17246 452662000654 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 452662000655 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 452662000656 homodimer interface [polypeptide binding]; other site 452662000657 substrate-cofactor binding pocket; other site 452662000658 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662000659 catalytic residue [active] 452662000660 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 452662000661 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 452662000662 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 452662000663 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 452662000664 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 452662000665 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 452662000666 Walker A/P-loop; other site 452662000667 ATP binding site [chemical binding]; other site 452662000668 Q-loop/lid; other site 452662000669 ABC transporter signature motif; other site 452662000670 Walker B; other site 452662000671 D-loop; other site 452662000672 H-loop/switch region; other site 452662000673 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 452662000674 PQQ_like domain of the quinohemoprotein alcohol dehydrogenase (type II); Region: PQQ_ADH_II; cd10279 452662000675 Trp docking motif [polypeptide binding]; other site 452662000676 cytochrome domain interface [polypeptide binding]; other site 452662000677 active site 452662000678 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 452662000679 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 452662000680 CoA binding domain; Region: CoA_binding_2; pfam13380 452662000681 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 452662000682 benzoate transport; Region: 2A0115; TIGR00895 452662000683 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 452662000684 recognition site for restriction enzyme PmeI 452662000685 putative glutathione S-transferase; Provisional; Region: PRK10357 452662000686 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 452662000687 putative C-terminal domain interface [polypeptide binding]; other site 452662000688 putative GSH binding site (G-site) [chemical binding]; other site 452662000689 putative dimer interface [polypeptide binding]; other site 452662000690 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 452662000691 N-terminal domain interface [polypeptide binding]; other site 452662000692 dimer interface [polypeptide binding]; other site 452662000693 substrate binding pocket (H-site) [chemical binding]; other site 452662000694 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 452662000695 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 452662000696 active site 452662000697 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 452662000698 PQQ_like domain of the quinohemoprotein alcohol dehydrogenase (type II); Region: PQQ_ADH_II; cd10279 452662000699 Trp docking motif [polypeptide binding]; other site 452662000700 cytochrome domain interface [polypeptide binding]; other site 452662000701 active site 452662000702 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 452662000703 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 452662000704 DUF35 OB-fold domain; Region: DUF35; pfam01796 452662000705 acetyl-CoA acetyltransferase; Provisional; Region: PRK06064 452662000706 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 452662000707 active site 452662000708 enoyl-CoA hydratase; Provisional; Region: PRK08140 452662000709 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662000710 substrate binding site [chemical binding]; other site 452662000711 oxyanion hole (OAH) forming residues; other site 452662000712 trimer interface [polypeptide binding]; other site 452662000713 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662000714 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 452662000715 substrate binding site [chemical binding]; other site 452662000716 oxyanion hole (OAH) forming residues; other site 452662000717 trimer interface [polypeptide binding]; other site 452662000718 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 452662000719 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662000720 EthD domain; Region: EthD; cl17553 452662000721 EthD domain; Region: EthD; cl17553 452662000722 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 452662000723 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 452662000724 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 452662000725 EthD domain; Region: EthD; pfam07110 452662000726 EthD domain; Region: EthD; pfam07110 452662000727 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 452662000728 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 452662000729 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 452662000730 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662000731 Flagellin N-methylase; Region: FliB; cl00497 452662000732 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 452662000733 Domain of unknown function (DUF4286); Region: DUF4286; pfam14114 452662000734 Amidohydrolase; Region: Amidohydro_2; pfam04909 452662000735 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 452662000736 homotrimer interaction site [polypeptide binding]; other site 452662000737 putative active site [active] 452662000738 protocatechuate 4,5-dioxygenase subunit beta; Provisional; Region: PRK13363 452662000739 active site 452662000740 metal binding site [ion binding]; metal-binding site 452662000741 benzoate transport; Region: 2A0115; TIGR00895 452662000742 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 452662000743 putative substrate translocation pore; other site 452662000744 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 452662000745 CoA-transferase family III; Region: CoA_transf_3; pfam02515 452662000746 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 452662000747 putative glutathione S-transferase; Provisional; Region: PRK10357 452662000748 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 452662000749 N-terminal domain interface [polypeptide binding]; other site 452662000750 dimer interface [polypeptide binding]; other site 452662000751 substrate binding pocket (H-site) [chemical binding]; other site 452662000752 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 452662000753 phosphonates metabolism transcriptional regulator PhnF; Region: C_P_lyase_phnF; TIGR02325 452662000754 DNA-binding site [nucleotide binding]; DNA binding site 452662000755 UTRA domain; Region: UTRA; pfam07702 452662000756 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 452662000757 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 452662000758 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 452662000759 iron-sulfur cluster [ion binding]; other site 452662000760 [2Fe-2S] cluster binding site [ion binding]; other site 452662000761 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 452662000762 alpha subunit interface [polypeptide binding]; other site 452662000763 active site 452662000764 substrate binding site [chemical binding]; other site 452662000765 Fe binding site [ion binding]; other site 452662000766 putative glutathione S-transferase; Provisional; Region: PRK10357 452662000767 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 452662000768 putative C-terminal domain interface [polypeptide binding]; other site 452662000769 putative GSH binding site (G-site) [chemical binding]; other site 452662000770 putative dimer interface [polypeptide binding]; other site 452662000771 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 452662000772 dimer interface [polypeptide binding]; other site 452662000773 N-terminal domain interface [polypeptide binding]; other site 452662000774 putative substrate binding pocket (H-site) [chemical binding]; other site 452662000775 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 452662000776 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 452662000777 active site 452662000778 Demethylmenaquinone methyltransferase [Coenzyme metabolism]; Region: MenG; COG0684 452662000779 Demethylmenaquinone methyltransferase [Coenzyme metabolism]; Region: MenG; COG0684 452662000780 Transmembrane secretion effector; Region: MFS_3; pfam05977 452662000781 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 452662000782 Cytochrome c; Region: Cytochrom_C; cl11414 452662000783 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 452662000784 CoA binding domain; Region: CoA_binding_2; pfam13380 452662000785 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 452662000786 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 452662000787 p-hydroxycinnamoyl CoA hydratase/lyase; Validated; Region: PRK09120 452662000788 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662000789 substrate binding site [chemical binding]; other site 452662000790 oxyanion hole (OAH) forming residues; other site 452662000791 trimer interface [polypeptide binding]; other site 452662000792 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 452662000793 Streptomyces aureofaciens putative aldehyde dehydrogenase AldA (AAD23400)-like; Region: ALDH_AldA-AAD23400; cd07106 452662000794 NAD(P) binding site [chemical binding]; other site 452662000795 catalytic residues [active] 452662000796 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 452662000797 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 452662000798 active site 452662000799 dimer interface [polypeptide binding]; other site 452662000800 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 452662000801 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 452662000802 active site 452662000803 FMN binding site [chemical binding]; other site 452662000804 substrate binding site [chemical binding]; other site 452662000805 3Fe-4S cluster binding site [ion binding]; other site 452662000806 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 452662000807 domain interface; other site 452662000808 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; cl01243 452662000809 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 452662000810 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 452662000811 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 452662000812 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 452662000813 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 452662000814 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 452662000815 putative NAD(P) binding site [chemical binding]; other site 452662000816 active site 452662000817 Predicted membrane protein [Function unknown]; Region: COG2119 452662000818 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 452662000819 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 452662000820 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 452662000821 active site 452662000822 tetramer interface; other site 452662000823 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 452662000824 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 452662000825 Peptidase family M48; Region: Peptidase_M48; cl12018 452662000826 Heparinase II/III-like protein; Region: Hepar_II_III; cl15421 452662000827 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 452662000828 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 452662000829 hexamer interface [polypeptide binding]; other site 452662000830 metal binding site [ion binding]; metal-binding site 452662000831 substrate binding site [chemical binding]; other site 452662000832 NusB family; Region: NusB; pfam01029 452662000833 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 452662000834 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 452662000835 S-adenosylmethionine binding site [chemical binding]; other site 452662000836 Peptidase family M23; Region: Peptidase_M23; pfam01551 452662000837 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 452662000838 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 452662000839 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 452662000840 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 452662000841 active site 452662000842 (T/H)XGH motif; other site 452662000843 hypothetical protein; Provisional; Region: PRK06194 452662000844 classical (c) SDRs; Region: SDR_c; cd05233 452662000845 NAD(P) binding site [chemical binding]; other site 452662000846 active site 452662000847 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662000848 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662000849 NAD(P) binding site [chemical binding]; other site 452662000850 active site 452662000851 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 452662000852 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662000853 active site 452662000854 Uncharacterized conserved protein [Function unknown]; Region: COG5361 452662000855 Protein of unknown function (DUF1254); Region: DUF1254; pfam06863 452662000856 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 452662000857 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily 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: ACAD10_11_like; cd05154 452662000858 Phosphotransferase enzyme family; Region: APH; pfam01636 452662000859 putative active site [active] 452662000860 putative substrate binding site [chemical binding]; other site 452662000861 ATP binding site [chemical binding]; other site 452662000862 Protein of unknown function (DUF2889); Region: DUF2889; pfam11136 452662000863 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 452662000864 active site 452662000865 dimer interface [polypeptide binding]; other site 452662000866 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 452662000867 predicted 30S ribosome binding site; other site 452662000868 rRNA binding site [nucleotide binding]; other site 452662000869 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 452662000870 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 452662000871 inhibitor-cofactor binding pocket; inhibition site 452662000872 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662000873 catalytic residue [active] 452662000874 Domain of unknown function (DUF4168); Region: DUF4168; pfam13767 452662000875 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 452662000876 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 452662000877 active site 452662000878 Zn binding site [ion binding]; other site 452662000879 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 452662000880 AAA domain; Region: AAA_26; pfam13500 452662000881 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 452662000882 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 452662000883 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 452662000884 catalytic residue [active] 452662000885 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 452662000886 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 452662000887 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 452662000888 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 452662000889 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 452662000890 thiamine-monophosphate kinase; Region: thiL; TIGR01379 452662000891 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 452662000892 ATP binding site [chemical binding]; other site 452662000893 dimerization interface [polypeptide binding]; other site 452662000894 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 452662000895 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 452662000896 histidinol dehydrogenase; Region: hisD; TIGR00069 452662000897 NAD binding site [chemical binding]; other site 452662000898 dimerization interface [polypeptide binding]; other site 452662000899 product binding site; other site 452662000900 substrate binding site [chemical binding]; other site 452662000901 zinc binding site [ion binding]; other site 452662000902 catalytic residues [active] 452662000903 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 452662000904 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 452662000905 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 452662000906 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 452662000907 Ligand Binding Site [chemical binding]; other site 452662000908 Protein of unknown function (DUF1153); Region: DUF1153; pfam06627 452662000909 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 452662000910 Predicted membrane protein [Function unknown]; Region: COG2261 452662000911 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 452662000912 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662000913 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 452662000914 Protein of unknown function (DUF445); Region: DUF445; pfam04286 452662000915 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 452662000916 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 452662000917 catalytic motif [active] 452662000918 Zn binding site [ion binding]; other site 452662000919 RibD C-terminal domain; Region: RibD_C; cl17279 452662000920 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 452662000921 Lumazine binding domain; Region: Lum_binding; pfam00677 452662000922 Lumazine binding domain; Region: Lum_binding; pfam00677 452662000923 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 452662000924 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 452662000925 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 452662000926 dimerization interface [polypeptide binding]; other site 452662000927 active site 452662000928 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 452662000929 homopentamer interface [polypeptide binding]; other site 452662000930 active site 452662000931 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 452662000932 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; cd02933 452662000933 FMN binding site [chemical binding]; other site 452662000934 active site 452662000935 substrate binding site [chemical binding]; other site 452662000936 catalytic residue [active] 452662000937 rpsU-divergently transcribed protein; Region: diverge_rpsU; TIGR02396 452662000938 COQ9; Region: COQ9; pfam08511 452662000939 FeoA domain; Region: FeoA; pfam04023 452662000940 Elongation factor Tu GTP binding domain; Region: GTP_EFTU; pfam00009 452662000941 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 452662000942 G1 box; other site 452662000943 GTP/Mg2+ binding site [chemical binding]; other site 452662000944 Switch I region; other site 452662000945 G2 box; other site 452662000946 G3 box; other site 452662000947 Switch II region; other site 452662000948 G4 box; other site 452662000949 G5 box; other site 452662000950 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 452662000951 Nucleoside recognition; Region: Gate; pfam07670 452662000952 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 452662000953 Nucleoside recognition; Region: Gate; pfam07670 452662000954 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 452662000955 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 452662000956 dimer interface [polypeptide binding]; other site 452662000957 ssDNA binding site [nucleotide binding]; other site 452662000958 tetramer (dimer of dimers) interface [polypeptide binding]; other site 452662000959 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 452662000960 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 452662000961 purine monophosphate binding site [chemical binding]; other site 452662000962 dimer interface [polypeptide binding]; other site 452662000963 putative catalytic residues [active] 452662000964 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 452662000965 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 452662000966 hypothetical protein; Provisional; Region: PRK07208 452662000967 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 452662000968 methionine sulfoxide reductase B; Provisional; Region: PRK00222 452662000969 SelR domain; Region: SelR; pfam01641 452662000970 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 452662000971 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4152 452662000972 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662000973 Walker A/P-loop; other site 452662000974 ATP binding site [chemical binding]; other site 452662000975 Q-loop/lid; other site 452662000976 ABC transporter signature motif; other site 452662000977 Walker B; other site 452662000978 D-loop; other site 452662000979 H-loop/switch region; other site 452662000980 epoxyqueuosine reductase; Region: TIGR00276 452662000981 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 452662000982 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 452662000983 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 452662000984 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 452662000985 substrate binding site [chemical binding]; other site 452662000986 ATP binding site [chemical binding]; other site 452662000987 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 452662000988 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 452662000989 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 452662000990 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 452662000991 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 452662000992 UGMP family protein; Validated; Region: PRK09604 452662000993 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 452662000994 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 452662000995 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl17708 452662000996 domain interfaces; other site 452662000997 active site 452662000998 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 452662000999 active site 452662001000 Mitochondrial inner membrane protein; Region: Mitofilin; pfam09731 452662001001 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 452662001002 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 452662001003 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 452662001004 active site 452662001005 HIGH motif; other site 452662001006 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 452662001007 active site 452662001008 KMSKS motif; other site 452662001009 NAD synthetase; Provisional; Region: PRK13981 452662001010 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 452662001011 multimer interface [polypeptide binding]; other site 452662001012 active site 452662001013 catalytic triad [active] 452662001014 protein interface 1 [polypeptide binding]; other site 452662001015 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 452662001016 homodimer interface [polypeptide binding]; other site 452662001017 NAD binding pocket [chemical binding]; other site 452662001018 ATP binding pocket [chemical binding]; other site 452662001019 Mg binding site [ion binding]; other site 452662001020 active-site loop [active] 452662001021 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 452662001022 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 452662001023 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 452662001024 active site 452662001025 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_14; cd08355 452662001026 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662001027 Predominantly bacterial family of Mg++ dependend phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate fructose-1,6-bisphosphate, inositol monophospate, 3'-phosphoadenosine-5'-phosphate, or similar substrates; Region: Bacterial_IMPase_like_1; cd01641 452662001028 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 452662001029 active site 452662001030 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 452662001031 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 452662001032 acyl-activating enzyme (AAE) consensus motif; other site 452662001033 putative AMP binding site [chemical binding]; other site 452662001034 putative active site [active] 452662001035 putative CoA binding site [chemical binding]; other site 452662001036 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 452662001037 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 452662001038 dimer interface [polypeptide binding]; other site 452662001039 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662001040 active site 452662001041 metal binding site [ion binding]; metal-binding site 452662001042 glutathione binding site [chemical binding]; other site 452662001043 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2859 452662001044 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 452662001045 binding surface 452662001046 Tetratricopeptide repeat; Region: TPR_16; pfam13432 452662001047 TPR motif; other site 452662001048 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 452662001049 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 452662001050 integrase; Provisional; Region: PRK09692 452662001051 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 452662001052 active site 452662001053 Int/Topo IB signature motif; other site 452662001054 Domain of Unknown Function with PDB structure (DUF3857); Region: DUF3857; pfam12969 452662001055 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 452662001056 Helix-turn-helix domain; Region: HTH_17; cl17695 452662001057 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 452662001058 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 452662001059 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 452662001060 active site 452662001061 NTP binding site [chemical binding]; other site 452662001062 metal binding triad [ion binding]; metal-binding site 452662001063 antibiotic binding site [chemical binding]; other site 452662001064 Higher Eukarytoes and Prokaryotes Nucleotide-binding domain; Region: HEPN; smart00748 452662001065 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 452662001066 ParB-like nuclease domain; Region: ParB; smart00470 452662001067 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662001068 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662001069 metal binding site [ion binding]; metal-binding site 452662001070 active site 452662001071 I-site; other site 452662001072 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 452662001073 Superfamily II helicase [General function prediction only]; Region: COG1204 452662001074 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 452662001075 ATP binding site [chemical binding]; other site 452662001076 putative Mg++ binding site [ion binding]; other site 452662001077 Domain of unknown function (DUF1837); Region: DUF1837; pfam08878 452662001078 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 452662001079 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 452662001080 Predicted transcriptional regulators [Transcription]; Region: COG1510 452662001081 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 452662001082 putative DNA binding site [nucleotide binding]; other site 452662001083 putative Zn2+ binding site [ion binding]; other site 452662001084 Domain of unknown function (DUF4166); Region: DUF4166; pfam13761 452662001085 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 452662001086 TIGR01777 family protein; Region: yfcH 452662001087 putative NAD(P) binding site [chemical binding]; other site 452662001088 putative active site [active] 452662001089 Uncharacterized protein conserved in bacteria (DUF2236); Region: DUF2236; pfam09995 452662001090 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 452662001091 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 452662001092 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 452662001093 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 452662001094 N-terminal plug; other site 452662001095 ligand-binding site [chemical binding]; other site 452662001096 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 452662001097 Prostaglandin dehydrogenases; Region: PGDH; cd05288 452662001098 NAD(P) binding site [chemical binding]; other site 452662001099 substrate binding site [chemical binding]; other site 452662001100 dimer interface [polypeptide binding]; other site 452662001101 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662001102 substrate binding site [chemical binding]; other site 452662001103 oxyanion hole (OAH) forming residues; other site 452662001104 trimer interface [polypeptide binding]; other site 452662001105 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 452662001106 3-hydroxybutyryl-CoA dehydrogenase; Region: PLN02545 452662001107 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662001108 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662001109 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 452662001110 AMP-binding enzyme; Region: AMP-binding; pfam00501 452662001111 acyl-activating enzyme (AAE) consensus motif; other site 452662001112 AMP binding site [chemical binding]; other site 452662001113 active site 452662001114 CoA binding site [chemical binding]; other site 452662001115 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 452662001116 classical (c) SDRs; Region: SDR_c; cd05233 452662001117 NAD(P) binding site [chemical binding]; other site 452662001118 active site 452662001119 EthD domain; Region: EthD; cl17553 452662001120 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 452662001121 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662001122 substrate binding site [chemical binding]; other site 452662001123 oxyanion hole (OAH) forming residues; other site 452662001124 trimer interface [polypeptide binding]; other site 452662001125 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 452662001126 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 452662001127 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662001128 active site 452662001129 Phosphotransferase enzyme family; Region: APH; pfam01636 452662001130 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily 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: ACAD10_11_like; cd05154 452662001131 putative active site [active] 452662001132 putative substrate binding site [chemical binding]; other site 452662001133 ATP binding site [chemical binding]; other site 452662001134 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 452662001135 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662001136 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 452662001137 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 452662001138 Major Facilitator Superfamily; Region: MFS_1; pfam07690 452662001139 putative substrate translocation pore; other site 452662001140 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662001141 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662001142 NAD(P) binding site [chemical binding]; other site 452662001143 active site 452662001144 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 452662001145 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662001146 active site 452662001147 acetyl-CoA acetyltransferase; Provisional; Region: PRK06504 452662001148 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 452662001149 dimer interface [polypeptide binding]; other site 452662001150 active site 452662001151 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 452662001152 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662001153 active site 452662001154 acetyl-CoA acetyltransferase; Provisional; Region: PRK06064 452662001155 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 452662001156 active site 452662001157 DUF35 OB-fold domain; Region: DUF35; pfam01796 452662001158 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 452662001159 DNA binding residues [nucleotide binding] 452662001160 dimerization interface [polypeptide binding]; other site 452662001161 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662001162 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662001163 short chain dehydrogenase; Provisional; Region: PRK06949 452662001164 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662001165 NAD(P) binding site [chemical binding]; other site 452662001166 active site 452662001167 RmuC family; Region: RmuC; pfam02646 452662001168 hypothetical protein; Provisional; Region: PRK08912 452662001169 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 452662001170 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662001171 homodimer interface [polypeptide binding]; other site 452662001172 catalytic residue [active] 452662001173 Restriction endonuclease; Region: Mrr_cat; pfam04471 452662001174 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 452662001175 Family description; Region: UvrD_C_2; pfam13538 452662001176 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 452662001177 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662001178 Walker A/P-loop; other site 452662001179 ATP binding site [chemical binding]; other site 452662001180 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 452662001181 putative active site [active] 452662001182 putative metal-binding site [ion binding]; other site 452662001183 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like_2; cd04847 452662001184 active site 452662001185 catalytic triad [active] 452662001186 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 452662001187 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 452662001188 Walker A motif; other site 452662001189 ATP binding site [chemical binding]; other site 452662001190 Walker B motif; other site 452662001191 arginine finger; other site 452662001192 Uncharacterized conserved protein [Function unknown]; Region: COG4544 452662001193 DNA Polymerase Y-family; Region: PolY_like; cd03468 452662001194 active site 452662001195 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 452662001196 DNA binding site [nucleotide binding] 452662001197 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 452662001198 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 452662001199 putative active site [active] 452662001200 putative PHP Thumb interface [polypeptide binding]; other site 452662001201 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 452662001202 generic binding surface I; other site 452662001203 generic binding surface II; other site 452662001204 Uncharacterized conserved protein [Function unknown]; Region: COG2135 452662001205 Uncharacterized ACR, COG2135; Region: DUF159; cl03646 452662001206 GAF domain; Region: GAF; pfam01590 452662001207 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662001208 metal binding site [ion binding]; metal-binding site 452662001209 active site 452662001210 I-site; other site 452662001211 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 452662001212 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 452662001213 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 452662001214 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; pfam02899 452662001215 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 452662001216 active site 452662001217 DNA binding site [nucleotide binding] 452662001218 Int/Topo IB signature motif; other site 452662001219 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 452662001220 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 452662001221 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 452662001222 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 452662001223 putative DNA binding site [nucleotide binding]; other site 452662001224 putative Zn2+ binding site [ion binding]; other site 452662001225 Low molecular weight phosphatase family; Region: LMWPc; cd00115 452662001226 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 452662001227 active site 452662001228 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 452662001229 ArsC family; Region: ArsC; pfam03960 452662001230 catalytic residues [active] 452662001231 Sodium Bile acid symporter family; Region: SBF; cl17470 452662001232 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 452662001233 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 452662001234 Coenzyme A binding pocket [chemical binding]; other site 452662001235 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 452662001236 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 452662001237 Protein of unknown function (DUF2493); Region: DUF2493; pfam10686 452662001238 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 452662001239 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 452662001240 dimer interface [polypeptide binding]; other site 452662001241 ssDNA binding site [nucleotide binding]; other site 452662001242 tetramer (dimer of dimers) interface [polypeptide binding]; other site 452662001243 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]; Region: COG1525 452662001244 Protein of unknown function (DUF3768); Region: DUF3768; pfam12599 452662001245 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 452662001246 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 452662001247 P-loop; other site 452662001248 Magnesium ion binding site [ion binding]; other site 452662001249 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 452662001250 Magnesium ion binding site [ion binding]; other site 452662001251 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 452662001252 ParB-like nuclease domain; Region: ParB; smart00470 452662001253 KorB domain; Region: KorB; pfam08535 452662001254 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 452662001255 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 452662001256 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 452662001257 Helix-turn-helix domain; Region: HTH_28; pfam13518 452662001258 Winged helix-turn helix; Region: HTH_29; pfam13551 452662001259 Homeodomain-like domain; Region: HTH_32; pfam13565 452662001260 Integrase core domain; Region: rve; pfam00665 452662001261 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 452662001262 Helix-turn-helix domain; Region: HTH_38; pfam13936 452662001263 Integrase core domain; Region: rve; pfam00665 452662001264 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 452662001265 non-specific DNA binding site [nucleotide binding]; other site 452662001266 sequence-specific DNA binding site [nucleotide binding]; other site 452662001267 salt bridge; other site 452662001268 Domain of unknown function (DUF955); Region: DUF955; pfam06114 452662001269 Chagasin family peptidase inhibitor I42; Region: Inhibitor_I42; pfam09394 452662001270 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; cd02619 452662001271 active site 452662001272 thymidylate synthase, methanogen type; Region: thy_syn_methano; TIGR03283 452662001273 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_3; cd10035 452662001274 putative uracil binding site [chemical binding]; other site 452662001275 putative active site [active] 452662001276 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 452662001277 putative metal binding site [ion binding]; other site 452662001278 Type IV secretory system Conjugative DNA transfer; Region: T4SS-DNA_transf; pfam02534 452662001279 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 452662001280 Walker A motif; other site 452662001281 ATP binding site [chemical binding]; other site 452662001282 Walker B motif; other site 452662001283 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 452662001284 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 452662001285 Walker A motif; other site 452662001286 hexamer interface [polypeptide binding]; other site 452662001287 ATP binding site [chemical binding]; other site 452662001288 Walker B motif; other site 452662001289 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 452662001290 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 452662001291 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 452662001292 VirB7 interaction site; other site 452662001293 VirB8 protein; Region: VirB8; cl01500 452662001294 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 452662001295 P-type DNA transfer protein VirB5; Region: VirB5; TIGR02791 452662001296 Type IV secretion system proteins; Region: T4SS; pfam07996 452662001297 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 452662001298 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 452662001299 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 452662001300 TrbC/VIRB2 family; Region: TrbC; pfam04956 452662001301 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 452662001302 N-acetyl-D-glucosamine binding site [chemical binding]; other site 452662001303 catalytic residue [active] 452662001304 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 452662001305 Autoinducer synthetase; Region: Autoind_synth; cl17404 452662001306 transcriptional regulator TraR; Provisional; Region: PRK13870 452662001307 Autoinducer binding domain; Region: Autoind_bind; pfam03472 452662001308 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 452662001309 DNA binding residues [nucleotide binding] 452662001310 dimerization interface [polypeptide binding]; other site 452662001311 DNA-binding transcriptional activator SdiA; Provisional; Region: PRK10188 452662001312 Autoinducer binding domain; Region: Autoind_bind; pfam03472 452662001313 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 452662001314 DNA binding residues [nucleotide binding] 452662001315 dimerization interface [polypeptide binding]; other site 452662001316 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 452662001317 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 452662001318 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 452662001319 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 452662001320 Beta-Casp domain; Region: Beta-Casp; smart01027 452662001321 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 452662001322 thymidine phosphorylase; Provisional; Region: PRK04350 452662001323 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 452662001324 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 452662001325 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; cl06734 452662001326 phosphoribosylpyrophosphate synthetase; Provisional; Region: PRK07199 452662001327 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 452662001328 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 452662001329 active site 452662001330 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 452662001331 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 452662001332 active site 452662001333 phosphorylation site [posttranslational modification] 452662001334 intermolecular recognition site; other site 452662001335 dimerization interface [polypeptide binding]; other site 452662001336 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 452662001337 DNA binding residues [nucleotide binding] 452662001338 dimerization interface [polypeptide binding]; other site 452662001339 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 452662001340 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 452662001341 DNA binding residues [nucleotide binding] 452662001342 dimer interface [polypeptide binding]; other site 452662001343 copper binding site [ion binding]; other site 452662001344 YHS domain; Region: YHS; pfam04945 452662001345 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 452662001346 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 452662001347 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 452662001348 active site 452662001349 motif I; other site 452662001350 motif II; other site 452662001351 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 452662001352 S-adenosylmethionine binding site [chemical binding]; other site 452662001353 Copper resistance protein D; Region: CopD; pfam05425 452662001354 CopC domain; Region: CopC; pfam04234 452662001355 Heavy-metal resistance; Region: Metal_resist; pfam13801 452662001356 dimer interface [polypeptide binding]; other site 452662001357 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 452662001358 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 452662001359 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 452662001360 DNA binding residues [nucleotide binding] 452662001361 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 452662001362 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 452662001363 Multicopper oxidase; Region: Cu-oxidase; pfam00394 452662001364 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 452662001365 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 452662001366 Domain of unknown function (DUF305); Region: DUF305; cl17794 452662001367 PAS domain; Region: PAS_9; pfam13426 452662001368 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 452662001369 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662001370 putative active site [active] 452662001371 heme pocket [chemical binding]; other site 452662001372 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 452662001373 dimer interface [polypeptide binding]; other site 452662001374 phosphorylation site [posttranslational modification] 452662001375 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 452662001376 ATP binding site [chemical binding]; other site 452662001377 Mg2+ binding site [ion binding]; other site 452662001378 G-X-G motif; other site 452662001379 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 452662001380 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 452662001381 active site 452662001382 phosphorylation site [posttranslational modification] 452662001383 intermolecular recognition site; other site 452662001384 dimerization interface [polypeptide binding]; other site 452662001385 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 452662001386 DNA binding residues [nucleotide binding] 452662001387 dimerization interface [polypeptide binding]; other site 452662001388 Response regulator receiver domain; Region: Response_reg; pfam00072 452662001389 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 452662001390 active site 452662001391 phosphorylation site [posttranslational modification] 452662001392 intermolecular recognition site; other site 452662001393 dimerization interface [polypeptide binding]; other site 452662001394 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 452662001395 Mycobacterium tuberculosis CorA-like subfamily; Region: MtCorA-like; cd12830 452662001396 oligomer interface [polypeptide binding]; other site 452662001397 metal binding site [ion binding]; metal-binding site 452662001398 metal binding site [ion binding]; metal-binding site 452662001399 putative Cl binding site [ion binding]; other site 452662001400 basic sphincter; other site 452662001401 hydrophobic gate; other site 452662001402 periplasmic entrance; other site 452662001403 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 452662001404 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 452662001405 multiple promoter invertase; Provisional; Region: mpi; PRK13413 452662001406 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 452662001407 catalytic residues [active] 452662001408 catalytic nucleophile [active] 452662001409 Presynaptic Site I dimer interface [polypeptide binding]; other site 452662001410 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 452662001411 Synaptic Flat tetramer interface [polypeptide binding]; other site 452662001412 Synaptic Site I dimer interface [polypeptide binding]; other site 452662001413 DNA binding site [nucleotide binding] 452662001414 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 452662001415 DNA-binding interface [nucleotide binding]; DNA binding site 452662001416 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 452662001417 classical (c) SDRs; Region: SDR_c; cd05233 452662001418 NAD(P) binding site [chemical binding]; other site 452662001419 active site 452662001420 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662001421 NAD(P) binding site [chemical binding]; other site 452662001422 active site 452662001423 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041 452662001424 addiction module antitoxin, RelB/DinJ family; Region: RelB_DinJ; TIGR02384 452662001425 Protein of unknown function, DUF; Region: DUF411; cl01142 452662001426 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 452662001427 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 452662001428 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 452662001429 Multicopper oxidase; Region: Cu-oxidase; pfam00394 452662001430 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 452662001431 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 452662001432 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD3; cd08297 452662001433 NAD binding site [chemical binding]; other site 452662001434 substrate binding site [chemical binding]; other site 452662001435 catalytic Zn binding site [ion binding]; other site 452662001436 tetramer interface [polypeptide binding]; other site 452662001437 structural Zn binding site [ion binding]; other site 452662001438 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II and Staphylococcus aureus AldA1 (SACOL0154)-like; Region: ALDH_ACDHII_AcoD-like; cd07559 452662001439 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 452662001440 NAD(P) binding site [chemical binding]; other site 452662001441 catalytic residues [active] 452662001442 Cysteine-rich 4 helical bundle widely conserved in bacteria; Region: DUF326; cd08026 452662001443 dimerization interface [polypeptide binding]; other site 452662001444 Protein of unknown function (DUF1622); Region: DUF1622; pfam07784 452662001445 Seven times multi-haem cytochrome CxxCH; Region: Multi-haem_cyto; pfam13447 452662001446 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_3; cd06217 452662001447 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 452662001448 FAD binding pocket [chemical binding]; other site 452662001449 FAD binding motif [chemical binding]; other site 452662001450 phosphate binding motif [ion binding]; other site 452662001451 beta-alpha-beta structure motif; other site 452662001452 NAD binding pocket [chemical binding]; other site 452662001453 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 452662001454 catalytic loop [active] 452662001455 iron binding site [ion binding]; other site 452662001456 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 452662001457 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 452662001458 DNA binding residues [nucleotide binding] 452662001459 dimer interface [polypeptide binding]; other site 452662001460 metal binding site [ion binding]; metal-binding site 452662001461 Outer membrane efflux protein; Region: OEP; pfam02321 452662001462 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 452662001463 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662001464 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 452662001465 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 452662001466 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 452662001467 may be target duplication site 452662001468 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 452662001469 Coenzyme A binding pocket [chemical binding]; other site 452662001470 multiple promoter invertase; Provisional; Region: mpi; PRK13413 452662001471 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 452662001472 catalytic residues [active] 452662001473 catalytic nucleophile [active] 452662001474 Presynaptic Site I dimer interface [polypeptide binding]; other site 452662001475 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 452662001476 Synaptic Flat tetramer interface [polypeptide binding]; other site 452662001477 Synaptic Site I dimer interface [polypeptide binding]; other site 452662001478 DNA binding site [nucleotide binding] 452662001479 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 452662001480 DNA-binding interface [nucleotide binding]; DNA binding site 452662001481 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 452662001482 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 452662001483 may be target duplication site 452662001484 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 452662001485 Eukaryotic phosphomannomutase; Region: PMM; cl17107 452662001486 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 452662001487 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 452662001488 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 452662001489 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 452662001490 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_4; cd07822 452662001491 putative hydrophobic ligand binding site [chemical binding]; other site 452662001492 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 452662001493 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 452662001494 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662001495 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 452662001496 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 452662001497 High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism]; Region: FTR1; COG0672 452662001498 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 452662001499 Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Region: HTH_CadR-PbrR-like; cd04785 452662001500 DNA binding residues [nucleotide binding] 452662001501 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 452662001502 dimer interface [polypeptide binding]; other site 452662001503 putative metal binding site [ion binding]; other site 452662001504 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 452662001505 catalytic motif [active] 452662001506 Catalytic residue [active] 452662001507 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 452662001508 protein binding site [polypeptide binding]; other site 452662001509 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 452662001510 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 452662001511 catalytic residues [active] 452662001512 catalytic nucleophile [active] 452662001513 Presynaptic Site I dimer interface [polypeptide binding]; other site 452662001514 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 452662001515 Synaptic Flat tetramer interface [polypeptide binding]; other site 452662001516 Synaptic Site I dimer interface [polypeptide binding]; other site 452662001517 DNA binding site [nucleotide binding] 452662001518 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl17393 452662001519 DNA-binding interface [nucleotide binding]; DNA binding site 452662001520 may be target duplication site 452662001521 Helix-turn-helix domain; Region: HTH_28; pfam13518 452662001522 Winged helix-turn helix; Region: HTH_29; pfam13551 452662001523 Homeodomain-like domain; Region: HTH_32; pfam13565 452662001524 Integrase core domain; Region: rve; pfam00665 452662001525 Integrase core domain; Region: rve_3; cl15866 452662001526 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 452662001527 AAA domain; Region: AAA_22; pfam13401 452662001528 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 452662001529 may be target duplication site 452662001530 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 452662001531 active site 452662001532 DNA binding site [nucleotide binding] 452662001533 Int/Topo IB signature motif; other site 452662001534 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 452662001535 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 452662001536 catalytic residues [active] 452662001537 catalytic nucleophile [active] 452662001538 Presynaptic Site I dimer interface [polypeptide binding]; other site 452662001539 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 452662001540 Synaptic Flat tetramer interface [polypeptide binding]; other site 452662001541 Synaptic Site I dimer interface [polypeptide binding]; other site 452662001542 DNA binding site [nucleotide binding] 452662001543 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 452662001544 DNA-binding interface [nucleotide binding]; DNA binding site 452662001545 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 452662001546 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 452662001547 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 452662001548 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662001549 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 452662001550 EthD domain; Region: EthD; pfam07110 452662001551 classical (c) SDRs; Region: SDR_c; cd05233 452662001552 NAD(P) binding site [chemical binding]; other site 452662001553 active site 452662001554 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 452662001555 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 452662001556 [2Fe-2S] cluster binding site [ion binding]; other site 452662001557 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 452662001558 alpha subunit interface [polypeptide binding]; other site 452662001559 active site 452662001560 substrate binding site [chemical binding]; other site 452662001561 Fe binding site [ion binding]; other site 452662001562 EthD domain; Region: EthD; pfam07110 452662001563 short chain dehydrogenase; Provisional; Region: PRK06172 452662001564 classical (c) SDRs; Region: SDR_c; cd05233 452662001565 NAD(P) binding site [chemical binding]; other site 452662001566 active site 452662001567 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 452662001568 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662001569 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662001570 Integrase core domain; Region: rve; pfam00665 452662001571 Autotransporter beta-domain; Region: Autotransporter; pfam03797 452662001572 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 452662001573 Fic family protein [Function unknown]; Region: COG3177 452662001574 Fic/DOC family; Region: Fic; pfam02661 452662001575 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 452662001576 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662001577 NAD(P) binding site [chemical binding]; other site 452662001578 active site 452662001579 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 452662001580 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 452662001581 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 452662001582 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 452662001583 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 452662001584 nucleophile elbow; other site 452662001585 Patatin phospholipase; Region: DUF3734; pfam12536 452662001586 acetoacetate decarboxylase; Provisional; Region: PRK02265 452662001587 Phasin protein; Region: Phasin_2; cl11491 452662001588 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; pfam05930 452662001589 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 452662001590 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 452662001591 active site 452662001592 Int/Topo IB signature motif; other site 452662001593 GMP synthase; Reviewed; Region: guaA; PRK00074 452662001594 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 452662001595 AMP/PPi binding site [chemical binding]; other site 452662001596 candidate oxyanion hole; other site 452662001597 catalytic triad [active] 452662001598 potential glutamine specificity residues [chemical binding]; other site 452662001599 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 452662001600 ATP Binding subdomain [chemical binding]; other site 452662001601 Ligand Binding sites [chemical binding]; other site 452662001602 Dimerization subdomain; other site 452662001603 Protein of unknown function (DUF1275); Region: DUF1275; cl01453 452662001604 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 452662001605 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 452662001606 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 452662001607 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 452662001608 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 452662001609 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 452662001610 alphaNTD homodimer interface [polypeptide binding]; other site 452662001611 alphaNTD - beta interaction site [polypeptide binding]; other site 452662001612 alphaNTD - beta' interaction site [polypeptide binding]; other site 452662001613 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 452662001614 30S ribosomal protein S11; Validated; Region: PRK05309 452662001615 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 452662001616 30S ribosomal protein S13; Region: bact_S13; TIGR03631 452662001617 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 452662001618 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 452662001619 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 452662001620 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662001621 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662001622 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 452662001623 putative effector binding pocket; other site 452662001624 dimerization interface [polypeptide binding]; other site 452662001625 Protein of unknown function (DUF3154); Region: DUF3154; pfam11351 452662001626 Glycosyl hydrolase 108; Region: Glyco_hydro_108; pfam05838 452662001627 Predicted Peptidoglycan domain; Region: PG_binding_3; pfam09374 452662001628 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 452662001629 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 452662001630 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 452662001631 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 452662001632 Protein export membrane protein; Region: SecD_SecF; pfam02355 452662001633 Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a...; Region: Mth938-like; cl00182 452662001634 exopolyphosphatase; Region: exo_poly_only; TIGR03706 452662001635 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 452662001636 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 452662001637 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 452662001638 S-adenosylmethionine binding site [chemical binding]; other site 452662001639 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 452662001640 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 452662001641 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 452662001642 Walker A motif; other site 452662001643 ATP binding site [chemical binding]; other site 452662001644 Walker B motif; other site 452662001645 arginine finger; other site 452662001646 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 452662001647 Transcriptional regulators [Transcription]; Region: FadR; COG2186 452662001648 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 452662001649 DNA-binding site [nucleotide binding]; DNA binding site 452662001650 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 452662001651 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 452662001652 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 452662001653 Uncharacterized protein conserved in bacteria [Function unknown]; Region: GguC; COG3802 452662001654 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 452662001655 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 452662001656 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 452662001657 dimer interface [polypeptide binding]; other site 452662001658 NADP binding site [chemical binding]; other site 452662001659 catalytic residues [active] 452662001660 dihydroxy-acid dehydratase; Provisional; Region: PRK13017 452662001661 2-keto-3-deoxy-galactonokinase [Carbohydrate transport and metabolism]; Region: DgoK; COG3734 452662001662 2-keto-3-deoxy-galactonokinase; Region: DGOK; pfam05035 452662001663 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; Reviewed; Region: PRK09140 452662001664 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 452662001665 active site 452662001666 intersubunit interface [polypeptide binding]; other site 452662001667 catalytic residue [active] 452662001668 PAS fold; Region: PAS_4; pfam08448 452662001669 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662001670 PAS domain; Region: PAS_9; pfam13426 452662001671 putative active site [active] 452662001672 heme pocket [chemical binding]; other site 452662001673 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 452662001674 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662001675 dimer interface [polypeptide binding]; other site 452662001676 phosphorylation site [posttranslational modification] 452662001677 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 452662001678 ATP binding site [chemical binding]; other site 452662001679 Mg2+ binding site [ion binding]; other site 452662001680 G-X-G motif; other site 452662001681 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cl00528 452662001682 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 452662001683 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 452662001684 active site 452662001685 phosphorylation site [posttranslational modification] 452662001686 intermolecular recognition site; other site 452662001687 dimerization interface [polypeptide binding]; other site 452662001688 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 452662001689 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 452662001690 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 452662001691 23S rRNA interface [nucleotide binding]; other site 452662001692 L3 interface [polypeptide binding]; other site 452662001693 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 452662001694 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 452662001695 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 452662001696 active site 452662001697 catalytic residues [active] 452662001698 DNA binding site [nucleotide binding] 452662001699 Int/Topo IB signature motif; other site 452662001700 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 452662001701 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662001702 Walker A/P-loop; other site 452662001703 ATP binding site [chemical binding]; other site 452662001704 Q-loop/lid; other site 452662001705 ABC transporter signature motif; other site 452662001706 Walker B; other site 452662001707 D-loop; other site 452662001708 H-loop/switch region; other site 452662001709 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 452662001710 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662001711 multiple promoter invertase; Provisional; Region: mpi; PRK13413 452662001712 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 452662001713 catalytic residues [active] 452662001714 catalytic nucleophile [active] 452662001715 Presynaptic Site I dimer interface [polypeptide binding]; other site 452662001716 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 452662001717 Synaptic Flat tetramer interface [polypeptide binding]; other site 452662001718 Synaptic Site I dimer interface [polypeptide binding]; other site 452662001719 DNA binding site [nucleotide binding] 452662001720 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 452662001721 DNA-binding interface [nucleotide binding]; DNA binding site 452662001722 DEAD-like helicases superfamily; Region: DEXDc; smart00487 452662001723 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 452662001724 ATP binding site [chemical binding]; other site 452662001725 putative Mg++ binding site [ion binding]; other site 452662001726 Transposase domain (DUF772); Region: DUF772; pfam05598 452662001727 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662001728 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 452662001729 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 452662001730 Peptidase family M23; Region: Peptidase_M23; pfam01551 452662001731 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 452662001732 S17 interaction site [polypeptide binding]; other site 452662001733 S8 interaction site; other site 452662001734 16S rRNA interaction site [nucleotide binding]; other site 452662001735 streptomycin interaction site [chemical binding]; other site 452662001736 23S rRNA interaction site [nucleotide binding]; other site 452662001737 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 452662001738 30S ribosomal protein S7; Validated; Region: PRK05302 452662001739 elongation factor G; Reviewed; Region: PRK00007 452662001740 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 452662001741 G1 box; other site 452662001742 putative GEF interaction site [polypeptide binding]; other site 452662001743 GTP/Mg2+ binding site [chemical binding]; other site 452662001744 Switch I region; other site 452662001745 G2 box; other site 452662001746 G3 box; other site 452662001747 Switch II region; other site 452662001748 G4 box; other site 452662001749 G5 box; other site 452662001750 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 452662001751 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 452662001752 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 452662001753 elongation factor Tu; Reviewed; Region: PRK00049 452662001754 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 452662001755 G1 box; other site 452662001756 GEF interaction site [polypeptide binding]; other site 452662001757 GTP/Mg2+ binding site [chemical binding]; other site 452662001758 Switch I region; other site 452662001759 G2 box; other site 452662001760 G3 box; other site 452662001761 Switch II region; other site 452662001762 G4 box; other site 452662001763 G5 box; other site 452662001764 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 452662001765 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 452662001766 Antibiotic Binding Site [chemical binding]; other site 452662001767 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 452662001768 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 452662001769 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 452662001770 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 452662001771 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 452662001772 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 452662001773 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 452662001774 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 452662001775 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 452662001776 putative translocon binding site; other site 452662001777 protein-rRNA interface [nucleotide binding]; other site 452662001778 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 452662001779 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 452662001780 G-X-X-G motif; other site 452662001781 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 452662001782 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 452662001783 23S rRNA interface [nucleotide binding]; other site 452662001784 5S rRNA interface [nucleotide binding]; other site 452662001785 putative antibiotic binding site [chemical binding]; other site 452662001786 L25 interface [polypeptide binding]; other site 452662001787 L27 interface [polypeptide binding]; other site 452662001788 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 452662001789 23S rRNA interface [nucleotide binding]; other site 452662001790 putative translocon interaction site; other site 452662001791 signal recognition particle (SRP54) interaction site; other site 452662001792 L23 interface [polypeptide binding]; other site 452662001793 trigger factor interaction site; other site 452662001794 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 452662001795 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 452662001796 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 452662001797 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 452662001798 RNA binding site [nucleotide binding]; other site 452662001799 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 452662001800 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 452662001801 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 452662001802 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 452662001803 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 452662001804 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 452662001805 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 452662001806 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 452662001807 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 452662001808 23S rRNA interface [nucleotide binding]; other site 452662001809 5S rRNA interface [nucleotide binding]; other site 452662001810 L27 interface [polypeptide binding]; other site 452662001811 L5 interface [polypeptide binding]; other site 452662001812 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 452662001813 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 452662001814 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 452662001815 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 452662001816 23S rRNA binding site [nucleotide binding]; other site 452662001817 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 452662001818 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 452662001819 SecY translocase; Region: SecY; pfam00344 452662001820 adenylate kinase; Reviewed; Region: adk; PRK00279 452662001821 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 452662001822 AMP-binding site [chemical binding]; other site 452662001823 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 452662001824 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 452662001825 hydrophobic ligand binding site; other site 452662001826 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 452662001827 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 452662001828 active site 452662001829 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 452662001830 MgtE intracellular N domain; Region: MgtE_N; smart00924 452662001831 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 452662001832 Divalent cation transporter; Region: MgtE; pfam01769 452662001833 Protein of unknown function (DUF1489); Region: DUF1489; cl11570 452662001834 probable DNA metabolism protein; Region: SAM_7_link_chp; TIGR03915 452662001835 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 452662001836 Fe-S cluster binding site [ion binding]; other site 452662001837 active site 452662001838 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 452662001839 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 452662001840 FeS/SAM binding site; other site 452662001841 CHASE3 domain; Region: CHASE3; pfam05227 452662001842 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662001843 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 452662001844 ATP binding site [chemical binding]; other site 452662001845 Mg2+ binding site [ion binding]; other site 452662001846 G-X-G motif; other site 452662001847 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 452662001848 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 452662001849 active site 452662001850 phosphorylation site [posttranslational modification] 452662001851 intermolecular recognition site; other site 452662001852 dimerization interface [polypeptide binding]; other site 452662001853 aldolase II superfamily protein; Provisional; Region: PRK07044 452662001854 intersubunit interface [polypeptide binding]; other site 452662001855 active site 452662001856 Zn2+ binding site [ion binding]; other site 452662001857 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 452662001858 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 452662001859 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 452662001860 Domain of unknown function DUF20; Region: UPF0118; pfam01594 452662001861 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 452662001862 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 452662001863 Catalytic site [active] 452662001864 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 452662001865 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 452662001866 pyridoxine 5'-phosphate synthase; Provisional; Region: PRK05265 452662001867 active site 452662001868 hydrophilic channel; other site 452662001869 dimerization interface [polypeptide binding]; other site 452662001870 catalytic residues [active] 452662001871 active site lid [active] 452662001872 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 452662001873 active site 452662001874 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 452662001875 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 452662001876 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 452662001877 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 452662001878 Subunit I/III interface [polypeptide binding]; other site 452662001879 D-pathway; other site 452662001880 Subunit I/VIIc interface [polypeptide binding]; other site 452662001881 Subunit I/IV interface [polypeptide binding]; other site 452662001882 Subunit I/II interface [polypeptide binding]; other site 452662001883 Low-spin heme (heme a) binding site [chemical binding]; other site 452662001884 Subunit I/VIIa interface [polypeptide binding]; other site 452662001885 Subunit I/VIa interface [polypeptide binding]; other site 452662001886 Dimer interface; other site 452662001887 Putative water exit pathway; other site 452662001888 Binuclear center (heme a3/CuB) [ion binding]; other site 452662001889 K-pathway; other site 452662001890 Subunit I/Vb interface [polypeptide binding]; other site 452662001891 Putative proton exit pathway; other site 452662001892 Subunit I/VIb interface; other site 452662001893 Subunit I/VIc interface [polypeptide binding]; other site 452662001894 Electron transfer pathway; other site 452662001895 Subunit I/VIIIb interface [polypeptide binding]; other site 452662001896 Subunit I/VIIb interface [polypeptide binding]; other site 452662001897 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 452662001898 UbiA prenyltransferase family; Region: UbiA; pfam01040 452662001899 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 452662001900 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 452662001901 Subunit III/VIIa interface [polypeptide binding]; other site 452662001902 Phospholipid binding site [chemical binding]; other site 452662001903 Subunit I/III interface [polypeptide binding]; other site 452662001904 Subunit III/VIb interface [polypeptide binding]; other site 452662001905 Subunit III/VIa interface; other site 452662001906 Subunit III/Vb interface [polypeptide binding]; other site 452662001907 Protein of unknown function (DUF983); Region: DUF983; cl02211 452662001908 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cl01321 452662001909 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 452662001910 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 452662001911 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662001912 catalytic residue [active] 452662001913 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 452662001914 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 452662001915 S-adenosylmethionine binding site [chemical binding]; other site 452662001916 MarC family integral membrane protein; Region: MarC; pfam01914 452662001917 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14188 452662001918 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 452662001919 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 452662001920 homodimer interface [polypeptide binding]; other site 452662001921 NADP binding site [chemical binding]; other site 452662001922 substrate binding site [chemical binding]; other site 452662001923 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 452662001924 YGGT family; Region: YGGT; pfam02325 452662001925 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 452662001926 feedback inhibition sensing region; other site 452662001927 homohexameric interface [polypeptide binding]; other site 452662001928 nucleotide binding site [chemical binding]; other site 452662001929 N-acetyl-L-glutamate binding site [chemical binding]; other site 452662001930 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 452662001931 beta-carotene hydroxylase; Region: PLN02601 452662001932 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 452662001933 mechanosensitive channel MscS; Provisional; Region: PRK10334 452662001934 Mechanosensitive ion channel; Region: MS_channel; pfam00924 452662001935 cystathionine beta-lyase; Provisional; Region: PRK09028 452662001936 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 452662001937 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 452662001938 catalytic residue [active] 452662001939 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 452662001940 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 452662001941 active site residue [active] 452662001942 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 452662001943 active site residue [active] 452662001944 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 452662001945 Peptidase family M1; Region: Peptidase_M1; pfam01433 452662001946 Peptidase M1 Aminopeptidase N family incudes tricorn interacting factor F3, Endoplasmic reticulum aminopeptidase 1 (ERAP1), Aminopeptidase Q (APQ); Region: M1_APN_2; cd09601 452662001947 Zn binding site [ion binding]; other site 452662001948 Domain of unknown function (DUF3358); Region: DUF3358; pfam11838 452662001949 Predicted membrane protein [Function unknown]; Region: COG1297 452662001950 putative oligopeptide transporter, OPT family; Region: TIGR00733 452662001951 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 452662001952 active site 452662001953 catalytic triad [active] 452662001954 oxyanion hole [active] 452662001955 Hemimethylated DNA-binding protein YccV like; Region: YccV-like; pfam08755 452662001956 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 452662001957 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662001958 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic); Region: Peptidase_C39_like; cl00296 452662001959 putative active site [active] 452662001960 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 452662001961 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 452662001962 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 452662001963 Walker A/P-loop; other site 452662001964 ATP binding site [chemical binding]; other site 452662001965 Q-loop/lid; other site 452662001966 ABC transporter signature motif; other site 452662001967 Walker B; other site 452662001968 D-loop; other site 452662001969 H-loop/switch region; other site 452662001970 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 452662001971 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662001972 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 452662001973 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 452662001974 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 452662001975 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 452662001976 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 452662001977 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 452662001978 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 452662001979 Spore Coat Protein U domain; Region: SCPU; pfam05229 452662001980 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 452662001981 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 452662001982 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 452662001983 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 452662001984 PapC C-terminal domain; Region: PapC_C; pfam13953 452662001985 Spore Coat Protein U domain; Region: SCPU; pfam05229 452662001986 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662001987 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662001988 metal binding site [ion binding]; metal-binding site 452662001989 active site 452662001990 I-site; other site 452662001991 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 452662001992 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 452662001993 ATPase, P-type (transporting), HAD superfamily, subfamily IC; Region: ATPase_P-type; TIGR01494 452662001994 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 452662001995 motif II; other site 452662001996 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 452662001997 Cytochrome c; Region: Cytochrom_C; cl11414 452662001998 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 452662001999 Cytochrome c; Region: Cytochrom_C; pfam00034 452662002000 YHS domain; Region: YHS; pfam04945 452662002001 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 452662002002 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 452662002003 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 452662002004 motif II; other site 452662002005 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662002006 CESA_CelA_like are involved in the elongation of the glucan chain of cellulose; Region: CESA_CelA_like; cd06421 452662002007 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 452662002008 DXD motif; other site 452662002009 PilZ domain; Region: PilZ; pfam07238 452662002010 Transcriptional regulators [Transcription]; Region: PurR; COG1609 452662002011 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 452662002012 DNA binding site [nucleotide binding] 452662002013 domain linker motif; other site 452662002014 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 452662002015 putative dimerization interface [polypeptide binding]; other site 452662002016 putative ligand binding site [chemical binding]; other site 452662002017 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662002018 HAMP domain; Region: HAMP; pfam00672 452662002019 dimerization interface [polypeptide binding]; other site 452662002020 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 452662002021 dimer interface [polypeptide binding]; other site 452662002022 phosphorylation site [posttranslational modification] 452662002023 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 452662002024 ATP binding site [chemical binding]; other site 452662002025 Mg2+ binding site [ion binding]; other site 452662002026 G-X-G motif; other site 452662002027 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 452662002028 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 452662002029 active site 452662002030 phosphorylation site [posttranslational modification] 452662002031 intermolecular recognition site; other site 452662002032 dimerization interface [polypeptide binding]; other site 452662002033 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 452662002034 DNA binding site [nucleotide binding] 452662002035 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 452662002036 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 452662002037 active site 452662002038 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 452662002039 Catalytic NodB homology domain of uncharacterized bacterial glycosyl transferase, group 2-like family proteins; Region: CE4_GT2-like; cd10962 452662002040 NodB motif; other site 452662002041 putative active site [active] 452662002042 putative catalytic site [active] 452662002043 putative Zn binding site [ion binding]; other site 452662002044 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 452662002045 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 452662002046 DXD motif; other site 452662002047 Nitroreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_2; cd02138 452662002048 putative FMN binding site [chemical binding]; other site 452662002049 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 452662002050 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 452662002051 PLD-like domain; Region: PLDc_2; pfam13091 452662002052 putative active site [active] 452662002053 catalytic site [active] 452662002054 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 452662002055 PLD-like domain; Region: PLDc_2; pfam13091 452662002056 putative active site [active] 452662002057 catalytic site [active] 452662002058 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 452662002059 hydroxyglutarate oxidase; Provisional; Region: PRK11728 452662002060 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 452662002061 Glycerol kinase [Energy production and conversion]; Region: GlpK; COG0554 452662002062 N- and C-terminal domain interface [polypeptide binding]; other site 452662002063 active site 452662002064 MgATP binding site [chemical binding]; other site 452662002065 catalytic site [active] 452662002066 metal binding site [ion binding]; metal-binding site 452662002067 glycerol binding site [chemical binding]; other site 452662002068 homotetramer interface [polypeptide binding]; other site 452662002069 homodimer interface [polypeptide binding]; other site 452662002070 FBP binding site [chemical binding]; other site 452662002071 protein IIAGlc interface [polypeptide binding]; other site 452662002072 MASE1; Region: MASE1; cl17823 452662002073 PAS domain S-box; Region: sensory_box; TIGR00229 452662002074 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662002075 putative active site [active] 452662002076 heme pocket [chemical binding]; other site 452662002077 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662002078 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662002079 metal binding site [ion binding]; metal-binding site 452662002080 active site 452662002081 I-site; other site 452662002082 MerC mercury resistance protein; Region: MerC; pfam03203 452662002083 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 452662002084 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 452662002085 putative active site [active] 452662002086 homoserine dehydrogenase; Provisional; Region: PRK06349 452662002087 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 452662002088 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 452662002089 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 452662002090 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 452662002091 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 452662002092 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 452662002093 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 452662002094 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 452662002095 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 452662002096 PilZ domain; Region: PilZ; cl01260 452662002097 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 452662002098 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 452662002099 TAP-like protein; Region: Abhydrolase_4; pfam08386 452662002100 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 452662002101 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 452662002102 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662002103 Walker A/P-loop; other site 452662002104 ATP binding site [chemical binding]; other site 452662002105 Q-loop/lid; other site 452662002106 ABC transporter signature motif; other site 452662002107 Walker B; other site 452662002108 D-loop; other site 452662002109 H-loop/switch region; other site 452662002110 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of...; Region: L-Ala-DL-Glu_epimerase; cd03319 452662002111 active site 452662002112 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 452662002113 Mechanosensitive ion channel; Region: MS_channel; pfam00924 452662002114 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 452662002115 DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of...; Region: Topo_IB_C; cd00659 452662002116 active site 452662002117 DNA binding site [nucleotide binding] 452662002118 Int/Topo IB signature motif; other site 452662002119 catalytic residues [active] 452662002120 O-Antigen ligase; Region: Wzy_C; cl04850 452662002121 PEP-CTERM/exosortase A-associated glycosyltransferase, Daro_2409 family; Region: stp3; TIGR04063 452662002122 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 452662002123 Predicted transcriptional regulator [Transcription]; Region: COG2932 452662002124 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 452662002125 Catalytic site [active] 452662002126 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 452662002127 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 452662002128 XdhC Rossmann domain; Region: XdhC_C; pfam13478 452662002129 Uncharacterized small protein [Function unknown]; Region: COG2879 452662002130 carbon starvation protein A; Provisional; Region: PRK15015 452662002131 Carbon starvation protein CstA; Region: CstA; pfam02554 452662002132 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 452662002133 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 452662002134 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 452662002135 PhnA protein; Region: PhnA; pfam03831 452662002136 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 452662002137 G1 box; other site 452662002138 GTP/Mg2+ binding site [chemical binding]; other site 452662002139 Switch I region; other site 452662002140 G2 box; other site 452662002141 G3 box; other site 452662002142 Switch II region; other site 452662002143 G4 box; other site 452662002144 G5 box; other site 452662002145 membrane protein insertase; Provisional; Region: PRK01318 452662002146 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 452662002147 Haemolytic domain; Region: Haemolytic; pfam01809 452662002148 Ribonuclease P; Region: Ribonuclease_P; cl00457 452662002149 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 452662002150 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 452662002151 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 452662002152 catalytic residues [active] 452662002153 Peptidase family M48; Region: Peptidase_M48; cl12018 452662002154 TPR repeat; Region: TPR_11; pfam13414 452662002155 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 452662002156 TPR motif; other site 452662002157 binding surface 452662002158 Tetratricopeptide repeat; Region: TPR_16; pfam13432 452662002159 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 452662002160 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 452662002161 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 452662002162 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 452662002163 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 452662002164 active site 452662002165 metal binding site [ion binding]; metal-binding site 452662002166 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 452662002167 Transglycosylase; Region: Transgly; pfam00912 452662002168 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 452662002169 Protein of unknown function DUF72; Region: DUF72; pfam01904 452662002170 PspC domain; Region: PspC; pfam04024 452662002171 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 452662002172 putative active site pocket [active] 452662002173 dimerization interface [polypeptide binding]; other site 452662002174 putative catalytic residue [active] 452662002175 Dienelactone hydrolase family; Region: DLH; pfam01738 452662002176 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 452662002177 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 452662002178 catalytic triad [active] 452662002179 peptide chain release factor 2; Validated; Region: prfB; PRK00578 452662002180 This domain is found in peptide chain release factors; Region: PCRF; smart00937 452662002181 RF-1 domain; Region: RF-1; pfam00472 452662002182 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 452662002183 S-adenosylmethionine binding site [chemical binding]; other site 452662002184 Toxic anion resistance protein (TelA); Region: TelA; pfam05816 452662002185 Protein of unknown function, DUF485; Region: DUF485; pfam04341 452662002186 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 452662002187 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 452662002188 Na binding site [ion binding]; other site 452662002189 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 452662002190 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 452662002191 G1 box; other site 452662002192 putative GEF interaction site [polypeptide binding]; other site 452662002193 GTP/Mg2+ binding site [chemical binding]; other site 452662002194 Switch I region; other site 452662002195 G2 box; other site 452662002196 G3 box; other site 452662002197 Switch II region; other site 452662002198 G4 box; other site 452662002199 G5 box; other site 452662002200 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 452662002201 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 452662002202 Peptidase family M48; Region: Peptidase_M48; cl12018 452662002203 Bacterial protein of unknown function (DUF898); Region: DUF898; pfam05987 452662002204 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 452662002205 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 452662002206 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 452662002207 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 452662002208 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 452662002209 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 452662002210 active site 452662002211 dimer interface [polypeptide binding]; other site 452662002212 motif 1; other site 452662002213 motif 2; other site 452662002214 motif 3; other site 452662002215 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 452662002216 anticodon binding site; other site 452662002217 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 452662002218 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 452662002219 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 452662002220 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662002221 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662002222 metal binding site [ion binding]; metal-binding site 452662002223 active site 452662002224 I-site; other site 452662002225 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 452662002226 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 452662002227 active site 452662002228 HIGH motif; other site 452662002229 nucleotide binding site [chemical binding]; other site 452662002230 active site 452662002231 KMSKS motif; other site 452662002232 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 452662002233 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 452662002234 active site 452662002235 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 452662002236 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 452662002237 ligand binding site [chemical binding]; other site 452662002238 flexible hinge region; other site 452662002239 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 452662002240 putative switch regulator; other site 452662002241 non-specific DNA interactions [nucleotide binding]; other site 452662002242 DNA binding site [nucleotide binding] 452662002243 sequence specific DNA binding site [nucleotide binding]; other site 452662002244 putative cAMP binding site [chemical binding]; other site 452662002245 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 452662002246 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 452662002247 hinge; other site 452662002248 active site 452662002249 GAF domain; Region: GAF; pfam01590 452662002250 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 452662002251 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662002252 PAS fold; Region: PAS_3; pfam08447 452662002253 putative active site [active] 452662002254 heme pocket [chemical binding]; other site 452662002255 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 452662002256 HWE histidine kinase; Region: HWE_HK; pfam07536 452662002257 response regulator; Provisional; Region: PRK13435 452662002258 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 452662002259 active site 452662002260 phosphorylation site [posttranslational modification] 452662002261 intermolecular recognition site; other site 452662002262 dimerization interface [polypeptide binding]; other site 452662002263 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 452662002264 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 452662002265 minor groove reading motif; other site 452662002266 helix-hairpin-helix signature motif; other site 452662002267 substrate binding pocket [chemical binding]; other site 452662002268 active site 452662002269 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 452662002270 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; cl00159 452662002271 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 452662002272 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 452662002273 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 452662002274 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 452662002275 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 452662002276 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 452662002277 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 452662002278 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 452662002279 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 452662002280 ABC transporter; Region: ABC_tran_2; pfam12848 452662002281 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 452662002282 Domain of unknown function DUF20; Region: UPF0118; pfam01594 452662002283 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 452662002284 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 452662002285 YceI-like domain; Region: YceI; pfam04264 452662002286 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 452662002287 active site 452662002288 Protein of unknown function (DUF983); Region: DUF983; cl02211 452662002289 aminodeoxychorismate synthase; Provisional; Region: PRK07508 452662002290 chorismate binding enzyme; Region: Chorismate_bind; cl10555 452662002291 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 452662002292 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 452662002293 substrate-cofactor binding pocket; other site 452662002294 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662002295 catalytic residue [active] 452662002296 aspartate aminotransferase; Provisional; Region: PRK05764 452662002297 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 452662002298 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662002299 homodimer interface [polypeptide binding]; other site 452662002300 catalytic residue [active] 452662002301 methionine sulfoxide reductase A; Provisional; Region: PRK13014 452662002302 2-enoyl thioester reductase (ETR) like proteins, child 1; Region: ETR_like_1; cd08291 452662002303 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 452662002304 NADP binding site [chemical binding]; other site 452662002305 dimer interface [polypeptide binding]; other site 452662002306 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 452662002307 ABC1 family; Region: ABC1; cl17513 452662002308 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 452662002309 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 452662002310 S-adenosylmethionine binding site [chemical binding]; other site 452662002311 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 452662002312 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 452662002313 DNA binding site [nucleotide binding] 452662002314 catalytic residue [active] 452662002315 H2TH interface [polypeptide binding]; other site 452662002316 putative catalytic residues [active] 452662002317 turnover-facilitating residue; other site 452662002318 intercalation triad [nucleotide binding]; other site 452662002319 8OG recognition residue [nucleotide binding]; other site 452662002320 putative reading head residues; other site 452662002321 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 452662002322 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 452662002323 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 452662002324 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 452662002325 DnaA N-terminal domain; Region: DnaA_N; pfam11638 452662002326 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 452662002327 Walker A motif; other site 452662002328 ATP binding site [chemical binding]; other site 452662002329 Walker B motif; other site 452662002330 arginine finger; other site 452662002331 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 452662002332 DnaA box-binding interface [nucleotide binding]; other site 452662002333 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 452662002334 active site 452662002335 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 452662002336 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 452662002337 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 452662002338 active site 452662002339 HIGH motif; other site 452662002340 dimer interface [polypeptide binding]; other site 452662002341 KMSKS motif; other site 452662002342 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 452662002343 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 452662002344 Preprotein translocase subunit SecB; Region: SecB; pfam02556 452662002345 SecA binding site; other site 452662002346 Preprotein binding site; other site 452662002347 Tim44-like domain; Region: Tim44; pfam04280 452662002348 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 452662002349 MltA specific insert domain; Region: MltA; smart00925 452662002350 3D domain; Region: 3D; pfam06725 452662002351 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 452662002352 Smr domain; Region: Smr; pfam01713 452662002353 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662002354 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662002355 metal binding site [ion binding]; metal-binding site 452662002356 active site 452662002357 I-site; other site 452662002358 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 452662002359 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 452662002360 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 452662002361 metal binding site [ion binding]; metal-binding site 452662002362 dimer interface [polypeptide binding]; other site 452662002363 Cupin domain; Region: Cupin_2; cl17218 452662002364 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 452662002365 dimer interface [polypeptide binding]; other site 452662002366 catalytic triad [active] 452662002367 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 452662002368 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 452662002369 glutamine binding [chemical binding]; other site 452662002370 catalytic triad [active] 452662002371 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 452662002372 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 452662002373 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 452662002374 active site 452662002375 ribulose/triose binding site [chemical binding]; other site 452662002376 phosphate binding site [ion binding]; other site 452662002377 substrate (anthranilate) binding pocket [chemical binding]; other site 452662002378 product (indole) binding pocket [chemical binding]; other site 452662002379 molybdenum cofactor biosynthesis protein MoaC; Provisional; Region: moaC; PRK09364 452662002380 trimer interface [polypeptide binding]; other site 452662002381 dimer interface [polypeptide binding]; other site 452662002382 putative active site [active] 452662002383 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 452662002384 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 452662002385 dimer interface [polypeptide binding]; other site 452662002386 putative functional site; other site 452662002387 putative MPT binding site; other site 452662002388 LexA repressor; Validated; Region: PRK00215 452662002389 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 452662002390 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 452662002391 Catalytic site [active] 452662002392 Competence protein; Region: Competence; pfam03772 452662002393 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 452662002394 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 452662002395 catalytic residues [active] 452662002396 catalytic nucleophile [active] 452662002397 Recombinase; Region: Recombinase; pfam07508 452662002398 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 452662002399 Terminase-like family; Region: Terminase_6; pfam03237 452662002400 Phage terminase large subunit; Region: Terminase_3; cl12054 452662002401 Uncharacterized conserved protein [Function unknown]; Region: COG5323 452662002402 Domain of unknown function (DUF4055); Region: DUF4055; pfam13264 452662002403 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 452662002404 Phage-related minor tail protein [Function unknown]; Region: COG5281 452662002405 tape measure domain; Region: tape_meas_nterm; TIGR02675 452662002406 multiple promoter invertase; Provisional; Region: mpi; PRK13413 452662002407 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 452662002408 catalytic residues [active] 452662002409 catalytic nucleophile [active] 452662002410 Presynaptic Site I dimer interface [polypeptide binding]; other site 452662002411 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 452662002412 Synaptic Flat tetramer interface [polypeptide binding]; other site 452662002413 Synaptic Site I dimer interface [polypeptide binding]; other site 452662002414 DNA binding site [nucleotide binding] 452662002415 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 452662002416 DNA-binding interface [nucleotide binding]; DNA binding site 452662002417 Predicted transcriptional regulator [Transcription]; Region: COG2944 452662002418 Protein of unknown function (DUF1044); Region: DUF1044; cl01955 452662002419 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 452662002420 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 452662002421 TIR domain; Region: TIR_2; pfam13676 452662002422 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 452662002423 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 452662002424 Competence protein; Region: Competence; pfam03772 452662002425 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 452662002426 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 452662002427 active site 452662002428 HIGH motif; other site 452662002429 nucleotide binding site [chemical binding]; other site 452662002430 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 452662002431 active site 452662002432 KMSKS motif; other site 452662002433 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 452662002434 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 452662002435 dimer interface [polypeptide binding]; other site 452662002436 active site 452662002437 citrylCoA binding site [chemical binding]; other site 452662002438 NADH binding [chemical binding]; other site 452662002439 cationic pore residues; other site 452662002440 oxalacetate/citrate binding site [chemical binding]; other site 452662002441 coenzyme A binding site [chemical binding]; other site 452662002442 catalytic triad [active] 452662002443 recombination protein F; Reviewed; Region: recF; PRK00064 452662002444 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662002445 Walker A/P-loop; other site 452662002446 ATP binding site [chemical binding]; other site 452662002447 Q-loop/lid; other site 452662002448 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662002449 ABC transporter signature motif; other site 452662002450 Walker B; other site 452662002451 D-loop; other site 452662002452 H-loop/switch region; other site 452662002453 CHAP domain; Region: CHAP; cl17642 452662002454 CHAP domain; Region: CHAP; cl17642 452662002455 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 452662002456 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 452662002457 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 452662002458 Predicted membrane protein [Function unknown]; Region: COG3766 452662002459 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 452662002460 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 452662002461 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 452662002462 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 452662002463 S-adenosylmethionine binding site [chemical binding]; other site 452662002464 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 452662002465 Moco binding site; other site 452662002466 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 452662002467 metal coordination site [ion binding]; other site 452662002468 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 452662002469 Thiosulfate reductase cytochrome B subunit (membrane anchoring protein) [Energy production and conversion]; Region: COG4117 452662002470 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 452662002471 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 452662002472 DNA polymerase III subunit beta; Validated; Region: PRK05643 452662002473 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 452662002474 putative DNA binding surface [nucleotide binding]; other site 452662002475 dimer interface [polypeptide binding]; other site 452662002476 beta-clamp/clamp loader binding surface; other site 452662002477 beta-clamp/translesion DNA polymerase binding surface; other site 452662002478 PAS domain; Region: PAS_9; pfam13426 452662002479 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662002480 putative active site [active] 452662002481 heme pocket [chemical binding]; other site 452662002482 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662002483 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662002484 metal binding site [ion binding]; metal-binding site 452662002485 active site 452662002486 I-site; other site 452662002487 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 452662002488 PilZ domain; Region: PilZ; pfam07238 452662002489 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 452662002490 DDE superfamily endonuclease; Region: DDE_3; pfam13358 452662002491 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 452662002492 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 452662002493 ApbE family; Region: ApbE; pfam02424 452662002494 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 452662002495 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 452662002496 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 452662002497 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 452662002498 VacJ like lipoprotein; Region: VacJ; cl01073 452662002499 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 452662002500 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 452662002501 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 452662002502 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 452662002503 DNA binding residues [nucleotide binding] 452662002504 Post-segregation antitoxin CcdA; Region: CcdA; pfam07362 452662002505 CcdB protein; Region: CcdB; cl03380 452662002506 Aspartate racemase [Cell envelope biogenesis, outer membrane]; Region: RacX; COG1794 452662002507 aspartate racemase; Region: asp_race; TIGR00035 452662002508 PilZ domain; Region: PilZ; pfam07238 452662002509 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 452662002510 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 452662002511 active site 452662002512 phosphorylation site [posttranslational modification] 452662002513 intermolecular recognition site; other site 452662002514 dimerization interface [polypeptide binding]; other site 452662002515 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 452662002516 DNA binding residues [nucleotide binding] 452662002517 Na binding site [ion binding]; other site 452662002518 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 452662002519 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662002520 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 452662002521 dimer interface [polypeptide binding]; other site 452662002522 phosphorylation site [posttranslational modification] 452662002523 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 452662002524 ATP binding site [chemical binding]; other site 452662002525 Mg2+ binding site [ion binding]; other site 452662002526 G-X-G motif; other site 452662002527 Response regulator receiver domain; Region: Response_reg; pfam00072 452662002528 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 452662002529 active site 452662002530 phosphorylation site [posttranslational modification] 452662002531 intermolecular recognition site; other site 452662002532 dimerization interface [polypeptide binding]; other site 452662002533 HupE / UreJ protein; Region: HupE_UreJ; pfam04955 452662002534 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 452662002535 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 452662002536 UreF; Region: UreF; pfam01730 452662002537 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; cd00571 452662002538 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 452662002539 dimer interface [polypeptide binding]; other site 452662002540 catalytic residues [active] 452662002541 urease subunit alpha; Reviewed; Region: ureC; PRK13207 452662002542 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 452662002543 subunit interactions [polypeptide binding]; other site 452662002544 active site 452662002545 flap region; other site 452662002546 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 452662002547 gamma-beta subunit interface [polypeptide binding]; other site 452662002548 alpha-beta subunit interface [polypeptide binding]; other site 452662002549 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 452662002550 alpha-gamma subunit interface [polypeptide binding]; other site 452662002551 beta-gamma subunit interface [polypeptide binding]; other site 452662002552 UreD urease accessory protein; Region: UreD; cl00530 452662002553 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 452662002554 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 452662002555 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 452662002556 putative ligand binding site [chemical binding]; other site 452662002557 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 452662002558 TM-ABC transporter signature motif; other site 452662002559 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 452662002560 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 452662002561 TM-ABC transporter signature motif; other site 452662002562 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 452662002563 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 452662002564 Walker A/P-loop; other site 452662002565 ATP binding site [chemical binding]; other site 452662002566 Q-loop/lid; other site 452662002567 ABC transporter signature motif; other site 452662002568 Walker B; other site 452662002569 D-loop; other site 452662002570 H-loop/switch region; other site 452662002571 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 452662002572 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 452662002573 Walker A/P-loop; other site 452662002574 ATP binding site [chemical binding]; other site 452662002575 Q-loop/lid; other site 452662002576 ABC transporter signature motif; other site 452662002577 Walker B; other site 452662002578 D-loop; other site 452662002579 H-loop/switch region; other site 452662002580 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 452662002581 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 452662002582 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl17208 452662002583 chlorocatechol 1,2-dioxygenase; Region: chlorocat_1_2; TIGR02465 452662002584 active site 452662002585 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 452662002586 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 452662002587 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 452662002588 YciI-like protein; Reviewed; Region: PRK12863 452662002589 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 452662002590 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 452662002591 AsnC family; Region: AsnC_trans_reg; pfam01037 452662002592 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 452662002593 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662002594 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 452662002595 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662002596 M20 Peptidase Aminoacylase 1-like protein 2 aminobenzoyl-glutamate utilization protein B subfamily; Region: M20_Acy1L2_AbgB; cd05673 452662002597 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 452662002598 putative metal binding site [ion binding]; other site 452662002599 M20 Peptidase Aminoacylase 1-like protein 2 aminobenzoyl-glutamate utilization protein B subfamily; Region: M20_Acy1L2_AbgB; cd05673 452662002600 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 452662002601 putative metal binding site [ion binding]; other site 452662002602 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 452662002603 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 452662002604 putative substrate translocation pore; other site 452662002605 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 452662002606 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 452662002607 active site 452662002608 catalytic residues [active] 452662002609 Protein of unknown function (DUF461); Region: DUF461; pfam04314 452662002610 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 452662002611 Nucleotide-binding domain of human HSPA9, Escherichia coli DnaK, and similar proteins; Region: HSPA9-like_NBD; cd11733 452662002612 nucleotide binding site [chemical binding]; other site 452662002613 NEF interaction site [polypeptide binding]; other site 452662002614 SBD interface [polypeptide binding]; other site 452662002615 chaperone protein DnaJ; Provisional; Region: PRK10767 452662002616 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 452662002617 HSP70 interaction site [polypeptide binding]; other site 452662002618 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 452662002619 substrate binding site [polypeptide binding]; other site 452662002620 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 452662002621 Zn binding sites [ion binding]; other site 452662002622 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 452662002623 dimer interface [polypeptide binding]; other site 452662002624 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 452662002625 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 452662002626 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662002627 active site 452662002628 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 452662002629 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 452662002630 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 452662002631 DNA binding residues [nucleotide binding] 452662002632 putative dimer interface [polypeptide binding]; other site 452662002633 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 452662002634 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 452662002635 N-terminal plug; other site 452662002636 ligand-binding site [chemical binding]; other site 452662002637 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 452662002638 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 452662002639 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 452662002640 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 452662002641 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 452662002642 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 452662002643 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 452662002644 putative ADP-binding pocket [chemical binding]; other site 452662002645 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662002646 Gram-negative bacterial tonB protein; Region: TonB; cl10048 452662002647 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]; Region: COG1525 452662002648 Catalytic site; other site 452662002649 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 452662002650 Abi-like protein; Region: Abi_2; pfam07751 452662002651 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 452662002652 non-specific DNA binding site [nucleotide binding]; other site 452662002653 salt bridge; other site 452662002654 sequence-specific DNA binding site [nucleotide binding]; other site 452662002655 DDE superfamily endonuclease; Region: DDE_3; pfam13358 452662002656 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 452662002657 Winged helix-turn helix; Region: HTH_29; pfam13551 452662002658 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 452662002659 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 452662002660 Int/Topo IB signature motif; other site 452662002661 Helix-turn-helix domain; Region: HTH_17; pfam12728 452662002662 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 452662002663 active site 452662002664 metal binding site [ion binding]; metal-binding site 452662002665 interdomain interaction site; other site 452662002666 AAA domain; Region: AAA_25; pfam13481 452662002667 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 452662002668 Walker A motif; other site 452662002669 ATP binding site [chemical binding]; other site 452662002670 Walker B motif; other site 452662002671 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 452662002672 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 452662002673 ATP binding site [chemical binding]; other site 452662002674 Mg2+ binding site [ion binding]; other site 452662002675 G-X-G motif; other site 452662002676 YcfA-like protein; Region: YcfA; pfam07927 452662002677 Domain of unknown function (DUF1902); Region: DUF1902; pfam08972 452662002678 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 452662002679 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 452662002680 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 452662002681 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 452662002682 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 452662002683 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 452662002684 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 452662002685 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 452662002686 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 452662002687 DNA binding site [nucleotide binding] 452662002688 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 452662002689 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 452662002690 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 452662002691 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 452662002692 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 452662002693 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 452662002694 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 452662002695 RPB3 interaction site [polypeptide binding]; other site 452662002696 RPB1 interaction site [polypeptide binding]; other site 452662002697 RPB11 interaction site [polypeptide binding]; other site 452662002698 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662002699 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 452662002700 N-terminal plug; other site 452662002701 ligand-binding site [chemical binding]; other site 452662002702 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 452662002703 DNA binding residues [nucleotide binding] 452662002704 dimerization interface [polypeptide binding]; other site 452662002705 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 452662002706 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 452662002707 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 452662002708 dimer interface [polypeptide binding]; other site 452662002709 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662002710 catalytic residue [active] 452662002711 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 452662002712 putative substrate translocation pore; other site 452662002713 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 452662002714 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 452662002715 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 452662002716 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 452662002717 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 452662002718 protein binding site [polypeptide binding]; other site 452662002719 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 452662002720 protein binding site [polypeptide binding]; other site 452662002721 HflC protein; Region: hflC; TIGR01932 452662002722 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 452662002723 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 452662002724 HflK protein; Region: hflK; TIGR01933 452662002725 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 452662002726 Predicted CoA-binding protein [General function prediction only]; Region: COG1832 452662002727 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 452662002728 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 452662002729 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 452662002730 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 452662002731 ferrochelatase; Reviewed; Region: hemH; PRK00035 452662002732 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 452662002733 C-terminal domain interface [polypeptide binding]; other site 452662002734 active site 452662002735 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 452662002736 active site 452662002737 N-terminal domain interface [polypeptide binding]; other site 452662002738 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 452662002739 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 452662002740 NAD(P) binding site [chemical binding]; other site 452662002741 homotetramer interface [polypeptide binding]; other site 452662002742 homodimer interface [polypeptide binding]; other site 452662002743 active site 452662002744 Ribbon-helix-helix domain; Region: RHH_4; pfam13467 452662002745 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 452662002746 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 452662002747 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 452662002748 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 452662002749 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 452662002750 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 452662002751 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 452662002752 Methyltransferase domain; Region: Methyltransf_18; pfam12847 452662002753 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 452662002754 ADP-ribose binding site [chemical binding]; other site 452662002755 dimer interface [polypeptide binding]; other site 452662002756 active site 452662002757 nudix motif; other site 452662002758 metal binding site [ion binding]; metal-binding site 452662002759 Repair protein; Region: Repair_PSII; cl01535 452662002760 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 452662002761 Repair protein; Region: Repair_PSII; pfam04536 452662002762 LemA family; Region: LemA; cl00742 452662002763 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 452662002764 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 452662002765 Transposase domain (DUF772); Region: DUF772; pfam05598 452662002766 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662002767 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 452662002768 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 452662002769 putative binding surface; other site 452662002770 active site 452662002771 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 452662002772 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 452662002773 ATP binding site [chemical binding]; other site 452662002774 Mg2+ binding site [ion binding]; other site 452662002775 G-X-G motif; other site 452662002776 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 452662002777 CheW-like domain; Region: CheW; pfam01584 452662002778 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 452662002779 Response regulator receiver domain; Region: Response_reg; pfam00072 452662002780 active site 452662002781 phosphorylation site [posttranslational modification] 452662002782 intermolecular recognition site; other site 452662002783 dimerization interface [polypeptide binding]; other site 452662002784 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 452662002785 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 452662002786 active site 452662002787 phosphorylation site [posttranslational modification] 452662002788 intermolecular recognition site; other site 452662002789 dimerization interface [polypeptide binding]; other site 452662002790 CheB methylesterase; Region: CheB_methylest; pfam01339 452662002791 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 452662002792 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 452662002793 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 452662002794 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 452662002795 amidase catalytic site [active] 452662002796 Zn binding residues [ion binding]; other site 452662002797 substrate binding site [chemical binding]; other site 452662002798 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 452662002799 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 452662002800 putative catalytic site [active] 452662002801 putative metal binding site [ion binding]; other site 452662002802 putative phosphate binding site [ion binding]; other site 452662002803 DNA repair protein RadA; Provisional; Region: PRK11823 452662002804 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 452662002805 Walker A motif; other site 452662002806 ATP binding site [chemical binding]; other site 452662002807 Walker B motif; other site 452662002808 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 452662002809 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 452662002810 Colicin V production protein; Region: Colicin_V; pfam02674 452662002811 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 452662002812 Aminopeptidase P, N-terminal domain; Region: AMP_N; smart01011 452662002813 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 452662002814 active site 452662002815 signal recognition particle protein; Provisional; Region: PRK10867 452662002816 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 452662002817 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 452662002818 P loop; other site 452662002819 GTP binding site [chemical binding]; other site 452662002820 Signal peptide binding domain; Region: SRP_SPB; pfam02978 452662002821 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 452662002822 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 452662002823 RimM N-terminal domain; Region: RimM; pfam01782 452662002824 PRC-barrel domain; Region: PRC; pfam05239 452662002825 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 452662002826 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 452662002827 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 452662002828 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 452662002829 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 452662002830 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 452662002831 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 452662002832 Coenzyme A binding pocket [chemical binding]; other site 452662002833 metabolite-proton symporter; Region: 2A0106; TIGR00883 452662002834 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 452662002835 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 452662002836 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 452662002837 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 452662002838 active site 452662002839 dimerization interface [polypeptide binding]; other site 452662002840 ribonuclease PH; Reviewed; Region: rph; PRK00173 452662002841 Ribonuclease PH; Region: RNase_PH_bact; cd11362 452662002842 hexamer interface [polypeptide binding]; other site 452662002843 active site 452662002844 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 452662002845 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 452662002846 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 452662002847 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 452662002848 dimer interface [polypeptide binding]; other site 452662002849 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 452662002850 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 452662002851 dimer interface [polypeptide binding]; other site 452662002852 putative CheW interface [polypeptide binding]; other site 452662002853 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 452662002854 proximal quinone binding site [chemical binding]; other site 452662002855 SdhD (CybS) interface [polypeptide binding]; other site 452662002856 proximal heme binding site [chemical binding]; other site 452662002857 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 452662002858 putative SdhC subunit interface [polypeptide binding]; other site 452662002859 putative proximal heme binding site [chemical binding]; other site 452662002860 putative Iron-sulfur protein interface [polypeptide binding]; other site 452662002861 putative proximal quinone binding site; other site 452662002862 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 452662002863 L-aspartate oxidase; Provisional; Region: PRK06175 452662002864 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 452662002865 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 452662002866 GAF domain; Region: GAF; pfam01590 452662002867 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662002868 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662002869 metal binding site [ion binding]; metal-binding site 452662002870 active site 452662002871 I-site; other site 452662002872 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 452662002873 dimerization domain swap beta strand [polypeptide binding]; other site 452662002874 regulatory protein interface [polypeptide binding]; other site 452662002875 active site 452662002876 regulatory phosphorylation site [posttranslational modification]; other site 452662002877 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cd00006 452662002878 active pocket/dimerization site; other site 452662002879 active site 452662002880 phosphorylation site [posttranslational modification] 452662002881 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 452662002882 Serine kinase of the HPr protein, regulates carbohydrate metabolism [Signal transduction mechanisms]; Region: HprK; COG1493 452662002883 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 452662002884 Hpr binding site; other site 452662002885 active site 452662002886 homohexamer subunit interaction site [polypeptide binding]; other site 452662002887 Stimulus-sensing domain; Region: Stimulus_sens_1; pfam13756 452662002888 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662002889 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 452662002890 dimer interface [polypeptide binding]; other site 452662002891 phosphorylation site [posttranslational modification] 452662002892 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 452662002893 ATP binding site [chemical binding]; other site 452662002894 Mg2+ binding site [ion binding]; other site 452662002895 G-X-G motif; other site 452662002896 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 452662002897 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 452662002898 active site 452662002899 phosphorylation site [posttranslational modification] 452662002900 intermolecular recognition site; other site 452662002901 dimerization interface [polypeptide binding]; other site 452662002902 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 452662002903 DNA binding site [nucleotide binding] 452662002904 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 452662002905 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 452662002906 active site 452662002907 substrate-binding site [chemical binding]; other site 452662002908 metal-binding site [ion binding] 452662002909 ATP binding site [chemical binding]; other site 452662002910 ATP phosphoribosyltransferase, regulatory subunit; Region: hisZ_biosyn_reg; TIGR00443 452662002911 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 452662002912 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 452662002913 FAD binding pocket [chemical binding]; other site 452662002914 FAD binding motif [chemical binding]; other site 452662002915 phosphate binding motif [ion binding]; other site 452662002916 beta-alpha-beta structure motif; other site 452662002917 NAD binding pocket [chemical binding]; other site 452662002918 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 452662002919 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 452662002920 active site 452662002921 phosphorylation site [posttranslational modification] 452662002922 intermolecular recognition site; other site 452662002923 dimerization interface [polypeptide binding]; other site 452662002924 Manganese catalase, ferritin-like diiron-binding domain; Region: Mn_catalase; cd01051 452662002925 dimanganese center [ion binding]; other site 452662002926 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 452662002927 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 452662002928 PAS domain S-box; Region: sensory_box; TIGR00229 452662002929 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662002930 putative active site [active] 452662002931 heme pocket [chemical binding]; other site 452662002932 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 452662002933 HWE histidine kinase; Region: HWE_HK; smart00911 452662002934 cheY-homologous receiver domain; Region: REC; smart00448 452662002935 Competence-damaged protein; Region: CinA; pfam02464 452662002936 NAD synthetase; Reviewed; Region: nadE; PRK02628 452662002937 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 452662002938 multimer interface [polypeptide binding]; other site 452662002939 active site 452662002940 catalytic triad [active] 452662002941 protein interface 1 [polypeptide binding]; other site 452662002942 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 452662002943 homodimer interface [polypeptide binding]; other site 452662002944 NAD binding pocket [chemical binding]; other site 452662002945 ATP binding pocket [chemical binding]; other site 452662002946 Mg binding site [ion binding]; other site 452662002947 active-site loop [active] 452662002948 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 452662002949 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; cl00047 452662002950 ligand binding site [chemical binding]; other site 452662002951 flexible hinge region; other site 452662002952 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 452662002953 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 452662002954 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 452662002955 Protein of unknown function (DUF4254); Region: DUF4254; pfam14063 452662002956 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 452662002957 Coenzyme F420-reducing hydrogenase, beta subunit [Energy production and conversion]; Region: FrhB; COG1035 452662002958 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term; Region: FrhB_FdhB_N; pfam04422 452662002959 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus; Region: FrhB_FdhB_C; pfam04432 452662002960 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 452662002961 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 452662002962 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 452662002963 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 452662002964 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH9; cd08269 452662002965 putative NAD(P) binding site [chemical binding]; other site 452662002966 catalytic Zn binding site [ion binding]; other site 452662002967 Myo-inositol-1-phosphate synthase [Lipid metabolism]; Region: INO1; COG1260 452662002968 Myo-inositol-1-phosphate synthase; Region: NAD_binding_5; cl00554 452662002969 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3664 452662002970 Methyltransferase domain; Region: Methyltransf_31; pfam13847 452662002971 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 452662002972 S-adenosylmethionine binding site [chemical binding]; other site 452662002973 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 452662002974 catalytic core [active] 452662002975 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662002976 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 452662002977 NAD(P) binding site [chemical binding]; other site 452662002978 active site 452662002979 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662002980 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 452662002981 NAD(P) binding site [chemical binding]; other site 452662002982 active site 452662002983 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 452662002984 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662002985 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4641 452662002986 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 452662002987 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4641 452662002988 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 452662002989 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4641 452662002990 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 452662002991 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662002992 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 452662002993 NAD(P) binding site [chemical binding]; other site 452662002994 active site 452662002995 Response regulator receiver domain; Region: Response_reg; pfam00072 452662002996 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 452662002997 active site 452662002998 phosphorylation site [posttranslational modification] 452662002999 intermolecular recognition site; other site 452662003000 dimerization interface [polypeptide binding]; other site 452662003001 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 452662003002 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 452662003003 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 452662003004 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 452662003005 ligand binding site [chemical binding]; other site 452662003006 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 452662003007 putative switch regulator; other site 452662003008 non-specific DNA interactions [nucleotide binding]; other site 452662003009 DNA binding site [nucleotide binding] 452662003010 sequence specific DNA binding site [nucleotide binding]; other site 452662003011 putative cAMP binding site [chemical binding]; other site 452662003012 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 452662003013 HWE histidine kinase; Region: HWE_HK; smart00911 452662003014 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 452662003015 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 452662003016 ligand binding site [chemical binding]; other site 452662003017 flexible hinge region; other site 452662003018 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 452662003019 non-specific DNA interactions [nucleotide binding]; other site 452662003020 DNA binding site [nucleotide binding] 452662003021 sequence specific DNA binding site [nucleotide binding]; other site 452662003022 putative cAMP binding site [chemical binding]; other site 452662003023 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 452662003024 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 452662003025 active site 452662003026 phosphorylation site [posttranslational modification] 452662003027 intermolecular recognition site; other site 452662003028 dimerization interface [polypeptide binding]; other site 452662003029 Sensors of blue-light using FAD; Region: BLUF; pfam04940 452662003030 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 452662003031 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 452662003032 active site 452662003033 phosphorylation site [posttranslational modification] 452662003034 intermolecular recognition site; other site 452662003035 dimerization interface [polypeptide binding]; other site 452662003036 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 452662003037 DNA binding residues [nucleotide binding] 452662003038 Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins; Region: AmyAc_OligoGlu; cd11330 452662003039 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 452662003040 active site 452662003041 catalytic site [active] 452662003042 Cytochrome c2 [Energy production and conversion]; Region: COG3474 452662003043 Predicted small integral membrane protein [Function unknown]; Region: COG5605 452662003044 Heme-copper oxidase subunit III subfamily. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane; Region: Heme_Cu_Oxidase_III_1; cd02864 452662003045 Subunit I/III interface [polypeptide binding]; other site 452662003046 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 452662003047 Subunit I/III interface [polypeptide binding]; other site 452662003048 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 452662003049 cytochrome c oxidase, subunit I; Region: CtaD_CoxA; TIGR02891 452662003050 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 452662003051 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 452662003052 Uncharacterized conserved protein [Function unknown]; Region: COG4544 452662003053 DNA Polymerase Y-family; Region: PolY_like; cd03468 452662003054 active site 452662003055 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 452662003056 DNA binding site [nucleotide binding] 452662003057 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 452662003058 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 452662003059 putative active site [active] 452662003060 putative PHP Thumb interface [polypeptide binding]; other site 452662003061 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 452662003062 generic binding surface II; other site 452662003063 generic binding surface I; other site 452662003064 TadE-like protein; Region: TadE; pfam07811 452662003065 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 452662003066 TadE-like protein; Region: TadE; pfam07811 452662003067 rod shape-determining protein MreB; Provisional; Region: PRK13927 452662003068 MreB and similar proteins; Region: MreB_like; cd10225 452662003069 nucleotide binding site [chemical binding]; other site 452662003070 Mg binding site [ion binding]; other site 452662003071 putative protofilament interaction site [polypeptide binding]; other site 452662003072 RodZ interaction site [polypeptide binding]; other site 452662003073 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 452662003074 AMP binding site [chemical binding]; other site 452662003075 metal binding site [ion binding]; metal-binding site 452662003076 active site 452662003077 Putative transmembrane protein (Alph_Pro_TM); Region: Alph_Pro_TM; pfam09608 452662003078 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 452662003079 Predicted permeases [General function prediction only]; Region: COG0730 452662003080 bacteriophage N4 adsorption protein B; Provisional; Region: PRK14716 452662003081 active site 452662003082 Glycosyl transferase family group 2; Region: Glyco_trans_2_3; pfam13632 452662003083 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09560 452662003084 Low affinity iron permease; Region: Iron_permease; pfam04120 452662003085 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 452662003086 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 452662003087 CoA-ligase; Region: Ligase_CoA; pfam00549 452662003088 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 452662003089 Ligand binding site [chemical binding]; other site 452662003090 Electron transfer flavoprotein domain; Region: ETF; pfam01012 452662003091 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 452662003092 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 452662003093 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 452662003094 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 452662003095 DNA-binding site [nucleotide binding]; DNA binding site 452662003096 RNA-binding motif; other site 452662003097 Domain of unknown function DUF1828; Region: DUF1828; pfam08861 452662003098 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 452662003099 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 452662003100 recA bacterial DNA recombination protein; Region: RecA; cl17211 452662003101 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 452662003102 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 452662003103 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 452662003104 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 452662003105 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 452662003106 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 452662003107 active site 452662003108 phosphorylation site [posttranslational modification] 452662003109 intermolecular recognition site; other site 452662003110 dimerization interface [polypeptide binding]; other site 452662003111 LytTr DNA-binding domain; Region: LytTR; smart00850 452662003112 Histidine kinase; Region: His_kinase; pfam06580 452662003113 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 452662003114 ATP binding site [chemical binding]; other site 452662003115 Mg2+ binding site [ion binding]; other site 452662003116 G-X-G motif; other site 452662003117 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662003118 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 452662003119 N-terminal plug; other site 452662003120 ligand-binding site [chemical binding]; other site 452662003121 short chain dehydrogenase; Provisional; Region: PRK08267 452662003122 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662003123 NAD(P) binding site [chemical binding]; other site 452662003124 active site 452662003125 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 452662003126 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 452662003127 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 452662003128 iron-sulfur cluster [ion binding]; other site 452662003129 [2Fe-2S] cluster binding site [ion binding]; other site 452662003130 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 452662003131 hydrophobic ligand binding site; other site 452662003132 Activator of aromatic catabolism; Region: XylR_N; pfam06505 452662003133 The V4R (vinyl 4 reductase) domain is a predicted small molecular binding domain, that may bind to hydrocarbons; Region: V4R; smart00989 452662003134 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 452662003135 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 452662003136 Walker A motif; other site 452662003137 ATP binding site [chemical binding]; other site 452662003138 Walker B motif; other site 452662003139 arginine finger; other site 452662003140 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 452662003141 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 452662003142 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662003143 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 452662003144 dimerization interface [polypeptide binding]; other site 452662003145 substrate binding pocket [chemical binding]; other site 452662003146 2-hydroxymuconic semialdehyde dehydrogenase; Region: OH_muco_semi_DH; TIGR03216 452662003147 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 452662003148 NAD binding site [chemical binding]; other site 452662003149 catalytic residues [active] 452662003150 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 452662003151 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 452662003152 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 452662003153 active site 1 [active] 452662003154 dimer interface [polypeptide binding]; other site 452662003155 hexamer interface [polypeptide binding]; other site 452662003156 active site 2 [active] 452662003157 acetaldehyde dehydrogenase; Validated; Region: PRK08300 452662003158 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 452662003159 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 452662003160 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 452662003161 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 452662003162 active site 452662003163 catalytic residues [active] 452662003164 metal binding site [ion binding]; metal-binding site 452662003165 DmpG-like communication domain; Region: DmpG_comm; pfam07836 452662003166 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662003167 NAD(P) binding site [chemical binding]; other site 452662003168 active site 452662003169 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 452662003170 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 452662003171 hexamer interface [polypeptide binding]; other site 452662003172 active site 2 [active] 452662003173 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 452662003174 catalytic loop [active] 452662003175 iron binding site [ion binding]; other site 452662003176 Domain of unknown function (DUF336); Region: DUF336; pfam03928 452662003177 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 452662003178 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; cl14632 452662003179 active site 452662003180 metal binding site [ion binding]; metal-binding site 452662003181 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; cl14632 452662003182 active site 452662003183 metal binding site [ion binding]; metal-binding site 452662003184 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662003185 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 452662003186 N-terminal plug; other site 452662003187 ligand-binding site [chemical binding]; other site 452662003188 Phenol hydroxylase subunit; Region: Phenol_hyd_sub; pfam06099 452662003189 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 452662003190 dinuclear metal binding motif [ion binding]; other site 452662003191 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 452662003192 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 452662003193 dinuclear metal binding motif [ion binding]; other site 452662003194 Phenol hydroxylase conserved region; Region: Phenol_monoox; pfam04663 452662003195 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 452662003196 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 452662003197 catalytic loop [active] 452662003198 iron binding site [ion binding]; other site 452662003199 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 452662003200 FAD binding pocket [chemical binding]; other site 452662003201 conserved FAD binding motif [chemical binding]; other site 452662003202 phosphate binding motif [ion binding]; other site 452662003203 beta-alpha-beta structure motif; other site 452662003204 NAD binding pocket [chemical binding]; other site 452662003205 Activator of aromatic catabolism; Region: XylR_N; pfam06505 452662003206 V4R domain; Region: V4R; pfam02830 452662003207 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 452662003208 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 452662003209 Walker A motif; other site 452662003210 ATP binding site [chemical binding]; other site 452662003211 Walker B motif; other site 452662003212 arginine finger; other site 452662003213 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 452662003214 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 452662003215 Sulfatase; Region: Sulfatase; pfam00884 452662003216 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662003217 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 452662003218 N-terminal plug; other site 452662003219 ligand-binding site [chemical binding]; other site 452662003220 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662003221 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662003222 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 452662003223 dimerization interface [polypeptide binding]; other site 452662003224 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 452662003225 Integrase core domain; Region: rve; pfam00665 452662003226 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 452662003227 Helix-turn-helix domain; Region: HTH_38; pfam13936 452662003228 Integrase core domain; Region: rve; pfam00665 452662003229 Domain of unknown function (DUF1993); Region: DUF1993; cl01567 452662003230 tRNA (guanine-N(7)-)-methyltransferase; Reviewed; Region: trmB; PRK00121 452662003231 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662003232 PAS domain; Region: PAS_9; pfam13426 452662003233 putative active site [active] 452662003234 heme pocket [chemical binding]; other site 452662003235 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 452662003236 dimer interface [polypeptide binding]; other site 452662003237 putative CheW interface [polypeptide binding]; other site 452662003238 S-adenosylmethionine synthetase; Validated; Region: PRK05250 452662003239 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 452662003240 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 452662003241 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 452662003242 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 452662003243 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 452662003244 putative active site [active] 452662003245 catalytic triad [active] 452662003246 putative dimer interface [polypeptide binding]; other site 452662003247 Predicted membrane protein [Function unknown]; Region: COG1238 452662003248 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 452662003249 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 452662003250 Coenzyme A binding pocket [chemical binding]; other site 452662003251 Uncharacterized conserved protein [Function unknown]; Region: COG5323 452662003252 Terminase-like family; Region: Terminase_6; pfam03237 452662003253 Phage-related protein [Function unknown]; Region: COG4695; cl01923 452662003254 Phage portal protein; Region: Phage_portal; pfam04860 452662003255 Caudovirus prohead protease; Region: Peptidase_U35; cl01521 452662003256 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 452662003257 Phage capsid family; Region: Phage_capsid; pfam05065 452662003258 phage conserved hypothetical protein, phiE125 gp8 family; Region: phage_chp_gp8; TIGR02215 452662003259 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 452662003260 Protein of unknown function (DUF3168); Region: DUF3168; pfam11367 452662003261 Phage major tail protein 2; Region: Phage_tail_2; pfam06199 452662003262 Protein of unknown function (DUF3356); Region: DUF3356; pfam11836 452662003263 Conserved hypothetical phage protein (DUF2376); Region: DUF2376; pfam09550 452662003264 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; pfam09343 452662003265 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 452662003266 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 452662003267 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 452662003268 Putative phage tail protein; Region: Phage-tail_3; pfam13550 452662003269 Protein of unknown function (DUF2793); Region: DUF2793; pfam10983 452662003270 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 452662003271 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 452662003272 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 452662003273 ligand binding site [chemical binding]; other site 452662003274 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 452662003275 E-class dimer interface [polypeptide binding]; other site 452662003276 P-class dimer interface [polypeptide binding]; other site 452662003277 active site 452662003278 Cu2+ binding site [ion binding]; other site 452662003279 Zn2+ binding site [ion binding]; other site 452662003280 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 452662003281 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 452662003282 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 452662003283 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 452662003284 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 452662003285 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 452662003286 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 452662003287 putative C-terminal domain interface [polypeptide binding]; other site 452662003288 putative GSH binding site (G-site) [chemical binding]; other site 452662003289 putative dimer interface [polypeptide binding]; other site 452662003290 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 452662003291 dimer interface [polypeptide binding]; other site 452662003292 N-terminal domain interface [polypeptide binding]; other site 452662003293 putative substrate binding pocket (H-site) [chemical binding]; other site 452662003294 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 452662003295 Clp amino terminal domain; Region: Clp_N; pfam02861 452662003296 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 452662003297 Walker A motif; other site 452662003298 ATP binding site [chemical binding]; other site 452662003299 Walker B motif; other site 452662003300 arginine finger; other site 452662003301 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 452662003302 Walker A motif; other site 452662003303 ATP binding site [chemical binding]; other site 452662003304 Walker B motif; other site 452662003305 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 452662003306 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662003307 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 452662003308 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 452662003309 NAD(P) binding site [chemical binding]; other site 452662003310 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 452662003311 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 452662003312 putative active site [active] 452662003313 putative metal binding site [ion binding]; other site 452662003314 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662003315 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_2; cd03814 452662003316 Protein of unknown function (DUF1013); Region: DUF1013; pfam06242 452662003317 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK05605 452662003318 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 452662003319 acyl-activating enzyme (AAE) consensus motif; other site 452662003320 putative AMP binding site [chemical binding]; other site 452662003321 putative active site [active] 452662003322 putative CoA binding site [chemical binding]; other site 452662003323 methionine sulfoxide reductase A; Provisional; Region: PRK14054 452662003324 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 452662003325 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 452662003326 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 452662003327 Protein of unknown function (DUF815); Region: DUF815; pfam05673 452662003328 Walker A motif; other site 452662003329 ATP binding site [chemical binding]; other site 452662003330 Walker B motif; other site 452662003331 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 452662003332 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 452662003333 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 452662003334 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 452662003335 NlpC/P60 family; Region: NLPC_P60; pfam00877 452662003336 Transcriptional regulators [Transcription]; Region: MarR; COG1846 452662003337 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 452662003338 putative Zn2+ binding site [ion binding]; other site 452662003339 putative DNA binding site [nucleotide binding]; other site 452662003340 dimerization interface [polypeptide binding]; other site 452662003341 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 452662003342 interface (dimer of trimers) [polypeptide binding]; other site 452662003343 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 452662003344 Substrate-binding/catalytic site; other site 452662003345 Zn-binding sites [ion binding]; other site 452662003346 Domain of unknown function (DUF4163); Region: DUF4163; pfam13739 452662003347 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 452662003348 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 452662003349 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 452662003350 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 452662003351 FeS/SAM binding site; other site 452662003352 Ion channel; Region: Ion_trans_2; pfam07885 452662003353 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 452662003354 TrkA-N domain; Region: TrkA_N; pfam02254 452662003355 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 452662003356 seryl-tRNA synthetase; Provisional; Region: PRK05431 452662003357 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 452662003358 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 452662003359 dimer interface [polypeptide binding]; other site 452662003360 active site 452662003361 motif 1; other site 452662003362 motif 2; other site 452662003363 motif 3; other site 452662003364 Protein required for attachment to host cells; Region: Host_attach; pfam10116 452662003365 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 452662003366 PilZ domain; Region: PilZ; cl01260 452662003367 Protein of unknown function (DUF465); Region: DUF465; pfam04325 452662003368 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]; Region: COG5481 452662003369 Protein of unknown function (DUF1465); Region: DUF1465; pfam07323 452662003370 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 452662003371 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 452662003372 Surface antigen; Region: Bac_surface_Ag; pfam01103 452662003373 Family of unknown function (DUF490); Region: DUF490; pfam04357 452662003374 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 452662003375 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 452662003376 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 452662003377 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 452662003378 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 452662003379 active site 452662003380 dimer interface [polypeptide binding]; other site 452662003381 aldose 1-epimerase, similar to Escherichia coli YphB; Region: Aldose_epim_Ec_YphB; cd09021 452662003382 active site 452662003383 catalytic residues [active] 452662003384 D-xylose transporter XylE; Provisional; Region: xylE; PRK10077 452662003385 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 452662003386 putative substrate translocation pore; other site 452662003387 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 452662003388 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 452662003389 short chain dehydrogenase; Provisional; Region: PRK12939 452662003390 classical (c) SDRs; Region: SDR_c; cd05233 452662003391 NAD(P) binding site [chemical binding]; other site 452662003392 active site 452662003393 Fumarylacetoacetate (FAA) hydrolase family protein [General function prediction only]; Region: COG3970 452662003394 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 452662003395 Ku protein, prokaryotic; Region: Ku_bact; TIGR02772 452662003396 Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku...; Region: KU_like; cd00789 452662003397 putative DNA binding site [nucleotide binding]; other site 452662003398 putative homodimer interface [polypeptide binding]; other site 452662003399 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 452662003400 DNA ligase D, 3'-phosphoesterase domain; Region: LigD_PE_dom; TIGR02777 452662003401 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 452662003402 active site 452662003403 DNA binding site [nucleotide binding] 452662003404 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_LigD; cd07971 452662003405 DNA binding site [nucleotide binding] 452662003406 PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for...; Region: PaeLigD_Pol_like; cd04862 452662003407 nucleotide binding site [chemical binding]; other site 452662003408 EF-hand domain pair; Region: EF_hand_5; pfam13499 452662003409 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 452662003410 Ca2+ binding site [ion binding]; other site 452662003411 adenylosuccinate lyase; Provisional; Region: PRK07492 452662003412 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 452662003413 tetramer interface [polypeptide binding]; other site 452662003414 active site 452662003415 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 452662003416 Transcriptional regulators [Transcription]; Region: PurR; COG1609 452662003417 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 452662003418 DNA binding site [nucleotide binding] 452662003419 domain linker motif; other site 452662003420 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 452662003421 putative dimerization interface [polypeptide binding]; other site 452662003422 putative ligand binding site [chemical binding]; other site 452662003423 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 452662003424 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 452662003425 putative DNA binding site [nucleotide binding]; other site 452662003426 putative Zn2+ binding site [ion binding]; other site 452662003427 AsnC family; Region: AsnC_trans_reg; pfam01037 452662003428 Mpr1p, Pad1p N-terminal (MPN) domains; Region: MPN; cl13996 452662003429 Thymidylate synthase; Region: Thymidylat_synt; pfam00303 452662003430 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 452662003431 dimerization interface [polypeptide binding]; other site 452662003432 active site 452662003433 2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal; Region: OxoDH_E1alpha_N; pfam12573 452662003434 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 452662003435 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 452662003436 tetramer interface [polypeptide binding]; other site 452662003437 TPP-binding site [chemical binding]; other site 452662003438 heterodimer interface [polypeptide binding]; other site 452662003439 phosphorylation loop region [posttranslational modification] 452662003440 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 452662003441 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 452662003442 alpha subunit interface [polypeptide binding]; other site 452662003443 TPP binding site [chemical binding]; other site 452662003444 heterodimer interface [polypeptide binding]; other site 452662003445 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 452662003446 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 452662003447 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 452662003448 E3 interaction surface; other site 452662003449 lipoyl attachment site [posttranslational modification]; other site 452662003450 e3 binding domain; Region: E3_binding; pfam02817 452662003451 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 452662003452 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4719 452662003453 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 452662003454 Domain of unknown function DUF20; Region: UPF0118; pfam01594 452662003455 Protein of unknown function (DUF2842); Region: DUF2842; pfam11003 452662003456 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 452662003457 Cell division protein ZapA; Region: ZapA; pfam05164 452662003458 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 452662003459 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 452662003460 TPP-binding site [chemical binding]; other site 452662003461 dimer interface [polypeptide binding]; other site 452662003462 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 452662003463 PYR/PP interface [polypeptide binding]; other site 452662003464 dimer interface [polypeptide binding]; other site 452662003465 TPP binding site [chemical binding]; other site 452662003466 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 452662003467 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 452662003468 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 452662003469 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 452662003470 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 452662003471 Phosphoglycerate kinase; Region: PGK; pfam00162 452662003472 substrate binding site [chemical binding]; other site 452662003473 hinge regions; other site 452662003474 ADP binding site [chemical binding]; other site 452662003475 catalytic site [active] 452662003476 fructose-1,6-bisphosphate aldolase; Reviewed; Region: PRK05377 452662003477 catalytic residue [active] 452662003478 Protein of unknown function DUF72; Region: DUF72; pfam01904 452662003479 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 452662003480 thiamine phosphate binding site [chemical binding]; other site 452662003481 active site 452662003482 pyrophosphate binding site [ion binding]; other site 452662003483 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 452662003484 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 452662003485 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 452662003486 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 452662003487 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 452662003488 Peptidase family M23; Region: Peptidase_M23; pfam01551 452662003489 elongation factor P; Validated; Region: PRK00529 452662003490 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 452662003491 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 452662003492 RNA binding site [nucleotide binding]; other site 452662003493 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 452662003494 RNA binding site [nucleotide binding]; other site 452662003495 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 452662003496 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 452662003497 active site 452662003498 dimerization interface [polypeptide binding]; other site 452662003499 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 452662003500 NADH dehydrogenase subunit B; Validated; Region: PRK06411 452662003501 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 452662003502 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 452662003503 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 452662003504 NADH dehydrogenase subunit D; Validated; Region: PRK06075 452662003505 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 452662003506 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 452662003507 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 452662003508 putative dimer interface [polypeptide binding]; other site 452662003509 [2Fe-2S] cluster binding site [ion binding]; other site 452662003510 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 452662003511 SLBB domain; Region: SLBB; pfam10531 452662003512 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 452662003513 NADH dehydrogenase subunit G; Validated; Region: PRK09130 452662003514 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 452662003515 catalytic loop [active] 452662003516 iron binding site [ion binding]; other site 452662003517 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 452662003518 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 452662003519 molybdopterin cofactor binding site; other site 452662003520 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 452662003521 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 452662003522 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 452662003523 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 452662003524 4Fe-4S binding domain; Region: Fer4; pfam00037 452662003525 4Fe-4S binding domain; Region: Fer4; pfam00037 452662003526 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 452662003527 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 452662003528 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 452662003529 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 452662003530 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 452662003531 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 452662003532 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 452662003533 NADH dehydrogenase subunit 5 C-terminus; Region: NADH5_C; pfam06455 452662003534 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 452662003535 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 452662003536 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 452662003537 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 452662003538 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 452662003539 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 452662003540 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 452662003541 pantothenate kinase; Reviewed; Region: PRK13318 452662003542 conserved hypothetical protein; Region: MG423; TIGR00649 452662003543 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 452662003544 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 452662003545 Protein of unknown function (DUF1467); Region: DUF1467; pfam07330 452662003546 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 452662003547 Coenzyme A binding pocket [chemical binding]; other site 452662003548 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662003549 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662003550 metal binding site [ion binding]; metal-binding site 452662003551 active site 452662003552 I-site; other site 452662003553 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 452662003554 enoyl-CoA hydratase; Validated; Region: PRK08788 452662003555 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662003556 substrate binding site [chemical binding]; other site 452662003557 oxyanion hole (OAH) forming residues; other site 452662003558 trimer interface [polypeptide binding]; other site 452662003559 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 452662003560 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 452662003561 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 452662003562 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 452662003563 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 452662003564 putative active site [active] 452662003565 putative substrate binding site [chemical binding]; other site 452662003566 putative cosubstrate binding site; other site 452662003567 catalytic site [active] 452662003568 Domain of unknown function (DUF1338); Region: DUF1338; pfam07063 452662003569 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 452662003570 Sel1-like repeats; Region: SEL1; smart00671 452662003571 Sporulation related domain; Region: SPOR; pfam05036 452662003572 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 452662003573 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 452662003574 P-loop; other site 452662003575 Magnesium ion binding site [ion binding]; other site 452662003576 Sporulation related domain; Region: SPOR; pfam05036 452662003577 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 452662003578 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662003579 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 452662003580 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 452662003581 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 452662003582 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 452662003583 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 452662003584 hypothetical protein; Provisional; Region: PRK06126 452662003585 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 452662003586 benzoate transport; Region: 2A0115; TIGR00895 452662003587 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 452662003588 putative substrate translocation pore; other site 452662003589 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09791 452662003590 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662003591 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662003592 dimerization interface [polypeptide binding]; other site 452662003593 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG2159 452662003594 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 452662003595 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 452662003596 N-terminal plug; other site 452662003597 ligand-binding site [chemical binding]; other site 452662003598 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 452662003599 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 452662003600 phosphate binding site [ion binding]; other site 452662003601 D-lactate dehydrogenase; Provisional; Region: PRK11183 452662003602 FAD binding domain; Region: FAD_binding_4; pfam01565 452662003603 D-lactate dehydrogenase, membrane binding; Region: Lact-deh-memb; pfam09330 452662003604 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662003605 classical (c) SDRs; Region: SDR_c; cd05233 452662003606 NAD(P) binding site [chemical binding]; other site 452662003607 active site 452662003608 Prokaryotic protein of unknown function (DUF849); Region: DUF849; pfam05853 452662003609 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09791 452662003610 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662003611 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662003612 dimerization interface [polypeptide binding]; other site 452662003613 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662003614 The single-domain 2,3-dihydroxybiphenyl 1,2-dioxygenases (BphC, EC 1.13.11.39) from Rhodococcus globerulus P6, BphC2-RGP6 and BphC3-RGP6, and similar proteins; Region: BphC2-C3-RGP6_C_like; cd08348 452662003615 putative active site [active] 452662003616 putative metal binding site [ion binding]; other site 452662003617 hypothetical protein; Provisional; Region: PRK06126 452662003618 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 452662003619 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 452662003620 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 452662003621 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 452662003622 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662003623 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 452662003624 N-terminal plug; other site 452662003625 ligand-binding site [chemical binding]; other site 452662003626 acetyl-CoA acetyltransferase; Provisional; Region: PRK07516 452662003627 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 452662003628 active site 452662003629 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662003630 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662003631 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 452662003632 substrate binding pocket [chemical binding]; other site 452662003633 dimerization interface [polypeptide binding]; other site 452662003634 SnoaL-like domain; Region: SnoaL_3; pfam13474 452662003635 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662003636 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662003637 NAD(P) binding site [chemical binding]; other site 452662003638 active site 452662003639 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR7; cd08276 452662003640 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 452662003641 putative NAD(P) binding site [chemical binding]; other site 452662003642 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 452662003643 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 452662003644 Amidohydrolase; Region: Amidohydro_4; pfam13147 452662003645 active site 452662003646 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 452662003647 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662003648 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 452662003649 The single-domain 2,3-dihydroxybiphenyl 1,2-dioxygenases (BphC, EC 1.13.11.39) from Rhodococcus globerulus P6, BphC2-RGP6 and BphC3-RGP6, and similar proteins; Region: BphC2-C3-RGP6_C_like; cd08348 452662003650 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662003651 putative active site [active] 452662003652 putative metal binding site [ion binding]; other site 452662003653 Prokaryotic protein of unknown function (DUF849); Region: DUF849; pfam05853 452662003654 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 452662003655 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 452662003656 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 452662003657 dimer interface [polypeptide binding]; other site 452662003658 active site 452662003659 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 452662003660 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662003661 NAD(P) binding site [chemical binding]; other site 452662003662 active site 452662003663 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 452662003664 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 452662003665 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 452662003666 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 452662003667 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 452662003668 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662003669 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 452662003670 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 452662003671 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662003672 NAD(P) binding site [chemical binding]; other site 452662003673 active site 452662003674 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662003675 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 452662003676 N-terminal plug; other site 452662003677 ligand-binding site [chemical binding]; other site 452662003678 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 452662003679 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 452662003680 NAD(P) binding site [chemical binding]; other site 452662003681 catalytic residues [active] 452662003682 Benzyl alcohol dehydrogenase; Region: benzyl_alcohol_DH; cd08278 452662003683 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 452662003684 catalytic Zn binding site [ion binding]; other site 452662003685 NAD binding site [chemical binding]; other site 452662003686 structural Zn binding site [ion binding]; other site 452662003687 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR7; cd08276 452662003688 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 452662003689 putative NAD(P) binding site [chemical binding]; other site 452662003690 enoyl-CoA hydratase; Provisional; Region: PRK06494 452662003691 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662003692 substrate binding site [chemical binding]; other site 452662003693 oxyanion hole (OAH) forming residues; other site 452662003694 trimer interface [polypeptide binding]; other site 452662003695 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 452662003696 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 452662003697 FMN binding site [chemical binding]; other site 452662003698 substrate binding site [chemical binding]; other site 452662003699 putative catalytic residue [active] 452662003700 acetyl-CoA acetyltransferase; Provisional; Region: PRK06064 452662003701 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 452662003702 active site 452662003703 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662003704 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 452662003705 active site 452662003706 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily 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: ACAD10_11_like; cd05154 452662003707 putative active site [active] 452662003708 putative substrate binding site [chemical binding]; other site 452662003709 ATP binding site [chemical binding]; other site 452662003710 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662003711 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 452662003712 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 452662003713 putative substrate translocation pore; other site 452662003714 Major Facilitator Superfamily; Region: MFS_1; pfam07690 452662003715 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662003716 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 452662003717 NAD(P) binding site [chemical binding]; other site 452662003718 active site 452662003719 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 452662003720 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 452662003721 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 452662003722 FMN binding site [chemical binding]; other site 452662003723 substrate binding site [chemical binding]; other site 452662003724 putative catalytic residue [active] 452662003725 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 452662003726 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 452662003727 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662003728 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662003729 acyl-CoA synthetase; Validated; Region: PRK06188 452662003730 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 452662003731 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 452662003732 acyl-activating enzyme (AAE) consensus motif; other site 452662003733 putative AMP binding site [chemical binding]; other site 452662003734 putative active site [active] 452662003735 putative CoA binding site [chemical binding]; other site 452662003736 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662003737 classical (c) SDRs; Region: SDR_c; cd05233 452662003738 NAD(P) binding site [chemical binding]; other site 452662003739 active site 452662003740 beta-ketothiolase; Provisional; Region: PRK09051 452662003741 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 452662003742 dimer interface [polypeptide binding]; other site 452662003743 active site 452662003744 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 452662003745 Transposase; Region: HTH_Tnp_1; cl17663 452662003746 putative transposase OrfB; Reviewed; Region: PHA02517 452662003747 HTH-like domain; Region: HTH_21; pfam13276 452662003748 Integrase core domain; Region: rve; pfam00665 452662003749 Integrase core domain; Region: rve_3; pfam13683 452662003750 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 452662003751 ATP-NAD kinase; Region: NAD_kinase; pfam01513 452662003752 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 452662003753 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 452662003754 FeS/SAM binding site; other site 452662003755 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 452662003756 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662003757 metal binding site [ion binding]; metal-binding site 452662003758 active site 452662003759 I-site; other site 452662003760 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 452662003761 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 452662003762 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 452662003763 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 452662003764 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 452662003765 ATP binding site [chemical binding]; other site 452662003766 putative Mg++ binding site [ion binding]; other site 452662003767 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 452662003768 nucleotide binding region [chemical binding]; other site 452662003769 ATP-binding site [chemical binding]; other site 452662003770 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 452662003771 Flavinator of succinate dehydrogenase; Region: Sdh5; pfam03937 452662003772 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 452662003773 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 452662003774 ssDNA binding site; other site 452662003775 generic binding surface II; other site 452662003776 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 452662003777 ATP binding site [chemical binding]; other site 452662003778 putative Mg++ binding site [ion binding]; other site 452662003779 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 452662003780 nucleotide binding region [chemical binding]; other site 452662003781 ATP-binding site [chemical binding]; other site 452662003782 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 452662003783 Mechanosensitive ion channel; Region: MS_channel; pfam00924 452662003784 PilZ domain; Region: PilZ; pfam07238 452662003785 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 452662003786 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 452662003787 active site 452662003788 HIGH motif; other site 452662003789 dimer interface [polypeptide binding]; other site 452662003790 KMSKS motif; other site 452662003791 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 452662003792 RNA binding surface [nucleotide binding]; other site 452662003793 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 452662003794 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 452662003795 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 452662003796 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 452662003797 dimer interface [polypeptide binding]; other site 452662003798 putative CheW interface [polypeptide binding]; other site 452662003799 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; pfam04828 452662003800 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 452662003801 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 452662003802 Walker A motif; other site 452662003803 ATP binding site [chemical binding]; other site 452662003804 Walker B motif; other site 452662003805 arginine finger; other site 452662003806 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 452662003807 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 452662003808 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 452662003809 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 452662003810 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 452662003811 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 452662003812 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 452662003813 DNA binding residues [nucleotide binding] 452662003814 CHC2 zinc finger; Region: zf-CHC2; pfam01807 452662003815 DNA primase, catalytic core; Region: dnaG; TIGR01391 452662003816 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 452662003817 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 452662003818 active site 452662003819 metal binding site [ion binding]; metal-binding site 452662003820 interdomain interaction site; other site 452662003821 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 452662003822 GIY-YIG motif/motif A; other site 452662003823 putative active site [active] 452662003824 putative metal binding site [ion binding]; other site 452662003825 Yqey-like protein; Region: YqeY; pfam09424 452662003826 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 452662003827 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 452662003828 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 452662003829 catalytic site [active] 452662003830 subunit interface [polypeptide binding]; other site 452662003831 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 452662003832 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 452662003833 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 452662003834 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 452662003835 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 452662003836 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 452662003837 ATP-grasp domain; Region: ATP-grasp_4; cl17255 452662003838 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 452662003839 IMP binding site; other site 452662003840 dimer interface [polypeptide binding]; other site 452662003841 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 452662003842 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 452662003843 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 452662003844 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 452662003845 Domain of unknown function (DUF4170); Region: DUF4170; pfam13773 452662003846 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 452662003847 enolase; Provisional; Region: eno; PRK00077 452662003848 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 452662003849 dimer interface [polypeptide binding]; other site 452662003850 metal binding site [ion binding]; metal-binding site 452662003851 substrate binding pocket [chemical binding]; other site 452662003852 Septum formation initiator; Region: DivIC; cl17659 452662003853 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 452662003854 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 452662003855 tetramer interface [polypeptide binding]; other site 452662003856 TPP-binding site [chemical binding]; other site 452662003857 heterodimer interface [polypeptide binding]; other site 452662003858 phosphorylation loop region [posttranslational modification] 452662003859 pyruvate dehydrogenase subunit beta; Provisional; Region: PRK11892 452662003860 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 452662003861 E3 interaction surface; other site 452662003862 lipoyl attachment site [posttranslational modification]; other site 452662003863 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 452662003864 alpha subunit interface [polypeptide binding]; other site 452662003865 TPP binding site [chemical binding]; other site 452662003866 heterodimer interface [polypeptide binding]; other site 452662003867 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 452662003868 TadE-like protein; Region: TadE; pfam07811 452662003869 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 452662003870 Putative Flp pilus-assembly TadE/G-like; Region: Tad; pfam13400 452662003871 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 452662003872 EF-hand domain pair; Region: EF_hand_5; pfam13499 452662003873 Ca2+ binding site [ion binding]; other site 452662003874 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 452662003875 Glucose inhibited division protein A; Region: GIDA; pfam01134 452662003876 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 452662003877 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 452662003878 hypothetical protein; Provisional; Region: PRK09133 452662003879 M20 Peptidase, carboxypeptidase yscS-like; Region: M20_yscS_like; cd05675 452662003880 putative metal binding site [ion binding]; other site 452662003881 2-isopropylmalate synthase; Validated; Region: PRK03739 452662003882 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 452662003883 active site 452662003884 catalytic residues [active] 452662003885 metal binding site [ion binding]; metal-binding site 452662003886 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 452662003887 Uncharacterized conserved protein [Function unknown]; Region: COG2353 452662003888 ketol-acid reductoisomerase; Provisional; Region: PRK05479 452662003889 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 452662003890 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 452662003891 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 452662003892 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 452662003893 putative valine binding site [chemical binding]; other site 452662003894 dimer interface [polypeptide binding]; other site 452662003895 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 452662003896 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK09107 452662003897 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 452662003898 PYR/PP interface [polypeptide binding]; other site 452662003899 dimer interface [polypeptide binding]; other site 452662003900 TPP binding site [chemical binding]; other site 452662003901 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 452662003902 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 452662003903 TPP-binding site [chemical binding]; other site 452662003904 dimer interface [polypeptide binding]; other site 452662003905 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 452662003906 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 452662003907 phosphoserine phosphatase SerB; Region: serB; TIGR00338 452662003908 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 452662003909 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 452662003910 motif II; other site 452662003911 phosphoribosylformylglycinamidine synthase I; Provisional; Region: PRK03619 452662003912 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 452662003913 putative active site [active] 452662003914 catalytic triad [active] 452662003915 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; pfam02700 452662003916 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 452662003917 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 452662003918 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 452662003919 ATP binding site [chemical binding]; other site 452662003920 active site 452662003921 substrate binding site [chemical binding]; other site 452662003922 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 452662003923 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 452662003924 active site 452662003925 homotetramer interface [polypeptide binding]; other site 452662003926 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 452662003927 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 452662003928 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 452662003929 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 452662003930 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 452662003931 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662003932 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 452662003933 dimerization interface [polypeptide binding]; other site 452662003934 substrate binding pocket [chemical binding]; other site 452662003935 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 452662003936 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 452662003937 CAP-like domain; other site 452662003938 active site 452662003939 primary dimer interface [polypeptide binding]; other site 452662003940 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662003941 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662003942 metal binding site [ion binding]; metal-binding site 452662003943 active site 452662003944 I-site; other site 452662003945 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 452662003946 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 452662003947 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 452662003948 active site 452662003949 NTP binding site [chemical binding]; other site 452662003950 metal binding triad [ion binding]; metal-binding site 452662003951 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 452662003952 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 452662003953 putative active site [active] 452662003954 putative CoA binding site [chemical binding]; other site 452662003955 nudix motif; other site 452662003956 metal binding site [ion binding]; metal-binding site 452662003957 Protein of unknown function (DUF1285); Region: DUF1285; pfam06938 452662003958 Predicted acetyltransferase [General function prediction only]; Region: COG3153 452662003959 Coenzyme A binding pocket [chemical binding]; other site 452662003960 Dihydroneopterin aldolase; Region: FolB; smart00905 452662003961 active site 452662003962 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 452662003963 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 452662003964 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 452662003965 EVE domain; Region: EVE; pfam01878 452662003966 Cupin superfamily (DUF985); Region: Cupin_5; pfam06172 452662003967 recombination factor protein RarA; Reviewed; Region: PRK13342 452662003968 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 452662003969 Walker A motif; other site 452662003970 ATP binding site [chemical binding]; other site 452662003971 Walker B motif; other site 452662003972 arginine finger; other site 452662003973 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 452662003974 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662003975 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_2; cd03814 452662003976 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 452662003977 MOSC domain; Region: MOSC; pfam03473 452662003978 3-alpha domain; Region: 3-alpha; pfam03475 452662003979 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 452662003980 acyl-CoA ligase (AMP-forming), exosortase A-associated; Region: ligase_PEP_1; TIGR03098 452662003981 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 452662003982 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 452662003983 acyl-activating enzyme (AAE) consensus motif; other site 452662003984 acyl-activating enzyme (AAE) consensus motif; other site 452662003985 AMP binding site [chemical binding]; other site 452662003986 active site 452662003987 CoA binding site [chemical binding]; other site 452662003988 pyridoxal-dependent decarboxylase, exosortase A system-associated; Region: dCO2ase_PEP1; TIGR03099 452662003989 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase; Region: PLPDE_III_Btrk_like; cd06839 452662003990 dimer interface [polypeptide binding]; other site 452662003991 active site 452662003992 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 452662003993 catalytic residues [active] 452662003994 substrate binding site [chemical binding]; other site 452662003995 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 452662003996 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 452662003997 SLBB domain; Region: SLBB; pfam10531 452662003998 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 452662003999 Chain length determinant protein; Region: Wzz; cl15801 452662004000 exopolysaccharide/PEP-CTERM locus tyrosine autokinase; Region: pepcterm_TyrKin; TIGR03018 452662004001 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 452662004002 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 452662004003 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 452662004004 Walker A motif; other site 452662004005 ATP binding site [chemical binding]; other site 452662004006 Walker B motif; other site 452662004007 arginine finger; other site 452662004008 polysaccharide deacetylase family protein, PEP-CTERM locus subfamily; Region: pepcterm_polyde; TIGR03006 452662004009 Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA); Region: CE4_PuuE_HpPgdA_like_2; cd10941 452662004010 putative active site [active] 452662004011 putative catalytic site [active] 452662004012 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 452662004013 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp1; TIGR03087 452662004014 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 452662004015 Predicted membrane protein [Function unknown]; Region: COG4083; cl15694 452662004016 Transmembrane exosortase (Exosortase_EpsH); Region: Exosortase_EpsH; pfam09721 452662004017 Protein of unknown function (DUF3485); Region: DUF3485; cl11827 452662004018 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 452662004019 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 452662004020 active site 452662004021 dimer interface [polypeptide binding]; other site 452662004022 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 452662004023 Ligand Binding Site [chemical binding]; other site 452662004024 Molecular Tunnel; other site 452662004025 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 452662004026 Bacterial sugar transferase; Region: Bac_transf; pfam02397 452662004027 CESA_like_1 is a member of the cellulose synthase (CESA) superfamily; Region: CESA_like_1; cd06439 452662004028 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 452662004029 DXD motif; other site 452662004030 Methyltransferase domain; Region: Methyltransf_23; pfam13489 452662004031 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 452662004032 Glycosyl transferase 4-like domain; Region: Glyco_trans_4_4; cl17183 452662004033 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662004034 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 452662004035 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 452662004036 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 452662004037 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 452662004038 Amidohydrolase family; Region: Amidohydro_3; pfam07969 452662004039 active site 452662004040 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 452662004041 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 452662004042 threonine dehydratase; Provisional; Region: PRK07334 452662004043 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 452662004044 tetramer interface [polypeptide binding]; other site 452662004045 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662004046 catalytic residue [active] 452662004047 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 452662004048 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 452662004049 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 452662004050 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 452662004051 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662004052 PAS fold; Region: PAS_3; pfam08447 452662004053 putative active site [active] 452662004054 heme pocket [chemical binding]; other site 452662004055 PAS domain S-box; Region: sensory_box; TIGR00229 452662004056 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662004057 putative active site [active] 452662004058 heme pocket [chemical binding]; other site 452662004059 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662004060 metal binding site [ion binding]; metal-binding site 452662004061 active site 452662004062 I-site; other site 452662004063 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 452662004064 Domain of unknown function (DUF3315); Region: DUF3315; cl02275 452662004065 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 452662004066 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 452662004067 hypothetical protein; Provisional; Region: PRK09256 452662004068 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 452662004069 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 452662004070 active site 452662004071 Acyltransferase family; Region: Acyl_transf_3; pfam01757 452662004072 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 452662004073 RNA polymerase sigma factor SigJ; Provisional; Region: PRK09636 452662004074 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 452662004075 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 452662004076 Uncharacterized conserved protein [Function unknown]; Region: COG2128 452662004077 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 452662004078 Glutamine cyclotransferase; Region: Glu_cyclase_2; pfam05096 452662004079 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 452662004080 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 452662004081 dihydroorotase; Validated; Region: PRK09060 452662004082 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 452662004083 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 452662004084 active site 452662004085 Predicted permeases [General function prediction only]; Region: RarD; COG2962 452662004086 camphor resistance protein CrcB; Provisional; Region: PRK14195 452662004087 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 452662004088 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 452662004089 active site 452662004090 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 452662004091 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 452662004092 motif II; other site 452662004093 ATP12 chaperone protein; Region: ATP12; pfam07542 452662004094 L,D-transpeptidase catalytic domain; Region: YkuD_2; pfam13645 452662004095 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 452662004096 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 452662004097 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 452662004098 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 452662004099 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 452662004100 Histone deacetylase class IV also known as histone deacetylase 11; Region: HDAC_classIV; cd09993 452662004101 putative active site [active] 452662004102 Zn binding site [ion binding]; other site 452662004103 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 452662004104 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 452662004105 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 452662004106 substrate binding site [chemical binding]; other site 452662004107 glutamase interaction surface [polypeptide binding]; other site 452662004108 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 452662004109 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 452662004110 catalytic residues [active] 452662004111 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 452662004112 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 452662004113 putative active site [active] 452662004114 oxyanion strand; other site 452662004115 catalytic triad [active] 452662004116 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 452662004117 putative active site pocket [active] 452662004118 4-fold oligomerization interface [polypeptide binding]; other site 452662004119 metal binding residues [ion binding]; metal-binding site 452662004120 3-fold/trimer interface [polypeptide binding]; other site 452662004121 Stringent starvation protein B; Region: SspB; pfam04386 452662004122 fumarate hydratase; Reviewed; Region: fumC; PRK00485 452662004123 Class II fumarases; Region: Fumarase_classII; cd01362 452662004124 active site 452662004125 tetramer interface [polypeptide binding]; other site 452662004126 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 452662004127 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 452662004128 catalytic site [active] 452662004129 G-X2-G-X-G-K; other site 452662004130 Uncharacterized conserved protein [Function unknown]; Region: COG1565 452662004131 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 452662004132 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 452662004133 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662004134 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 452662004135 NAD(P)H:quinone oxidoreductase; Provisional; Region: PRK03767 452662004136 Pirin-related protein [General function prediction only]; Region: COG1741 452662004137 Pirin; Region: Pirin; pfam02678 452662004138 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662004139 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662004140 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 452662004141 putative effector binding pocket; other site 452662004142 dimerization interface [polypeptide binding]; other site 452662004143 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 452662004144 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 452662004145 active site 452662004146 phosphorylation site [posttranslational modification] 452662004147 intermolecular recognition site; other site 452662004148 dimerization interface [polypeptide binding]; other site 452662004149 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 452662004150 DNA binding site [nucleotide binding] 452662004151 PilZ domain; Region: PilZ; cl01260 452662004152 Peptidase S8 family domain, uncharacterized subfamily 4; Region: Peptidases_S8_4; cd05561 452662004153 active site 452662004154 catalytic triad [active] 452662004155 RNA polymerase sigma factor; Provisional; Region: PRK12547 452662004156 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 452662004157 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 452662004158 DNA binding residues [nucleotide binding] 452662004159 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 452662004160 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662004161 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 452662004162 N-terminal plug; other site 452662004163 ligand-binding site [chemical binding]; other site 452662004164 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 452662004165 active site 452662004166 metal binding site [ion binding]; metal-binding site 452662004167 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 452662004168 trimer interface [polypeptide binding]; other site 452662004169 active site 452662004170 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 452662004171 active site 452662004172 catalytic motif [active] 452662004173 Zn binding site [ion binding]; other site 452662004174 Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues; Region: GH25_muramidase; cd00599 452662004175 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 452662004176 active site 452662004177 hypothetical protein; Provisional; Region: PRK02853 452662004178 replicative DNA helicase; Provisional; Region: PRK09165 452662004179 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 452662004180 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 452662004181 Walker A motif; other site 452662004182 ATP binding site [chemical binding]; other site 452662004183 Walker B motif; other site 452662004184 DNA binding loops [nucleotide binding] 452662004185 MAPEG family; Region: MAPEG; cl09190 452662004186 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 452662004187 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 452662004188 Active Sites [active] 452662004189 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 452662004190 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 452662004191 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 452662004192 Animal heme peroxidases and related proteins; Region: An_peroxidase_like; cl14561 452662004193 substrate binding site [chemical binding]; other site 452662004194 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 452662004195 Protein of unknown function (DUF2849); Region: DUF2849; pfam11011 452662004196 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 452662004197 active site 452662004198 SAM binding site [chemical binding]; other site 452662004199 homodimer interface [polypeptide binding]; other site 452662004200 succinylglutamic semialdehyde dehydrogenase; Reviewed; Region: astD; PRK09457 452662004201 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 452662004202 NAD(P) binding site [chemical binding]; other site 452662004203 catalytic residues [active] 452662004204 hypothetical protein; Validated; Region: PRK00029 452662004205 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; pfam02696 452662004206 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 452662004207 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp2; TIGR03088 452662004208 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 452662004209 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 452662004210 FMN binding site [chemical binding]; other site 452662004211 substrate binding site [chemical binding]; other site 452662004212 putative catalytic residue [active] 452662004213 Uncharacterized protein conserved in bacteria (DUF2093); Region: DUF2093; pfam09866 452662004214 Cytochrome c2 [Energy production and conversion]; Region: COG3474 452662004215 putative heme-binding domain, Pirellula/Verrucomicrobium type; Region: CxxCH_TIGR02603 452662004216 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 452662004217 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 452662004218 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 452662004219 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 452662004220 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 452662004221 Citrate transporter; Region: CitMHS; pfam03600 452662004222 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 452662004223 Domain of unknown function (DUF3315); Region: DUF3315; cl02275 452662004224 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 452662004225 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 452662004226 FtsX-like permease family; Region: FtsX; pfam02687 452662004227 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 452662004228 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 452662004229 Walker A/P-loop; other site 452662004230 ATP binding site [chemical binding]; other site 452662004231 Q-loop/lid; other site 452662004232 ABC transporter signature motif; other site 452662004233 Walker B; other site 452662004234 D-loop; other site 452662004235 H-loop/switch region; other site 452662004236 macrolide transporter subunit MacA; Provisional; Region: PRK11578 452662004237 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 452662004238 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662004239 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 452662004240 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 452662004241 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 452662004242 enoyl-CoA hydratase; Provisional; Region: PRK09245 452662004243 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662004244 substrate binding site [chemical binding]; other site 452662004245 oxyanion hole (OAH) forming residues; other site 452662004246 trimer interface [polypeptide binding]; other site 452662004247 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662004248 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662004249 NAD(P) binding site [chemical binding]; other site 452662004250 active site 452662004251 acyl carrier protein; Provisional; Region: acpP; PRK00982 452662004252 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 452662004253 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 452662004254 dimer interface [polypeptide binding]; other site 452662004255 active site 452662004256 YceG-like family; Region: YceG; pfam02618 452662004257 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 452662004258 dimerization interface [polypeptide binding]; other site 452662004259 anthranilate synthase component I; Provisional; Region: PRK13573 452662004260 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 452662004261 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 452662004262 SurA N-terminal domain; Region: SurA_N_3; cl07813 452662004263 periplasmic folding chaperone; Provisional; Region: PRK10788 452662004264 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 452662004265 triosephosphate isomerase; Provisional; Region: PRK14565 452662004266 substrate binding site [chemical binding]; other site 452662004267 dimer interface [polypeptide binding]; other site 452662004268 catalytic triad [active] 452662004269 Preprotein translocase SecG subunit; Region: SecG; pfam03840 452662004270 CTP synthetase; Validated; Region: pyrG; PRK05380 452662004271 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 452662004272 Catalytic site [active] 452662004273 active site 452662004274 UTP binding site [chemical binding]; other site 452662004275 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 452662004276 active site 452662004277 putative oxyanion hole; other site 452662004278 catalytic triad [active] 452662004279 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 452662004280 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 452662004281 hypothetical protein; Provisional; Region: PRK14636 452662004282 Sm and related proteins; Region: Sm_like; cl00259 452662004283 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 452662004284 putative oligomer interface [polypeptide binding]; other site 452662004285 putative RNA binding site [nucleotide binding]; other site 452662004286 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 452662004287 NusA N-terminal domain; Region: NusA_N; pfam08529 452662004288 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 452662004289 RNA binding site [nucleotide binding]; other site 452662004290 homodimer interface [polypeptide binding]; other site 452662004291 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 452662004292 G-X-X-G motif; other site 452662004293 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 452662004294 G-X-X-G motif; other site 452662004295 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 452662004296 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 452662004297 active site 1 [active] 452662004298 dimer interface [polypeptide binding]; other site 452662004299 hexamer interface [polypeptide binding]; other site 452662004300 active site 2 [active] 452662004301 hypothetical protein; Provisional; Region: PRK09190 452662004302 Protein of unknown function (DUF448); Region: DUF448; pfam04296 452662004303 putative RNA binding cleft [nucleotide binding]; other site 452662004304 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 452662004305 translation initiation factor IF-2; Region: IF-2; TIGR00487 452662004306 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 452662004307 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 452662004308 G1 box; other site 452662004309 putative GEF interaction site [polypeptide binding]; other site 452662004310 GTP/Mg2+ binding site [chemical binding]; other site 452662004311 Switch I region; other site 452662004312 G2 box; other site 452662004313 G3 box; other site 452662004314 Switch II region; other site 452662004315 G4 box; other site 452662004316 G5 box; other site 452662004317 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 452662004318 Translation-initiation factor 2; Region: IF-2; pfam11987 452662004319 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 452662004320 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 452662004321 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 452662004322 thymidine kinase; Provisional; Region: PRK04296 452662004323 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05389 452662004324 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 452662004325 RNA binding site [nucleotide binding]; other site 452662004326 active site 452662004327 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 452662004328 16S/18S rRNA binding site [nucleotide binding]; other site 452662004329 S13e-L30e interaction site [polypeptide binding]; other site 452662004330 25S rRNA binding site [nucleotide binding]; other site 452662004331 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 452662004332 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 452662004333 RNase E interface [polypeptide binding]; other site 452662004334 trimer interface [polypeptide binding]; other site 452662004335 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 452662004336 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 452662004337 RNase E interface [polypeptide binding]; other site 452662004338 trimer interface [polypeptide binding]; other site 452662004339 active site 452662004340 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 452662004341 putative nucleic acid binding region [nucleotide binding]; other site 452662004342 G-X-X-G motif; other site 452662004343 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 452662004344 RNA binding site [nucleotide binding]; other site 452662004345 domain interface; other site 452662004346 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 452662004347 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 452662004348 Histidine kinase; Region: HisKA_2; pfam07568 452662004349 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 452662004350 ATP binding site [chemical binding]; other site 452662004351 Mg2+ binding site [ion binding]; other site 452662004352 G-X-G motif; other site 452662004353 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 452662004354 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 452662004355 binding surface 452662004356 TPR motif; other site 452662004357 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 452662004358 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 452662004359 Walker A/P-loop; other site 452662004360 ATP binding site [chemical binding]; other site 452662004361 Q-loop/lid; other site 452662004362 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 452662004363 ABC transporter signature motif; other site 452662004364 Walker B; other site 452662004365 D-loop; other site 452662004366 H-loop/switch region; other site 452662004367 Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family) [Carbohydrate transport and metabolism]; Region: GlpF; COG0580 452662004368 amphipathic channel; other site 452662004369 Asn-Pro-Ala signature motifs; other site 452662004370 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 452662004371 ArsC family; Region: ArsC; pfam03960 452662004372 catalytic residues [active] 452662004373 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 452662004374 dimerization interface [polypeptide binding]; other site 452662004375 putative DNA binding site [nucleotide binding]; other site 452662004376 putative Zn2+ binding site [ion binding]; other site 452662004377 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 452662004378 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 452662004379 nucleotide binding pocket [chemical binding]; other site 452662004380 K-X-D-G motif; other site 452662004381 catalytic site [active] 452662004382 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 452662004383 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 452662004384 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 452662004385 Dimer interface [polypeptide binding]; other site 452662004386 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 452662004387 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 452662004388 putative DNA binding site [nucleotide binding]; other site 452662004389 putative Zn2+ binding site [ion binding]; other site 452662004390 AsnC family; Region: AsnC_trans_reg; pfam01037 452662004391 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662004392 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 452662004393 dimer interface [polypeptide binding]; other site 452662004394 phosphorylation site [posttranslational modification] 452662004395 Putative catalytic domain of lipopolysaccharide biosynthesis protein WalW and its bacterial homologs; Region: CE4_WalW; cd10935 452662004396 putative active site [active] 452662004397 putative catalytic site [active] 452662004398 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 452662004399 NMT1-like family; Region: NMT1_2; pfam13379 452662004400 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 452662004401 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 452662004402 dimer interface [polypeptide binding]; other site 452662004403 conserved gate region; other site 452662004404 putative PBP binding loops; other site 452662004405 ABC-ATPase subunit interface; other site 452662004406 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 452662004407 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 452662004408 Walker A/P-loop; other site 452662004409 ATP binding site [chemical binding]; other site 452662004410 Q-loop/lid; other site 452662004411 ABC transporter signature motif; other site 452662004412 Walker B; other site 452662004413 D-loop; other site 452662004414 H-loop/switch region; other site 452662004415 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 452662004416 PA_M28_2: Protease-associated (PA) domain, peptidase family M28, subfamily-2. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions; Region: PA_M28_2; cd04815 452662004417 PA/protease or protease-like domain interface [polypeptide binding]; other site 452662004418 M28 Zn-Peptidase Plasma glutamate carboxypeptidase; Region: M28_Pgcp_like; cd03883 452662004419 Peptidase family M28; Region: Peptidase_M28; pfam04389 452662004420 metal binding site [ion binding]; metal-binding site 452662004421 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 452662004422 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 452662004423 Walker A/P-loop; other site 452662004424 ATP binding site [chemical binding]; other site 452662004425 Q-loop/lid; other site 452662004426 ABC transporter signature motif; other site 452662004427 Walker B; other site 452662004428 D-loop; other site 452662004429 H-loop/switch region; other site 452662004430 ABC transporter; Region: ABC_tran_2; pfam12848 452662004431 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 452662004432 PAS fold; Region: PAS_7; pfam12860 452662004433 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 452662004434 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 452662004435 dimer interface [polypeptide binding]; other site 452662004436 phosphorylation site [posttranslational modification] 452662004437 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 452662004438 ATP binding site [chemical binding]; other site 452662004439 Mg2+ binding site [ion binding]; other site 452662004440 G-X-G motif; other site 452662004441 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 452662004442 Phosphotransferase enzyme family; Region: APH; pfam01636 452662004443 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 452662004444 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 452662004445 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 452662004446 Substrate binding site; other site 452662004447 metal-binding site 452662004448 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 452662004449 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 452662004450 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 452662004451 Part of AAA domain; Region: AAA_19; pfam13245 452662004452 Family description; Region: UvrD_C_2; pfam13538 452662004453 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 452662004454 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 452662004455 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 452662004456 catalytic residues [active] 452662004457 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 452662004458 GST_N family, unknown subfamily 2; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_2; cd03047 452662004459 putative C-terminal domain interface [polypeptide binding]; other site 452662004460 putative GSH binding site (G-site) [chemical binding]; other site 452662004461 putative dimer interface [polypeptide binding]; other site 452662004462 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 452662004463 putative N-terminal domain interface [polypeptide binding]; other site 452662004464 putative dimer interface [polypeptide binding]; other site 452662004465 putative substrate binding pocket (H-site) [chemical binding]; other site 452662004466 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 452662004467 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 452662004468 active site 452662004469 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 452662004470 heterotetramer interface [polypeptide binding]; other site 452662004471 active site pocket [active] 452662004472 cleavage site 452662004473 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 452662004474 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 452662004475 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 452662004476 nucleotide binding region [chemical binding]; other site 452662004477 SEC-C motif; Region: SEC-C; pfam02810 452662004478 Protein of unknown function (DUF983); Region: DUF983; cl02211 452662004479 Transglycosylase SLT domain; Region: SLT_2; pfam13406 452662004480 murein hydrolase B; Provisional; Region: PRK10760; cl17906 452662004481 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 452662004482 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 452662004483 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 452662004484 thymidylate kinase; Validated; Region: tmk; PRK00698 452662004485 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 452662004486 TMP-binding site; other site 452662004487 ATP-binding site [chemical binding]; other site 452662004488 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 452662004489 DNA polymerase III subunit delta'; Validated; Region: PRK08485 452662004490 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 452662004491 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 452662004492 active site 452662004493 HIGH motif; other site 452662004494 KMSKS motif; other site 452662004495 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 452662004496 tRNA binding surface [nucleotide binding]; other site 452662004497 anticodon binding site; other site 452662004498 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 452662004499 active site 452662004500 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 452662004501 putative hydrolase; Provisional; Region: PRK02113 452662004502 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 452662004503 catalytic motif [active] 452662004504 Catalytic residue [active] 452662004505 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 452662004506 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 452662004507 putative substrate translocation pore; other site 452662004508 may be target duplication site 452662004509 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 452662004510 Helix-turn-helix domain; Region: HTH_38; pfam13936 452662004511 Integrase core domain; Region: rve; pfam00665 452662004512 may be target duplication site 452662004513 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 452662004514 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 452662004515 homodimer interface [polypeptide binding]; other site 452662004516 metal binding site [ion binding]; metal-binding site 452662004517 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 452662004518 homodimer interface [polypeptide binding]; other site 452662004519 active site 452662004520 putative chemical substrate binding site [chemical binding]; other site 452662004521 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 452662004522 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 452662004523 HflX GTPase family; Region: HflX; cd01878 452662004524 G1 box; other site 452662004525 GTP/Mg2+ binding site [chemical binding]; other site 452662004526 Switch I region; other site 452662004527 G2 box; other site 452662004528 G3 box; other site 452662004529 Switch II region; other site 452662004530 G4 box; other site 452662004531 G5 box; other site 452662004532 RNA-binding protein Hfq; Provisional; Region: PRK14091 452662004533 bacterial Hfq-like; Region: Hfq; cd01716 452662004534 hexamer interface [polypeptide binding]; other site 452662004535 Sm1 motif; other site 452662004536 RNA binding site [nucleotide binding]; other site 452662004537 Sm2 motif; other site 452662004538 bacterial Hfq-like; Region: Hfq; cd01716 452662004539 hexamer interface [polypeptide binding]; other site 452662004540 Sm1 motif; other site 452662004541 RNA binding site [nucleotide binding]; other site 452662004542 Sm2 motif; other site 452662004543 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 452662004544 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 452662004545 active site 452662004546 phosphorylation site [posttranslational modification] 452662004547 intermolecular recognition site; other site 452662004548 dimerization interface [polypeptide binding]; other site 452662004549 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 452662004550 Walker A motif; other site 452662004551 ATP binding site [chemical binding]; other site 452662004552 Walker B motif; other site 452662004553 arginine finger; other site 452662004554 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 452662004555 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 452662004556 dimerization interface [polypeptide binding]; other site 452662004557 PAS domain; Region: PAS; smart00091 452662004558 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 452662004559 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 452662004560 dimer interface [polypeptide binding]; other site 452662004561 phosphorylation site [posttranslational modification] 452662004562 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 452662004563 ATP binding site [chemical binding]; other site 452662004564 Mg2+ binding site [ion binding]; other site 452662004565 G-X-G motif; other site 452662004566 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 452662004567 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 452662004568 active site 452662004569 phosphorylation site [posttranslational modification] 452662004570 intermolecular recognition site; other site 452662004571 dimerization interface [polypeptide binding]; other site 452662004572 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 452662004573 Walker A motif; other site 452662004574 ATP binding site [chemical binding]; other site 452662004575 Walker B motif; other site 452662004576 arginine finger; other site 452662004577 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 452662004578 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 452662004579 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 452662004580 phosphorylation site [posttranslational modification] 452662004581 dimer interface [polypeptide binding]; other site 452662004582 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 452662004583 ATP binding site [chemical binding]; other site 452662004584 Mg2+ binding site [ion binding]; other site 452662004585 G-X-G motif; other site 452662004586 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 452662004587 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 452662004588 FMN binding site [chemical binding]; other site 452662004589 active site 452662004590 catalytic residues [active] 452662004591 substrate binding site [chemical binding]; other site 452662004592 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 452662004593 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 452662004594 substrate binding site; other site 452662004595 dimer interface; other site 452662004596 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 452662004597 homotrimer interaction site [polypeptide binding]; other site 452662004598 zinc binding site [ion binding]; other site 452662004599 CDP-binding sites; other site 452662004600 Competence-damaged protein; Region: CinA; pfam02464 452662004601 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 452662004602 putative coenzyme Q binding site [chemical binding]; other site 452662004603 lipoyl synthase; Provisional; Region: PRK05481 452662004604 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 452662004605 FeS/SAM binding site; other site 452662004606 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 452662004607 active site clefts [active] 452662004608 zinc binding site [ion binding]; other site 452662004609 dimer interface [polypeptide binding]; other site 452662004610 Uncharacterized conserved protein [Function unknown]; Region: COG1432 452662004611 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 452662004612 putative metal binding site [ion binding]; other site 452662004613 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 452662004614 Acylphosphatases [Energy production and conversion]; Region: AcyP; COG1254 452662004615 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 452662004616 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 452662004617 homotetramer interface [polypeptide binding]; other site 452662004618 ligand binding site [chemical binding]; other site 452662004619 catalytic site [active] 452662004620 NAD binding site [chemical binding]; other site 452662004621 Uncharacterized ACR, COG1678; Region: DUF179; pfam02622 452662004622 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 452662004623 catalytic triad [active] 452662004624 dimer interface [polypeptide binding]; other site 452662004625 AMP nucleosidase; Provisional; Region: PRK08292 452662004626 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 452662004627 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 452662004628 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 452662004629 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 452662004630 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 452662004631 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 452662004632 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 452662004633 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 452662004634 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 452662004635 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 452662004636 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 452662004637 active site 452662004638 HslU subunit interaction site [polypeptide binding]; other site 452662004639 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 452662004640 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 452662004641 Walker A motif; other site 452662004642 ATP binding site [chemical binding]; other site 452662004643 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 452662004644 Walker B motif; other site 452662004645 arginine finger; other site 452662004646 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 452662004647 prolyl-tRNA synthetase; Provisional; Region: PRK08661 452662004648 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 452662004649 dimer interface [polypeptide binding]; other site 452662004650 motif 1; other site 452662004651 active site 452662004652 motif 2; other site 452662004653 motif 3; other site 452662004654 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 452662004655 anticodon binding site; other site 452662004656 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 452662004657 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 452662004658 poly(R)-hydroxyalkanoic acid synthase, class III, PhaC subunit; Region: PHA_synth_III_C; TIGR01836 452662004659 putative acyltransferase; Provisional; Region: PRK05790 452662004660 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 452662004661 dimer interface [polypeptide binding]; other site 452662004662 active site 452662004663 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 452662004664 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 452662004665 active site 452662004666 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 452662004667 dimer interface [polypeptide binding]; other site 452662004668 substrate binding site [chemical binding]; other site 452662004669 catalytic residues [active] 452662004670 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 452662004671 putative substrate translocation pore; other site 452662004672 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 452662004673 dimer interface [polypeptide binding]; other site 452662004674 putative tRNA-binding site [nucleotide binding]; other site 452662004675 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 452662004676 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 452662004677 ATP-grasp domain; Region: ATP-grasp_4; cl17255 452662004678 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 452662004679 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 452662004680 carboxyltransferase (CT) interaction site; other site 452662004681 biotinylation site [posttranslational modification]; other site 452662004682 biotin synthase; Region: bioB; TIGR00433 452662004683 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 452662004684 FeS/SAM binding site; other site 452662004685 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 452662004686 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 452662004687 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 452662004688 active site 452662004689 substrate binding site [chemical binding]; other site 452662004690 coenzyme B12 binding site [chemical binding]; other site 452662004691 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 452662004692 B12 binding site [chemical binding]; other site 452662004693 cobalt ligand [ion binding]; other site 452662004694 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662004695 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 452662004696 dimer interface [polypeptide binding]; other site 452662004697 substrate binding site [chemical binding]; other site 452662004698 metal binding site [ion binding]; metal-binding site 452662004699 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 452662004700 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 452662004701 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 452662004702 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 452662004703 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 452662004704 non-specific DNA binding site [nucleotide binding]; other site 452662004705 salt bridge; other site 452662004706 sequence-specific DNA binding site [nucleotide binding]; other site 452662004707 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 452662004708 Domain of unknown function (DUF955); Region: DUF955; pfam06114 452662004709 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 452662004710 Biofilm formation and stress response factor; Region: BsmA; pfam10014 452662004711 glutathione reductase; Validated; Region: PRK06116 452662004712 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 452662004713 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 452662004714 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 452662004715 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 452662004716 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 452662004717 active site 452662004718 dimer interface [polypeptide binding]; other site 452662004719 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 452662004720 dimer interface [polypeptide binding]; other site 452662004721 active site 452662004722 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 452662004723 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 452662004724 Catalytic site [active] 452662004725 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 452662004726 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 452662004727 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 452662004728 dimerization interface [polypeptide binding]; other site 452662004729 active site 452662004730 metal binding site [ion binding]; metal-binding site 452662004731 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 452662004732 dsRNA binding site [nucleotide binding]; other site 452662004733 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 452662004734 GIY-YIG motif/motif A; other site 452662004735 putative active site [active] 452662004736 putative metal binding site [ion binding]; other site 452662004737 GTPase Era; Reviewed; Region: era; PRK00089 452662004738 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 452662004739 G1 box; other site 452662004740 GTP/Mg2+ binding site [chemical binding]; other site 452662004741 Switch I region; other site 452662004742 G2 box; other site 452662004743 Switch II region; other site 452662004744 G3 box; other site 452662004745 G4 box; other site 452662004746 G5 box; other site 452662004747 KH domain; Region: KH_2; pfam07650 452662004748 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 452662004749 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 452662004750 active site 452662004751 interdomain interaction site; other site 452662004752 putative metal-binding site [ion binding]; other site 452662004753 nucleotide binding site [chemical binding]; other site 452662004754 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 452662004755 domain I; other site 452662004756 DNA binding groove [nucleotide binding] 452662004757 phosphate binding site [ion binding]; other site 452662004758 domain II; other site 452662004759 domain III; other site 452662004760 nucleotide binding site [chemical binding]; other site 452662004761 catalytic site [active] 452662004762 domain IV; other site 452662004763 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 452662004764 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 452662004765 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 452662004766 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 452662004767 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 452662004768 DNA protecting protein DprA; Region: dprA; TIGR00732 452662004769 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 452662004770 glutamate racemase; Provisional; Region: PRK00865 452662004771 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 452662004772 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 452662004773 substrate-cofactor binding pocket; other site 452662004774 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662004775 catalytic residue [active] 452662004776 putative exonuclease, DNA ligase-associated; Region: Xnuc_lig_assoc; TIGR04122 452662004777 DNA ligase, ATP-dependent, PP_1105 family; Region: DNA_lig_bact; TIGR04120 452662004778 Adenylation domain of putative bacterial ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_Bac1; cd07897 452662004779 active site 452662004780 DNA binding site [nucleotide binding] 452662004781 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_Arch_LigB; cd07972 452662004782 DNA binding site [nucleotide binding] 452662004783 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 452662004784 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662004785 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 452662004786 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 452662004787 dimer interface [polypeptide binding]; other site 452662004788 active site 452662004789 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 452662004790 catalytic residues [active] 452662004791 substrate binding site [chemical binding]; other site 452662004792 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 452662004793 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 452662004794 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 452662004795 catalytic residue [active] 452662004796 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 452662004797 Uncharacterized conserved protein [Function unknown]; Region: COG0062 452662004798 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 452662004799 putative ATP binding site [chemical binding]; other site 452662004800 putative substrate binding site [chemical binding]; other site 452662004801 N-formylglutamate amidohydrolase; Region: FGase; cl01522 452662004802 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14608 452662004803 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 452662004804 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 452662004805 hydroxyglutarate oxidase; Provisional; Region: PRK11728 452662004806 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 452662004807 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 452662004808 active site 452662004809 Fe-S cluster binding site [ion binding]; other site 452662004810 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 452662004811 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 452662004812 N-acetyl-D-glucosamine binding site [chemical binding]; other site 452662004813 catalytic residue [active] 452662004814 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 452662004815 MPT binding site; other site 452662004816 trimer interface [polypeptide binding]; other site 452662004817 Putative bacterial sensory transduction regulator; Region: YbjN; pfam10722 452662004818 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 452662004819 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 452662004820 FeS/SAM binding site; other site 452662004821 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 452662004822 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 452662004823 putative active site [active] 452662004824 putative PHP Thumb interface [polypeptide binding]; other site 452662004825 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 452662004826 generic binding surface II; other site 452662004827 generic binding surface I; other site 452662004828 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 452662004829 dimerization interface [polypeptide binding]; other site 452662004830 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662004831 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662004832 metal binding site [ion binding]; metal-binding site 452662004833 active site 452662004834 I-site; other site 452662004835 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 452662004836 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 452662004837 Walker A/P-loop; other site 452662004838 ATP binding site [chemical binding]; other site 452662004839 Q-loop/lid; other site 452662004840 ABC transporter signature motif; other site 452662004841 Walker B; other site 452662004842 D-loop; other site 452662004843 H-loop/switch region; other site 452662004844 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 452662004845 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 452662004846 FtsX-like permease family; Region: FtsX; pfam02687 452662004847 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 452662004848 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 452662004849 putative dimer interface [polypeptide binding]; other site 452662004850 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 452662004851 potassium uptake protein; Region: kup; TIGR00794 452662004852 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 452662004853 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 452662004854 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 452662004855 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 452662004856 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 452662004857 CcmE; Region: CcmE; pfam03100 452662004858 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 452662004859 amidophosphoribosyltransferase; Provisional; Region: PRK09123 452662004860 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 452662004861 active site 452662004862 tetramer interface [polypeptide binding]; other site 452662004863 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 452662004864 active site 452662004865 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662004866 short chain dehydrogenase; Provisional; Region: PRK08219 452662004867 NAD(P) binding site [chemical binding]; other site 452662004868 active site 452662004869 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 452662004870 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 452662004871 S-adenosylmethionine binding site [chemical binding]; other site 452662004872 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 452662004873 DNA photolyase; Region: DNA_photolyase; pfam00875 452662004874 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 452662004875 putative active site [active] 452662004876 Ap4A binding site [chemical binding]; other site 452662004877 nudix motif; other site 452662004878 putative metal binding site [ion binding]; other site 452662004879 Protein of unknown function, DUF481; Region: DUF481; pfam04338 452662004880 hypothetical protein; Provisional; Region: PRK07338 452662004881 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 452662004882 metal binding site [ion binding]; metal-binding site 452662004883 dimer interface [polypeptide binding]; other site 452662004884 Arginine N-succinyltransferase beta subunit; Region: AstA; pfam04958 452662004885 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 452662004886 succinylarginine dihydrolase; Provisional; Region: PRK13281 452662004887 cobyric acid synthase; Provisional; Region: PRK00784 452662004888 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 452662004889 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 452662004890 catalytic triad [active] 452662004891 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 452662004892 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 452662004893 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 452662004894 Walker A/P-loop; other site 452662004895 ATP binding site [chemical binding]; other site 452662004896 Q-loop/lid; other site 452662004897 ABC transporter signature motif; other site 452662004898 Walker B; other site 452662004899 D-loop; other site 452662004900 H-loop/switch region; other site 452662004901 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 452662004902 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 452662004903 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662004904 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_3; cd03813 452662004905 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662004906 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 452662004907 TM1410 hypothetical-related protein; Region: DUF297; pfam03537 452662004908 Predicted membrane protein [Function unknown]; Region: COG4267 452662004909 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 452662004910 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 452662004911 Ca2+ binding site [ion binding]; other site 452662004912 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 452662004913 Ca2+ binding site [ion binding]; other site 452662004914 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 452662004915 Ca2+ binding site [ion binding]; other site 452662004916 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 452662004917 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 452662004918 TM1410 hypothetical-related protein; Region: DUF297; pfam03537 452662004919 Uncharacterized conserved protein [Function unknown]; Region: COG3743 452662004920 pyruvate phosphate dikinase; Provisional; Region: PRK09279 452662004921 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 452662004922 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 452662004923 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 452662004924 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 452662004925 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 452662004926 dimer interface [polypeptide binding]; other site 452662004927 motif 1; other site 452662004928 active site 452662004929 motif 2; other site 452662004930 motif 3; other site 452662004931 TraB family; Region: TraB; pfam01963 452662004932 TraB family; Region: TraB; pfam01963 452662004933 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 452662004934 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 452662004935 5S rRNA interface [nucleotide binding]; other site 452662004936 CTC domain interface [polypeptide binding]; other site 452662004937 L16 interface [polypeptide binding]; other site 452662004938 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 452662004939 putative active site [active] 452662004940 catalytic residue [active] 452662004941 phosphoglucomutase; Region: PLN02307 452662004942 Phosphoglucomutase 1 (PGM1) catalyzes the bidirectional interconversion of glucose-1-phosphate (G-1-P) and glucose-6-phosphate (G-6-P) via a glucose 1,6-diphosphate intermediate, an important metabolic step in prokaryotes and eukaryotes. In one direction; Region: PGM1; cd03085 452662004943 substrate binding site [chemical binding]; other site 452662004944 dimer interface [polypeptide binding]; other site 452662004945 active site 452662004946 metal binding site [ion binding]; metal-binding site 452662004947 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 452662004948 GTP-binding protein YchF; Reviewed; Region: PRK09601 452662004949 YchF GTPase; Region: YchF; cd01900 452662004950 G1 box; other site 452662004951 GTP/Mg2+ binding site [chemical binding]; other site 452662004952 Switch I region; other site 452662004953 G2 box; other site 452662004954 Switch II region; other site 452662004955 G3 box; other site 452662004956 G4 box; other site 452662004957 G5 box; other site 452662004958 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 452662004959 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 452662004960 putative active site [active] 452662004961 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 452662004962 phosphonoacetate hydrolase; Region: hydr_PhnA; TIGR02335 452662004963 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 452662004964 putative active site [active] 452662004965 putative catalytic site [active] 452662004966 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 452662004967 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 452662004968 ATP binding site [chemical binding]; other site 452662004969 Mg2+ binding site [ion binding]; other site 452662004970 G-X-G motif; other site 452662004971 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 452662004972 ATP binding site [chemical binding]; other site 452662004973 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 452662004974 rod shape-determining protein MreB; Provisional; Region: PRK13927 452662004975 MreB and similar proteins; Region: MreB_like; cd10225 452662004976 nucleotide binding site [chemical binding]; other site 452662004977 Mg binding site [ion binding]; other site 452662004978 putative protofilament interaction site [polypeptide binding]; other site 452662004979 RodZ interaction site [polypeptide binding]; other site 452662004980 rod shape-determining protein MreC; Provisional; Region: PRK13922 452662004981 rod shape-determining protein MreC; Region: MreC; pfam04085 452662004982 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 452662004983 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 452662004984 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 452662004985 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 452662004986 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; pfam05930 452662004987 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 452662004988 Restriction endonuclease; Region: Mrr_cat; pfam04471 452662004989 TrwC relaxase; Region: TrwC; pfam08751 452662004990 conjugative relaxase domain, TrwC/TraI family; Region: relax_trwC; TIGR02686 452662004991 AAA domain; Region: AAA_30; pfam13604 452662004992 Family description; Region: UvrD_C_2; pfam13538 452662004993 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 452662004994 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 452662004995 Walker A motif; other site 452662004996 ATP binding site [chemical binding]; other site 452662004997 Walker B motif; other site 452662004998 Protein of unknown function (DUF2493); Region: DUF2493; pfam10686 452662004999 Protein of unknown function (DUF736); Region: DUF736; pfam05284 452662005000 Homeodomain-like domain; Region: HTH_23; cl17451 452662005001 Winged helix-turn helix; Region: HTH_29; pfam13551 452662005002 Homeodomain-like domain; Region: HTH_32; pfam13565 452662005003 DDE superfamily endonuclease; Region: DDE_3; pfam13358 452662005004 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 452662005005 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 452662005006 ATP binding site [chemical binding]; other site 452662005007 Mg2+ binding site [ion binding]; other site 452662005008 G-X-G motif; other site 452662005009 PRTRC system ThiF family protein; Region: PRTRC_ThiF; TIGR03736 452662005010 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cl17196 452662005011 substrate interface [chemical binding]; other site 452662005012 Domain of unknown function (DUF2016); Region: DUF2016; pfam09436 452662005013 Prokaryotic homologs of the JAB domain; Region: Prok-JAB; pfam14464 452662005014 Prokaryotic E2 family D; Region: Prok-E2_D; cl14019 452662005015 Alpha-helical domain 2; Region: alpha-hel2; pfam14456 452662005016 Prokaryotic Ubiquitin; Region: Prok_Ub; cl14020 452662005017 PRTRC system protein E; Region: PRTRC_E; TIGR03741 452662005018 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 452662005019 ParB-like nuclease domain; Region: ParB; smart00470 452662005020 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662005021 Walker A/P-loop; other site 452662005022 ATP binding site [chemical binding]; other site 452662005023 Q-loop/lid; other site 452662005024 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 452662005025 Protein of unknown function (DUF1419); Region: DUF1419; pfam07215 452662005026 Domain of unknown function (DUF4262); Region: DUF4262; pfam14081 452662005027 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 452662005028 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662005029 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662005030 Integrase core domain; Region: rve; pfam00665 452662005031 Members of the ICL/PEPM_KPHMT enzyme superfamily catalyze the formation and cleavage of either P-C or C-C bonds. Typical members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate...; Region: ICL_KPHMT; cl00435 452662005032 Predicted esterase [General function prediction only]; Region: COG0400 452662005033 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 452662005034 SnoaL-like domain; Region: SnoaL_4; pfam13577 452662005035 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662005036 NAD(P) binding site [chemical binding]; other site 452662005037 active site 452662005038 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662005039 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662005040 NAD(P) binding site [chemical binding]; other site 452662005041 active site 452662005042 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 452662005043 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662005044 active site 452662005045 glutathione reductase; Validated; Region: PRK06116 452662005046 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 452662005047 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 452662005048 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 452662005049 MoeA_like. This domain is similar to a domain found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. There this domain is presumed to bind molybdopterin. The exact function of this subgroup is...; Region: MoeA_like; cd03522 452662005050 putative MPT binding site; other site 452662005051 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 452662005052 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 452662005053 XdhC Rossmann domain; Region: XdhC_C; pfam13478 452662005054 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 452662005055 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 452662005056 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 452662005057 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes [Energy production and conversion]; Region: AceF; COG0508 452662005058 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 452662005059 E3 interaction surface; other site 452662005060 lipoyl attachment site [posttranslational modification]; other site 452662005061 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 452662005062 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 452662005063 alpha subunit interface [polypeptide binding]; other site 452662005064 TPP binding site [chemical binding]; other site 452662005065 heterodimer interface [polypeptide binding]; other site 452662005066 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 452662005067 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 452662005068 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 452662005069 tetramer interface [polypeptide binding]; other site 452662005070 TPP-binding site [chemical binding]; other site 452662005071 heterodimer interface [polypeptide binding]; other site 452662005072 phosphorylation loop region [posttranslational modification] 452662005073 cyclohexanecarboxylate-CoA ligase; Reviewed; Region: PRK13295 452662005074 Cyclohexanecarboxylate-CoA ligase (also called cyclohex-1-ene-1-carboxylate:CoA ligase); Region: CHC_CoA_lg; cd05903 452662005075 acyl-activating enzyme (AAE) consensus motif; other site 452662005076 putative AMP binding site [chemical binding]; other site 452662005077 putative active site [active] 452662005078 putative CoA binding site [chemical binding]; other site 452662005079 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662005080 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662005081 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 452662005082 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 452662005083 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662005084 NAD(P) binding site [chemical binding]; other site 452662005085 active site 452662005086 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily 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: ACAD10_11_like; cd05154 452662005087 putative active site [active] 452662005088 putative substrate binding site [chemical binding]; other site 452662005089 ATP binding site [chemical binding]; other site 452662005090 Prostaglandin dehydrogenases; Region: PGDH; cd05288 452662005091 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 452662005092 NAD(P) binding site [chemical binding]; other site 452662005093 substrate binding site [chemical binding]; other site 452662005094 dimer interface [polypeptide binding]; other site 452662005095 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662005096 active site 452662005097 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662005098 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662005099 Integrase core domain; Region: rve; pfam00665 452662005100 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 452662005101 NAD(P) binding site [chemical binding]; other site 452662005102 catalytic residues [active] 452662005103 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 452662005104 putative substrate translocation pore; other site 452662005105 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662005106 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662005107 NAD(P) binding site [chemical binding]; other site 452662005108 active site 452662005109 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 452662005110 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 452662005111 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 452662005112 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 452662005113 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 452662005114 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 452662005115 Transcriptional regulator [Transcription]; Region: IclR; COG1414 452662005116 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 452662005117 Amidase; Region: Amidase; cl11426 452662005118 Transposase, Mutator family; Region: Transposase_mut; pfam00872 452662005119 potential frameshift: common BLAST hit: gi|85373170|ref|YP_457232.1| dipeptidyl aminopeptidase 452662005120 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 452662005121 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 452662005122 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 452662005123 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 452662005124 Protein of unknown function (DUF1826); Region: DUF1826; pfam08856 452662005125 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 452662005126 metal binding site 2 [ion binding]; metal-binding site 452662005127 putative DNA binding helix; other site 452662005128 metal binding site 1 [ion binding]; metal-binding site 452662005129 dimer interface [polypeptide binding]; other site 452662005130 structural Zn2+ binding site [ion binding]; other site 452662005131 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 452662005132 metal binding site 2 [ion binding]; metal-binding site 452662005133 putative DNA binding helix; other site 452662005134 metal binding site 1 [ion binding]; metal-binding site 452662005135 dimer interface [polypeptide binding]; other site 452662005136 structural Zn2+ binding site [ion binding]; other site 452662005137 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662005138 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 452662005139 N-terminal plug; other site 452662005140 ligand-binding site [chemical binding]; other site 452662005141 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 452662005142 metal binding site 2 [ion binding]; metal-binding site 452662005143 putative DNA binding helix; other site 452662005144 metal binding site 1 [ion binding]; metal-binding site 452662005145 dimer interface [polypeptide binding]; other site 452662005146 structural Zn2+ binding site [ion binding]; other site 452662005147 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 452662005148 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 452662005149 N-terminal plug; other site 452662005150 ligand-binding site [chemical binding]; other site 452662005151 Protein of unknown function (DUF3299); Region: DUF3299; cl01387 452662005152 Protein of unknown function (DUF3299); Region: DUF3299; cl01387 452662005153 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 452662005154 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 452662005155 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 452662005156 Walker A/P-loop; other site 452662005157 ATP binding site [chemical binding]; other site 452662005158 Q-loop/lid; other site 452662005159 ABC transporter signature motif; other site 452662005160 Walker B; other site 452662005161 D-loop; other site 452662005162 H-loop/switch region; other site 452662005163 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 452662005164 catalytic residues [active] 452662005165 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 452662005166 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 452662005167 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 452662005168 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 452662005169 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 452662005170 metal binding site 2 [ion binding]; metal-binding site 452662005171 putative DNA binding helix; other site 452662005172 metal binding site 1 [ion binding]; metal-binding site 452662005173 dimer interface [polypeptide binding]; other site 452662005174 structural Zn2+ binding site [ion binding]; other site 452662005175 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 452662005176 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 452662005177 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 452662005178 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 452662005179 Walker A/P-loop; other site 452662005180 ATP binding site [chemical binding]; other site 452662005181 Q-loop/lid; other site 452662005182 ABC transporter signature motif; other site 452662005183 Walker B; other site 452662005184 D-loop; other site 452662005185 H-loop/switch region; other site 452662005186 Domain of unknown function (DUF3526); Region: DUF3526; pfam12040 452662005187 ABC-type transport system involved in multi-copper enzyme maturation, permease component [General function prediction only]; Region: NosY; COG1277 452662005188 Domain of unknown function (DUF3526); Region: DUF3526; pfam12040 452662005189 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 452662005190 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 452662005191 N-terminal plug; other site 452662005192 ligand-binding site [chemical binding]; other site 452662005193 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 452662005194 active site 452662005195 DNA binding site [nucleotide binding] 452662005196 Int/Topo IB signature motif; other site 452662005197 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 452662005198 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 452662005199 putative DNA binding site [nucleotide binding]; other site 452662005200 putative Zn2+ binding site [ion binding]; other site 452662005201 AsnC family; Region: AsnC_trans_reg; pfam01037 452662005202 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 452662005203 Bacterial sugar transferase; Region: Bac_transf; pfam02397 452662005204 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; pfam10082 452662005205 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 452662005206 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 452662005207 SLBB domain; Region: SLBB; pfam10531 452662005208 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 452662005209 AAA domain; Region: AAA_22; pfam13401 452662005210 Walker A motif; other site 452662005211 ATP binding site [chemical binding]; other site 452662005212 Walker B motif; other site 452662005213 arginine finger; other site 452662005214 chain length determinant protein EpsF; Region: EpsF; TIGR03017 452662005215 Chain length determinant protein; Region: Wzz; cl15801 452662005216 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 452662005217 chain length determinant protein tyrosine kinase EpsG; Region: EpsG; TIGR03029 452662005218 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 452662005219 Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]; Region: WecG; COG1922 452662005220 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 452662005221 Polysaccharide biosynthesis protein; Region: Polysacc_synt_3; pfam13440 452662005222 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 452662005223 O-Antigen ligase; Region: Wzy_C; pfam04932 452662005224 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 452662005225 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 452662005226 active site 452662005227 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 452662005228 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 452662005229 active site 452662005230 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 452662005231 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 452662005232 active site 452662005233 Glycosyl hydrolase family 10; Region: Glyco_hydro_10; cl01495 452662005234 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 452662005235 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 452662005236 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 452662005237 active site 452662005238 glycosyl hydrolase family 16; Region: Glyco_hydrolase_16; cl00218 452662005239 active site 452662005240 catalytic residues [active] 452662005241 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 452662005242 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 452662005243 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 452662005244 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 452662005245 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 452662005246 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 452662005247 putative MPT binding site; other site 452662005248 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 452662005249 active site 452662005250 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 452662005251 Nitrogen regulatory protein P-II; Region: P-II; smart00938 452662005252 glutamine synthetase; Provisional; Region: glnA; PRK09469 452662005253 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 452662005254 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 452662005255 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 452662005256 FMN binding site [chemical binding]; other site 452662005257 substrate binding site [chemical binding]; other site 452662005258 putative catalytic residue [active] 452662005259 Uncharacterized protein conserved in bacteria (DUF2328); Region: DUF2328; pfam10090 452662005260 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); Region: MPN_like; cd08070 452662005261 MPN+ (JAMM) motif; other site 452662005262 Zinc-binding site [ion binding]; other site 452662005263 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 452662005264 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 452662005265 RNA binding surface [nucleotide binding]; other site 452662005266 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 452662005267 active site 452662005268 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 452662005269 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 452662005270 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 452662005271 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 452662005272 DNA binding residues [nucleotide binding] 452662005273 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 452662005274 Transglycosylase; Region: Transgly; cl17702 452662005275 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662005276 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 452662005277 N-terminal plug; other site 452662005278 ligand-binding site [chemical binding]; other site 452662005279 recognition site for restriction enzyme SwaI 452662005280 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 452662005281 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 452662005282 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 452662005283 Walker A motif; other site 452662005284 ATP binding site [chemical binding]; other site 452662005285 Walker B motif; other site 452662005286 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 452662005287 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 452662005288 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 452662005289 oligomer interface [polypeptide binding]; other site 452662005290 active site residues [active] 452662005291 glycosyltransferase, TIGR04182 family; Region: glyco_TIGR04182 452662005292 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 452662005293 Ligand binding site; other site 452662005294 Putative Catalytic site; other site 452662005295 DXD motif; other site 452662005296 trigger factor; Provisional; Region: tig; PRK01490 452662005297 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 452662005298 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 452662005299 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 452662005300 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 452662005301 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 452662005302 DNA binding residues [nucleotide binding] 452662005303 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 452662005304 FecR protein; Region: FecR; pfam04773 452662005305 NAD-dependent deacetylase; Provisional; Region: PRK00481 452662005306 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 452662005307 NAD+ binding site [chemical binding]; other site 452662005308 substrate binding site [chemical binding]; other site 452662005309 Zn binding site [ion binding]; other site 452662005310 dihydrodipicolinate reductase; Provisional; Region: PRK00048 452662005311 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 452662005312 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 452662005313 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 452662005314 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 452662005315 minor groove reading motif; other site 452662005316 helix-hairpin-helix signature motif; other site 452662005317 substrate binding pocket [chemical binding]; other site 452662005318 active site 452662005319 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 452662005320 FixH; Region: FixH; pfam05751 452662005321 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 452662005322 C-terminal domain interface [polypeptide binding]; other site 452662005323 GSH binding site (G-site) [chemical binding]; other site 452662005324 dimer interface [polypeptide binding]; other site 452662005325 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 452662005326 N-terminal domain interface [polypeptide binding]; other site 452662005327 dimer interface [polypeptide binding]; other site 452662005328 substrate binding pocket (H-site) [chemical binding]; other site 452662005329 haloalkane dehalogenase; Provisional; Region: PRK03592 452662005330 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 452662005331 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 452662005332 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 452662005333 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 452662005334 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 452662005335 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 452662005336 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 452662005337 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cd00531 452662005338 SnoaL-like domain; Region: SnoaL_3; pfam13474 452662005339 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3558 452662005340 SnoaL-like domain; Region: SnoaL_2; pfam12680 452662005341 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 452662005342 Uncharacterized conserved protein [Function unknown]; Region: COG2128 452662005343 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 452662005344 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662005345 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662005346 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662005347 dimerization interface [polypeptide binding]; other site 452662005348 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 452662005349 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 452662005350 active site 452662005351 FMN binding site [chemical binding]; other site 452662005352 substrate binding site [chemical binding]; other site 452662005353 putative catalytic residue [active] 452662005354 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 452662005355 classical (c) SDR, subgroup 10; Region: SDR_c10; cd05373 452662005356 putative NAD(P) binding site [chemical binding]; other site 452662005357 active site 452662005358 YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgH_like; cd02198 452662005359 homotrimer interaction site [polypeptide binding]; other site 452662005360 putative active site [active] 452662005361 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662005362 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662005363 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 452662005364 putative effector binding pocket; other site 452662005365 dimerization interface [polypeptide binding]; other site 452662005366 potential frameshift: common BLAST hit: gi|254784278|ref|YP_003071706.1| antioxidant, AhpC/TSA family protein 452662005367 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these...; Region: PRX_like2; cd02970 452662005368 putative catalytic residues [active] 452662005369 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 452662005370 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these...; Region: PRX_like2; cd02970 452662005371 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 452662005372 putative catalytic residues [active] 452662005373 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 452662005374 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 452662005375 C-terminal domain interface [polypeptide binding]; other site 452662005376 GSH binding site (G-site) [chemical binding]; other site 452662005377 dimer interface [polypeptide binding]; other site 452662005378 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 452662005379 N-terminal domain interface [polypeptide binding]; other site 452662005380 dimer interface [polypeptide binding]; other site 452662005381 substrate binding pocket (H-site) [chemical binding]; other site 452662005382 putative S-transferase; Provisional; Region: PRK11752 452662005383 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 452662005384 C-terminal domain interface [polypeptide binding]; other site 452662005385 GSH binding site (G-site) [chemical binding]; other site 452662005386 dimer interface [polypeptide binding]; other site 452662005387 C-terminal, alpha helical domain of Escherichia coli Yghu Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YghU_like; cd10292 452662005388 dimer interface [polypeptide binding]; other site 452662005389 N-terminal domain interface [polypeptide binding]; other site 452662005390 active site 452662005391 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 452662005392 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662005393 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 452662005394 dimerization interface [polypeptide binding]; other site 452662005395 substrate binding pocket [chemical binding]; other site 452662005396 Protein of unknown function (DUF2274); Region: DUF2274; pfam10038 452662005397 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 452662005398 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 452662005399 VirB7 interaction site; other site 452662005400 conjugal transfer protein TrbF; Provisional; Region: PRK13872 452662005401 conjugal transfer protein TrbL; Provisional; Region: PRK13875 452662005402 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 452662005403 conjugative transfer region protein TrbK; Region: other_trbK; TIGR04360 452662005404 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 452662005405 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 452662005406 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 452662005407 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662005408 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 452662005409 Walker A motif; other site 452662005410 Walker A/P-loop; other site 452662005411 ATP binding site [chemical binding]; other site 452662005412 ATP binding site [chemical binding]; other site 452662005413 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 452662005414 Type IV secretory pathway, TrbD component [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TrbD; COG5268 452662005415 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 452662005416 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 452662005417 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 452662005418 ATP binding site [chemical binding]; other site 452662005419 Walker A motif; other site 452662005420 hexamer interface [polypeptide binding]; other site 452662005421 Walker B motif; other site 452662005422 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 452662005423 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 452662005424 Walker A motif; other site 452662005425 ATP binding site [chemical binding]; other site 452662005426 Walker B motif; other site 452662005427 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 452662005428 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 452662005429 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 452662005430 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 452662005431 N-acetyl-D-glucosamine binding site [chemical binding]; other site 452662005432 catalytic residue [active] 452662005433 Protein of unknown function (DUF736); Region: DUF736; pfam05284 452662005434 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 452662005435 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 452662005436 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 452662005437 Antitoxin ParD; Region: ParD; pfam09386 452662005438 ParA-like protein; Provisional; Region: PHA02518 452662005439 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 452662005440 P-loop; other site 452662005441 Magnesium ion binding site [ion binding]; other site 452662005442 Replication initiator protein A; Region: RPA; pfam10134 452662005443 Helix-turn-helix domain; Region: HTH_17; pfam12728 452662005444 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 452662005445 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 452662005446 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 452662005447 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 452662005448 dimer interface [polypeptide binding]; other site 452662005449 ssDNA binding site [nucleotide binding]; other site 452662005450 tetramer (dimer of dimers) interface [polypeptide binding]; other site 452662005451 Protein of unknown function (DUF2493); Region: DUF2493; pfam10686 452662005452 Toprim domain; Region: Toprim_3; pfam13362 452662005453 Methyltransferase domain; Region: Methyltransf_26; pfam13659 452662005454 P-loop containing NTP hydrolase pore-1; Region: AAA_34; pfam13872 452662005455 Helicase_C-like; Region: Helicase_C_4; pfam13871 452662005456 ParB-like nuclease domain; Region: ParB; smart00470 452662005457 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 452662005458 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 452662005459 Protein of unknwon function (DUF2893); Region: DUF2893; pfam11459 452662005460 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 452662005461 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 452662005462 Domain of unknown function (DUF955); Region: DUF955; pfam06114 452662005463 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 452662005464 Part of AAA domain; Region: AAA_19; pfam13245 452662005465 Family description; Region: UvrD_C_2; pfam13538 452662005466 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 452662005467 Bacterial multiubiquitin; Region: Bac_multiUb; pfam14452 452662005468 Bacterial multiubiquitin; Region: Bac_multiUb; pfam14452 452662005469 Bacterial multiubiquitin; Region: Bac_multiUb; pfam14452 452662005470 hypothetical protein; Provisional; Region: PRK06153 452662005471 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cd01483 452662005472 ATP binding site [chemical binding]; other site 452662005473 substrate interface [chemical binding]; other site 452662005474 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 452662005475 active site 452662005476 DNA binding site [nucleotide binding] 452662005477 Int/Topo IB signature motif; other site 452662005478 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 452662005479 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 452662005480 DNA binding site [nucleotide binding] 452662005481 active site 452662005482 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 452662005483 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 452662005484 Protein export membrane protein; Region: SecD_SecF; cl14618 452662005485 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 452662005486 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 452662005487 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662005488 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662005489 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662005490 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 452662005491 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 452662005492 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 452662005493 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 452662005494 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 452662005495 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 452662005496 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 452662005497 ATP binding site [chemical binding]; other site 452662005498 Mg++ binding site [ion binding]; other site 452662005499 motif III; other site 452662005500 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 452662005501 nucleotide binding region [chemical binding]; other site 452662005502 ATP-binding site [chemical binding]; other site 452662005503 Uncharacterized stress protein (general stress protein 26) [General function prediction only]; Region: COG3871 452662005504 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 452662005505 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 452662005506 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 452662005507 Glycoprotease family; Region: Peptidase_M22; pfam00814 452662005508 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 452662005509 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 452662005510 Coenzyme A binding pocket [chemical binding]; other site 452662005511 recognition site for restriction enzyme SwaI 452662005512 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 452662005513 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 452662005514 metal binding site 2 [ion binding]; metal-binding site 452662005515 putative DNA binding helix; other site 452662005516 metal binding site 1 [ion binding]; metal-binding site 452662005517 dimer interface [polypeptide binding]; other site 452662005518 structural Zn2+ binding site [ion binding]; other site 452662005519 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 452662005520 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 452662005521 putative acyl-acceptor binding pocket; other site 452662005522 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 452662005523 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 452662005524 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 452662005525 FeS/SAM binding site; other site 452662005526 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 452662005527 PhoH-like protein; Region: PhoH; pfam02562 452662005528 metal-binding heat shock protein; Provisional; Region: PRK00016 452662005529 FOG: CBS domain [General function prediction only]; Region: COG0517 452662005530 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 452662005531 Transporter associated domain; Region: CorC_HlyC; smart01091 452662005532 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 452662005533 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 452662005534 active site 452662005535 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 452662005536 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 452662005537 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 452662005538 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 452662005539 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 452662005540 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 452662005541 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 452662005542 E3 interaction surface; other site 452662005543 lipoyl attachment site [posttranslational modification]; other site 452662005544 e3 binding domain; Region: E3_binding; pfam02817 452662005545 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 452662005546 ABC-2 type transporter; Region: ABC2_membrane; cl17235 452662005547 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 452662005548 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 452662005549 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 452662005550 Walker A/P-loop; other site 452662005551 ATP binding site [chemical binding]; other site 452662005552 Q-loop/lid; other site 452662005553 ABC transporter signature motif; other site 452662005554 Walker B; other site 452662005555 D-loop; other site 452662005556 H-loop/switch region; other site 452662005557 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 452662005558 S-adenosylmethionine binding site [chemical binding]; other site 452662005559 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662005560 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662005561 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662005562 dimerization interface [polypeptide binding]; other site 452662005563 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 452662005564 Isobutyryl-CoA dehydrogenase; Region: IBD; cd01162 452662005565 substrate binding pocket [chemical binding]; other site 452662005566 FAD binding site [chemical binding]; other site 452662005567 catalytic base [active] 452662005568 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 452662005569 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662005570 substrate binding site [chemical binding]; other site 452662005571 oxyanion hole (OAH) forming residues; other site 452662005572 trimer interface [polypeptide binding]; other site 452662005573 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 452662005574 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 452662005575 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 452662005576 enoyl-CoA hydratase; Provisional; Region: PRK05862 452662005577 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662005578 substrate binding site [chemical binding]; other site 452662005579 oxyanion hole (OAH) forming residues; other site 452662005580 trimer interface [polypeptide binding]; other site 452662005581 short chain dehydrogenase; Provisional; Region: PRK09134 452662005582 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662005583 NAD(P) binding site [chemical binding]; other site 452662005584 active site 452662005585 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 452662005586 GTP cyclohydrolase I; Provisional; Region: PLN03044 452662005587 active site 452662005588 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 452662005589 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 452662005590 Ligand binding site; other site 452662005591 metal-binding site 452662005592 Transmembrane secretion effector; Region: MFS_3; pfam05977 452662005593 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 452662005594 acetyl-CoA acetyltransferase; Validated; Region: PRK08242 452662005595 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 452662005596 dimer interface [polypeptide binding]; other site 452662005597 active site 452662005598 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 452662005599 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662005600 substrate binding site [chemical binding]; other site 452662005601 oxyanion hole (OAH) forming residues; other site 452662005602 trimer interface [polypeptide binding]; other site 452662005603 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 452662005604 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662005605 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662005606 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 452662005607 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 452662005608 NAD binding site [chemical binding]; other site 452662005609 homodimer interface [polypeptide binding]; other site 452662005610 active site 452662005611 substrate binding site [chemical binding]; other site 452662005612 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 452662005613 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 452662005614 putative active site [active] 452662005615 aspartate aminotransferase; Provisional; Region: PRK05764 452662005616 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 452662005617 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662005618 homodimer interface [polypeptide binding]; other site 452662005619 catalytic residue [active] 452662005620 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 452662005621 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 452662005622 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 452662005623 phosphogluconate dehydratase; Validated; Region: PRK09054 452662005624 6-phosphogluconate dehydratase; Region: edd; TIGR01196 452662005625 Glucokinase; Region: Glucokinase; pfam02685 452662005626 glucokinase, proteobacterial type; Region: glk; TIGR00749 452662005627 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]; Region: Eda; COG0800 452662005628 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 452662005629 active site 452662005630 intersubunit interface [polypeptide binding]; other site 452662005631 catalytic residue [active] 452662005632 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 452662005633 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 452662005634 trimer interface [polypeptide binding]; other site 452662005635 putative metal binding site [ion binding]; other site 452662005636 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 452662005637 dimer interface [polypeptide binding]; other site 452662005638 allosteric magnesium binding site [ion binding]; other site 452662005639 active site 452662005640 aspartate-rich active site metal binding site; other site 452662005641 Schiff base residues; other site 452662005642 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 452662005643 PA_M28_1_1: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 1. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_1; cd04820 452662005644 PA/protease or protease-like domain interface [polypeptide binding]; other site 452662005645 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_2; cd05661 452662005646 Peptidase family M28; Region: Peptidase_M28; pfam04389 452662005647 metal binding site [ion binding]; metal-binding site 452662005648 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 452662005649 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 452662005650 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 452662005651 metabolite-proton symporter; Region: 2A0106; TIGR00883 452662005652 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 452662005653 putative substrate translocation pore; other site 452662005654 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 452662005655 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 452662005656 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 452662005657 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 452662005658 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 452662005659 D-pathway; other site 452662005660 Putative ubiquinol binding site [chemical binding]; other site 452662005661 Low-spin heme (heme b) binding site [chemical binding]; other site 452662005662 Putative water exit pathway; other site 452662005663 Binuclear center (heme o3/CuB) [ion binding]; other site 452662005664 K-pathway; other site 452662005665 Putative proton exit pathway; other site 452662005666 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 452662005667 Subunit I/III interface [polypeptide binding]; other site 452662005668 Subunit III/IV interface [polypeptide binding]; other site 452662005669 cytochrome o ubiquinol oxidase subunit IV; Region: CyoD; TIGR02847 452662005670 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 452662005671 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662005672 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 452662005673 ATP binding site [chemical binding]; other site 452662005674 Mg2+ binding site [ion binding]; other site 452662005675 G-X-G motif; other site 452662005676 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 452662005677 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 452662005678 active site 452662005679 phosphorylation site [posttranslational modification] 452662005680 intermolecular recognition site; other site 452662005681 dimerization interface [polypeptide binding]; other site 452662005682 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 452662005683 potential frameshift: common BLAST hit: gi|103486540|ref|YP_616101.1| DEAD/DEAH box helicase-like protein 452662005684 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 452662005685 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 452662005686 nucleotide binding region [chemical binding]; other site 452662005687 ATP-binding site [chemical binding]; other site 452662005688 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 452662005689 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 452662005690 ATP binding site [chemical binding]; other site 452662005691 Mg++ binding site [ion binding]; other site 452662005692 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 452662005693 FAD binding domain; Region: FAD_binding_4; pfam01565 452662005694 SapC; Region: SapC; pfam07277 452662005695 Tetratricopeptide repeat; Region: TPR_16; pfam13432 452662005696 Protein of unknown function (DUF560); Region: DUF560; pfam04575 452662005697 Transferrin binding protein-like solute binding protein; Region: Lipoprotein_5; pfam01298 452662005698 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 452662005699 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 452662005700 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 452662005701 Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived...; Region: MLE; cd03318 452662005702 octamer interface [polypeptide binding]; other site 452662005703 active site 452662005704 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662005705 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 452662005706 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662005707 dimerization interface [polypeptide binding]; other site 452662005708 chlorocatechol 1,2-dioxygenase; Region: chlorocat_1_2; TIGR02465 452662005709 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl17208 452662005710 active site 452662005711 Dienelactone hydrolase family; Region: DLH; pfam01738 452662005712 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 452662005713 catalytic site [active] 452662005714 FAD binding domain; Region: FAD_binding_3; pfam01494 452662005715 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 452662005716 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 452662005717 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662005718 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 452662005719 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]; Region: COG2355 452662005720 active site 452662005721 dimer interface [polypeptide binding]; other site 452662005722 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662005723 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 452662005724 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 452662005725 Protein of unknown function (DUF2877); Region: DUF2877; pfam11392 452662005726 Chromate resistance exported protein; Region: Chrome_Resist; cl01744 452662005727 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 452662005728 Chromate transporter; Region: Chromate_transp; pfam02417 452662005729 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 452662005730 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 452662005731 ring oligomerisation interface [polypeptide binding]; other site 452662005732 ATP/Mg binding site [chemical binding]; other site 452662005733 stacking interactions; other site 452662005734 hinge regions; other site 452662005735 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 452662005736 oligomerisation interface [polypeptide binding]; other site 452662005737 mobile loop; other site 452662005738 roof hairpin; other site 452662005739 putative S-transferase; Provisional; Region: PRK11752 452662005740 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 452662005741 C-terminal domain interface [polypeptide binding]; other site 452662005742 GSH binding site (G-site) [chemical binding]; other site 452662005743 dimer interface [polypeptide binding]; other site 452662005744 C-terminal, alpha helical domain of Escherichia coli Yghu Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YghU_like; cd10292 452662005745 dimer interface [polypeptide binding]; other site 452662005746 N-terminal domain interface [polypeptide binding]; other site 452662005747 active site 452662005748 DNA gyrase subunit A; Validated; Region: PRK05560 452662005749 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 452662005750 CAP-like domain; other site 452662005751 active site 452662005752 primary dimer interface [polypeptide binding]; other site 452662005753 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 452662005754 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 452662005755 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 452662005756 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 452662005757 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 452662005758 Protein of unknown function (DUF952); Region: DUF952; pfam06108 452662005759 Glycosyl transferase family 21; Region: Glyco_transf_21; pfam13506 452662005760 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 452662005761 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 452662005762 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 452662005763 putative acyl-acceptor binding pocket; other site 452662005764 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 452662005765 active site 452662005766 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 452662005767 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 452662005768 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662005769 catalytic residue [active] 452662005770 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 452662005771 substrate binding site [chemical binding]; other site 452662005772 active site 452662005773 catalytic residues [active] 452662005774 heterodimer interface [polypeptide binding]; other site 452662005775 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 452662005776 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 452662005777 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 452662005778 muropeptide transporter; Reviewed; Region: ampG; PRK11902 452662005779 muropeptide transporter; Validated; Region: ampG; cl17669 452662005780 Response regulator receiver domain; Region: Response_reg; pfam00072 452662005781 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 452662005782 active site 452662005783 phosphorylation site [posttranslational modification] 452662005784 intermolecular recognition site; other site 452662005785 dimerization interface [polypeptide binding]; other site 452662005786 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 452662005787 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 452662005788 RNA binding surface [nucleotide binding]; other site 452662005789 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 452662005790 active site 452662005791 Conserved hypothetical protein 95; Region: Cons_hypoth95; pfam03602 452662005792 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 452662005793 S-adenosylmethionine binding site [chemical binding]; other site 452662005794 Uncharacterized conserved protein [Function unknown]; Region: COG3791 452662005795 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 452662005796 Family description; Region: UvrD_C_2; pfam13538 452662005797 TIGR02300 family protein; Region: FYDLN_acid 452662005798 Protein of unknown function (FYDLN_acid); Region: FYDLN_acid; pfam09538 452662005799 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 452662005800 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 452662005801 hinge; other site 452662005802 active site 452662005803 cytidylate kinase; Provisional; Region: cmk; PRK00023 452662005804 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 452662005805 CMP-binding site; other site 452662005806 The sites determining sugar specificity; other site 452662005807 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 452662005808 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 452662005809 RNA binding site [nucleotide binding]; other site 452662005810 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 452662005811 RNA binding site [nucleotide binding]; other site 452662005812 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 452662005813 RNA binding site [nucleotide binding]; other site 452662005814 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec4; cd05689 452662005815 RNA binding site [nucleotide binding]; other site 452662005816 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 452662005817 RNA binding site [nucleotide binding]; other site 452662005818 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 452662005819 RNA binding site [nucleotide binding]; other site 452662005820 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 452662005821 IHF dimer interface [polypeptide binding]; other site 452662005822 IHF - DNA interface [nucleotide binding]; other site 452662005823 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 452662005824 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 452662005825 TrkA-N domain; Region: TrkA_N; pfam02254 452662005826 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 452662005827 glutaminase; Provisional; Region: PRK00971 452662005828 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 452662005829 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 452662005830 motif 1; other site 452662005831 active site 452662005832 motif 2; other site 452662005833 motif 3; other site 452662005834 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 452662005835 malate synthase G; Provisional; Region: PRK02999 452662005836 active site 452662005837 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662005838 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662005839 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 452662005840 putative effector binding pocket; other site 452662005841 dimerization interface [polypeptide binding]; other site 452662005842 malic enzyme; Reviewed; Region: PRK12862 452662005843 Malic enzyme, N-terminal domain; Region: malic; pfam00390 452662005844 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 452662005845 putative NAD(P) binding site [chemical binding]; other site 452662005846 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 452662005847 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 452662005848 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 452662005849 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 452662005850 putative substrate translocation pore; other site 452662005851 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 452662005852 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 452662005853 IHF dimer interface [polypeptide binding]; other site 452662005854 IHF - DNA interface [nucleotide binding]; other site 452662005855 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 452662005856 Found in ATP-dependent protease La (LON); Region: LON; smart00464 452662005857 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 452662005858 Walker A motif; other site 452662005859 ATP binding site [chemical binding]; other site 452662005860 Walker B motif; other site 452662005861 arginine finger; other site 452662005862 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 452662005863 hypothetical protein; Validated; Region: PRK00153 452662005864 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 452662005865 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 452662005866 Walker A motif; other site 452662005867 ATP binding site [chemical binding]; other site 452662005868 Walker B motif; other site 452662005869 arginine finger; other site 452662005870 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 452662005871 DNA polymerase III gamma and tau subunits C terminal; Region: DUF3646; pfam12362 452662005872 Beta-lactamase enzyme family; Region: Beta-lactamase2; pfam13354 452662005873 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 452662005874 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 452662005875 catalytic loop [active] 452662005876 iron binding site [ion binding]; other site 452662005877 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 452662005878 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 452662005879 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 452662005880 catalytic residue [active] 452662005881 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 452662005882 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 452662005883 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 452662005884 catalytic residue [active] 452662005885 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 452662005886 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 452662005887 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 452662005888 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 452662005889 dimer interface [polypeptide binding]; other site 452662005890 active site 452662005891 glycine-pyridoxal phosphate binding site [chemical binding]; other site 452662005892 folate binding site [chemical binding]; other site 452662005893 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 452662005894 ATP cone domain; Region: ATP-cone; pfam03477 452662005895 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 452662005896 GIY-YIG motif/motif A; other site 452662005897 putative active site [active] 452662005898 putative metal binding site [ion binding]; other site 452662005899 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 452662005900 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 452662005901 Chorismate mutase type II; Region: CM_2; smart00830 452662005902 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 452662005903 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 452662005904 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 452662005905 RNA binding surface [nucleotide binding]; other site 452662005906 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 452662005907 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 452662005908 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 452662005909 PA/protease or protease-like domain interface [polypeptide binding]; other site 452662005910 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 452662005911 metal binding site [ion binding]; metal-binding site 452662005912 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 452662005913 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 452662005914 FMN binding site [chemical binding]; other site 452662005915 substrate binding site [chemical binding]; other site 452662005916 putative catalytic residue [active] 452662005917 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 452662005918 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 452662005919 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 452662005920 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 452662005921 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 452662005922 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 452662005923 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 452662005924 putative active site; other site 452662005925 catalytic triad [active] 452662005926 putative dimer interface [polypeptide binding]; other site 452662005927 Uncharacterized conserved protein [Function unknown]; Region: COG1359 452662005928 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 452662005929 Fe-S cluster binding site [ion binding]; other site 452662005930 DNA binding site [nucleotide binding] 452662005931 active site 452662005932 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 452662005933 catalytic center binding site [active] 452662005934 ATP binding site [chemical binding]; other site 452662005935 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 452662005936 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 452662005937 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 452662005938 active site 452662005939 catalytic site [active] 452662005940 glycogen synthase; Provisional; Region: glgA; PRK00654 452662005941 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 452662005942 ADP-binding pocket [chemical binding]; other site 452662005943 homodimer interface [polypeptide binding]; other site 452662005944 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 452662005945 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 452662005946 ligand binding site; other site 452662005947 oligomer interface; other site 452662005948 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 452662005949 dimer interface [polypeptide binding]; other site 452662005950 N-terminal domain interface [polypeptide binding]; other site 452662005951 sulfate 1 binding site; other site 452662005952 glycogen branching enzyme; Provisional; Region: PRK05402 452662005953 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 452662005954 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 452662005955 active site 452662005956 catalytic site [active] 452662005957 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 452662005958 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 452662005959 homodimer interface [polypeptide binding]; other site 452662005960 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 452662005961 active site pocket [active] 452662005962 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 452662005963 Beta-lactamase; Region: Beta-lactamase; pfam00144 452662005964 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 452662005965 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 452662005966 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 452662005967 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 452662005968 FecR protein; Region: FecR; pfam04773 452662005969 Secretin and TonB N terminus short domain; Region: STN; smart00965 452662005970 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 452662005971 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 452662005972 Autotransporter beta-domain; Region: Autotransporter; pfam03797 452662005973 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 452662005974 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 452662005975 GatB domain; Region: GatB_Yqey; smart00845 452662005976 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 452662005977 putative active site [active] 452662005978 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 452662005979 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 452662005980 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 452662005981 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 452662005982 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 452662005983 Protein of unknown function (DUF3089); Region: DUF3089; pfam11288 452662005984 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 452662005985 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 452662005986 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 452662005987 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 452662005988 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 452662005989 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 452662005990 exopolysaccharide transport protein family; Region: eps_transp_fam; TIGR01005 452662005991 Chain length determinant protein; Region: Wzz; pfam02706 452662005992 Chain length determinant protein; Region: Wzz; cl15801 452662005993 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 452662005994 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 452662005995 SLBB domain; Region: SLBB; pfam10531 452662005996 UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional; Region: wecC; PRK11064 452662005997 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 452662005998 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 452662005999 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 452662006000 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 452662006001 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 452662006002 active site 452662006003 homodimer interface [polypeptide binding]; other site 452662006004 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 452662006005 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 452662006006 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 452662006007 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 452662006008 ABC-2 type transporter; Region: ABC2_membrane; cl17235 452662006009 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 452662006010 GcrA cell cycle regulator; Region: GcrA; cl11564 452662006011 GcrA cell cycle regulator; Region: GcrA; cl11564 452662006012 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 452662006013 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 452662006014 MarR family; Region: MarR; pfam01047 452662006015 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 452662006016 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 452662006017 ATP binding site [chemical binding]; other site 452662006018 Mg2+ binding site [ion binding]; other site 452662006019 G-X-G motif; other site 452662006020 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 452662006021 anchoring element; other site 452662006022 dimer interface [polypeptide binding]; other site 452662006023 ATP binding site [chemical binding]; other site 452662006024 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 452662006025 active site 452662006026 putative metal-binding site [ion binding]; other site 452662006027 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 452662006028 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 452662006029 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 452662006030 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 452662006031 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662006032 Cell wall hydrolyses involved in spore germination [Cell envelope biogenesis, outer membrane]; Region: SleB; COG3773 452662006033 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 452662006034 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic); Region: Peptidase_C39_like; cl00296 452662006035 putative active site [active] 452662006036 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 452662006037 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 452662006038 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662006039 Walker A/P-loop; other site 452662006040 ATP binding site [chemical binding]; other site 452662006041 Q-loop/lid; other site 452662006042 ABC transporter signature motif; other site 452662006043 Walker B; other site 452662006044 D-loop; other site 452662006045 H-loop/switch region; other site 452662006046 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 452662006047 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 452662006048 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 452662006049 ligand binding site [chemical binding]; other site 452662006050 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 452662006051 VCBS repeat; Region: VCBS_repeat; TIGR01965 452662006052 VCBS repeat; Region: VCBS_repeat; TIGR01965 452662006053 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 452662006054 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 452662006055 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 452662006056 Tetratricopeptide repeat; Region: TPR_12; pfam13424 452662006057 Tetratricopeptide repeat; Region: TPR_10; pfam13374 452662006058 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 452662006059 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662006060 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662006061 dimerization interface [polypeptide binding]; other site 452662006062 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 452662006063 O-succinylhomoserine sulfhydrylase; Reviewed; Region: PRK07504 452662006064 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 452662006065 homodimer interface [polypeptide binding]; other site 452662006066 substrate-cofactor binding pocket; other site 452662006067 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662006068 catalytic residue [active] 452662006069 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 452662006070 tartrate dehydrogenase; Region: TTC; TIGR02089 452662006071 Recombination protein O N terminal; Region: RecO_N; pfam11967 452662006072 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 452662006073 Recombination protein O C terminal; Region: RecO_C; pfam02565 452662006074 Histidine kinase; Region: HisKA_3; pfam07730 452662006075 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 452662006076 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 452662006077 active site 452662006078 phosphorylation site [posttranslational modification] 452662006079 intermolecular recognition site; other site 452662006080 dimerization interface [polypeptide binding]; other site 452662006081 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 452662006082 DNA binding residues [nucleotide binding] 452662006083 dimerization interface [polypeptide binding]; other site 452662006084 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 452662006085 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 452662006086 binding surface 452662006087 TPR motif; other site 452662006088 Tetratricopeptide repeat; Region: TPR_16; pfam13432 452662006089 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 452662006090 TPR motif; other site 452662006091 binding surface 452662006092 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 452662006093 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 452662006094 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 452662006095 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 452662006096 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 452662006097 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 452662006098 ATP binding site [chemical binding]; other site 452662006099 Walker A motif; other site 452662006100 hexamer interface [polypeptide binding]; other site 452662006101 Walker B motif; other site 452662006102 AAA domain; Region: AAA_31; pfam13614 452662006103 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 452662006104 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 452662006105 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 452662006106 TadE-like protein; Region: TadE; pfam07811 452662006107 Pilus biogenesis CpaD protein (pilus_cpaD); Region: Pilus_CpaD; pfam09476 452662006108 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 452662006109 BON domain; Region: BON; pfam04972 452662006110 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 452662006111 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 452662006112 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 452662006113 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 452662006114 Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion]; Region: Flp; COG3847 452662006115 Flp/Fap pilin component; Region: Flp_Fap; pfam04964 452662006116 Histidine kinase; Region: HisKA_3; pfam07730 452662006117 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 452662006118 ATP binding site [chemical binding]; other site 452662006119 Mg2+ binding site [ion binding]; other site 452662006120 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 452662006121 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 452662006122 GIY-YIG motif/motif A; other site 452662006123 active site 452662006124 catalytic site [active] 452662006125 putative DNA binding site [nucleotide binding]; other site 452662006126 metal binding site [ion binding]; metal-binding site 452662006127 UvrB/uvrC motif; Region: UVR; pfam02151 452662006128 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 452662006129 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 452662006130 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 452662006131 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 452662006132 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 452662006133 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 452662006134 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 452662006135 Protein of unknown function (DUF1318); Region: DUF1318; pfam07027 452662006136 YnbE-like lipoprotein; Region: Lipoprotein_19; pfam13617 452662006137 Dicarboxylate transport; Region: DctA-YdbH; pfam11739 452662006138 hypothetical protein; Reviewed; Region: PRK00024 452662006139 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 452662006140 MPN+ (JAMM) motif; other site 452662006141 Zinc-binding site [ion binding]; other site 452662006142 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 452662006143 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 452662006144 substrate binding site [chemical binding]; other site 452662006145 ATP binding site [chemical binding]; other site 452662006146 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662006147 PAS domain; Region: PAS_9; pfam13426 452662006148 putative active site [active] 452662006149 heme pocket [chemical binding]; other site 452662006150 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 452662006151 dimer interface [polypeptide binding]; other site 452662006152 phosphorylation site [posttranslational modification] 452662006153 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 452662006154 ATP binding site [chemical binding]; other site 452662006155 G-X-G motif; other site 452662006156 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 452662006157 active site 452662006158 phosphorylation site [posttranslational modification] 452662006159 intermolecular recognition site; other site 452662006160 dimerization interface [polypeptide binding]; other site 452662006161 Protein of unknown function (DUF2794); Region: DUF2794; pfam10984 452662006162 serine O-acetyltransferase; Region: cysE; TIGR01172 452662006163 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 452662006164 trimer interface [polypeptide binding]; other site 452662006165 active site 452662006166 substrate binding site [chemical binding]; other site 452662006167 CoA binding site [chemical binding]; other site 452662006168 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 452662006169 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662006170 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662006171 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 452662006172 dimerization interface [polypeptide binding]; other site 452662006173 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 452662006174 MoaE homodimer interface [polypeptide binding]; other site 452662006175 MoaD interaction [polypeptide binding]; other site 452662006176 active site residues [active] 452662006177 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 452662006178 MoaE interaction surface [polypeptide binding]; other site 452662006179 MoeB interaction surface [polypeptide binding]; other site 452662006180 thiocarboxylated glycine; other site 452662006181 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 452662006182 H+ Antiporter protein; Region: 2A0121; TIGR00900 452662006183 Transglycosylase; Region: Transgly; pfam00912 452662006184 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 452662006185 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 452662006186 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 452662006187 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 452662006188 trimerization site [polypeptide binding]; other site 452662006189 active site 452662006190 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 452662006191 TrkA-N domain; Region: TrkA_N; pfam02254 452662006192 Protein of unknown function (DUF423); Region: DUF423; pfam04241 452662006193 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 452662006194 metal binding site 2 [ion binding]; metal-binding site 452662006195 putative DNA binding helix; other site 452662006196 metal binding site 1 [ion binding]; metal-binding site 452662006197 dimer interface [polypeptide binding]; other site 452662006198 structural Zn2+ binding site [ion binding]; other site 452662006199 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 452662006200 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 452662006201 TPP-binding site; other site 452662006202 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 452662006203 PYR/PP interface [polypeptide binding]; other site 452662006204 dimer interface [polypeptide binding]; other site 452662006205 TPP binding site [chemical binding]; other site 452662006206 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 452662006207 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_5; cd08898 452662006208 putative hydrophobic ligand binding site [chemical binding]; other site 452662006209 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 452662006210 dimerization interface [polypeptide binding]; other site 452662006211 putative DNA binding site [nucleotide binding]; other site 452662006212 putative Zn2+ binding site [ion binding]; other site 452662006213 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 452662006214 Signal peptidase (SPase) II; Region: Peptidase_A8; pfam01252 452662006215 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 452662006216 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 452662006217 active site 452662006218 HIGH motif; other site 452662006219 nucleotide binding site [chemical binding]; other site 452662006220 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 452662006221 active site 452662006222 KMSKS motif; other site 452662006223 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 452662006224 tRNA binding surface [nucleotide binding]; other site 452662006225 anticodon binding site; other site 452662006226 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 452662006227 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 452662006228 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 452662006229 active site 452662006230 Riboflavin kinase; Region: Flavokinase; smart00904 452662006231 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 452662006232 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 452662006233 folate binding site [chemical binding]; other site 452662006234 NADP+ binding site [chemical binding]; other site 452662006235 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 452662006236 ATP-grasp domain; Region: ATP-grasp; pfam02222 452662006237 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 452662006238 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 452662006239 catalytic core [active] 452662006240 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 452662006241 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 452662006242 tandem repeat interface [polypeptide binding]; other site 452662006243 oligomer interface [polypeptide binding]; other site 452662006244 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 452662006245 active site residues [active] 452662006246 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 452662006247 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 452662006248 tandem repeat interface [polypeptide binding]; other site 452662006249 oligomer interface [polypeptide binding]; other site 452662006250 active site residues [active] 452662006251 ribonuclease R; Region: RNase_R; TIGR02063 452662006252 RNB domain; Region: RNB; pfam00773 452662006253 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 452662006254 RNA binding site [nucleotide binding]; other site 452662006255 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 452662006256 cation binding site [ion binding]; other site 452662006257 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2354 452662006258 Predicted membrane protein [Function unknown]; Region: COG2860 452662006259 UPF0126 domain; Region: UPF0126; pfam03458 452662006260 UPF0126 domain; Region: UPF0126; pfam03458 452662006261 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 452662006262 catalytic residues [active] 452662006263 dimer interface [polypeptide binding]; other site 452662006264 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 452662006265 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 452662006266 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 452662006267 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 452662006268 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 452662006269 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 452662006270 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 452662006271 active site 452662006272 phosphorylation site [posttranslational modification] 452662006273 intermolecular recognition site; other site 452662006274 dimerization interface [polypeptide binding]; other site 452662006275 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 452662006276 DNA binding site [nucleotide binding] 452662006277 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662006278 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 452662006279 ATP binding site [chemical binding]; other site 452662006280 Mg2+ binding site [ion binding]; other site 452662006281 G-X-G motif; other site 452662006282 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2832 452662006283 polyhydroxyalkanoate depolymerase, intracellular; Region: PHB_depoly_PhaZ; TIGR01849 452662006284 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 452662006285 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 452662006286 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 452662006287 putative C-terminal domain interface [polypeptide binding]; other site 452662006288 putative GSH binding site (G-site) [chemical binding]; other site 452662006289 putative dimer interface [polypeptide binding]; other site 452662006290 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 452662006291 putative N-terminal domain interface [polypeptide binding]; other site 452662006292 putative dimer interface [polypeptide binding]; other site 452662006293 putative substrate binding pocket (H-site) [chemical binding]; other site 452662006294 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 452662006295 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 452662006296 catalytic triad [active] 452662006297 aconitate hydratase; Validated; Region: PRK09277 452662006298 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 452662006299 substrate binding site [chemical binding]; other site 452662006300 ligand binding site [chemical binding]; other site 452662006301 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 452662006302 substrate binding site [chemical binding]; other site 452662006303 Protein of unknown function (DUF2614); Region: DUF2614; cl07936 452662006304 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 452662006305 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 452662006306 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 452662006307 Multicopper oxidase; Region: Cu-oxidase; pfam00394 452662006308 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 452662006309 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 452662006310 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 452662006311 dimerization interface [polypeptide binding]; other site 452662006312 ligand binding site [chemical binding]; other site 452662006313 NADP binding site [chemical binding]; other site 452662006314 catalytic site [active] 452662006315 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 452662006316 Bacterial SH3 domain; Region: SH3_4; pfam06347 452662006317 Bacterial SH3 domain; Region: SH3_4; pfam06347 452662006318 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 452662006319 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 452662006320 putative substrate translocation pore; other site 452662006321 POT family; Region: PTR2; cl17359 452662006322 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 452662006323 putative FMN binding site [chemical binding]; other site 452662006324 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 452662006325 DNA-binding site [nucleotide binding]; DNA binding site 452662006326 PEP-CTERM-box response regulator transcription factor; Region: PEP_resp_reg; TIGR02915 452662006327 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 452662006328 active site 452662006329 phosphorylation site [posttranslational modification] 452662006330 intermolecular recognition site; other site 452662006331 dimerization interface [polypeptide binding]; other site 452662006332 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 452662006333 Walker A motif; other site 452662006334 ATP binding site [chemical binding]; other site 452662006335 Walker B motif; other site 452662006336 arginine finger; other site 452662006337 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 452662006338 putative PEP-CTERM system histidine kinase; Region: PEP_his_kin; TIGR02916 452662006339 GAF domain; Region: GAF_3; pfam13492 452662006340 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 452662006341 ATP binding site [chemical binding]; other site 452662006342 Mg2+ binding site [ion binding]; other site 452662006343 G-X-G motif; other site 452662006344 sugar transferase, PEP-CTERM system associated; Region: EpsB_2; TIGR03013 452662006345 Bacterial sugar transferase; Region: Bac_transf; pfam02397 452662006346 RNA polymerase sigma factor; Provisional; Region: PRK12547 452662006347 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 452662006348 two-component response regulator; Provisional; Region: PRK09191 452662006349 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 452662006350 active site 452662006351 phosphorylation site [posttranslational modification] 452662006352 intermolecular recognition site; other site 452662006353 dimerization interface [polypeptide binding]; other site 452662006354 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 452662006355 Histidine kinase; Region: HisKA_2; pfam07568 452662006356 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 452662006357 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 452662006358 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 452662006359 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 452662006360 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 452662006361 active site 452662006362 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 452662006363 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 452662006364 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 452662006365 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 452662006366 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 452662006367 Uncharacterized conserved protein [Function unknown]; Region: COG2308 452662006368 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 452662006369 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 452662006370 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 452662006371 Type II secretion system (T2SS), protein M; Region: T2SM; pfam04612 452662006372 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 452662006373 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 452662006374 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 452662006375 Type II secretory pathway, component PulJ [Intracellular trafficking and secretion]; Region: PulJ; COG4795 452662006376 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 452662006377 type II secretion system protein I; Region: gspI; TIGR01707 452662006378 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 452662006379 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 452662006380 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 452662006381 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 452662006382 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 452662006383 type II secretion system protein F; Region: GspF; TIGR02120 452662006384 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 452662006385 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 452662006386 type II secretion system protein E; Region: type_II_gspE; TIGR02533 452662006387 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 452662006388 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 452662006389 Walker A motif; other site 452662006390 ATP binding site [chemical binding]; other site 452662006391 Walker B motif; other site 452662006392 type II secretion system protein D; Region: type_II_gspD; TIGR02517 452662006393 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 452662006394 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 452662006395 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 452662006396 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 452662006397 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 452662006398 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 452662006399 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 452662006400 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 452662006401 C2 domain; Region: C2; cl14603 452662006402 NRDE protein; Region: NRDE; cl01315 452662006403 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 452662006404 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 452662006405 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662006406 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 452662006407 ATP binding site [chemical binding]; other site 452662006408 Mg2+ binding site [ion binding]; other site 452662006409 G-X-G motif; other site 452662006410 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 452662006411 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 452662006412 Protein of unknown function (DUF4242); Region: DUF4242; pfam14026 452662006413 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 452662006414 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; cl00447 452662006415 nudix motif; other site 452662006416 Aldehyde dehydrogenase family 21A1-like; Region: ALDH_F21_RNP123; cd07147 452662006417 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 452662006418 NAD(P) binding site [chemical binding]; other site 452662006419 catalytic residues [active] 452662006420 choline dehydrogenase; Validated; Region: PRK02106 452662006421 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 452662006422 Transcriptional regulator [Transcription]; Region: IclR; COG1414 452662006423 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 452662006424 Bacterial transcriptional regulator; Region: IclR; pfam01614 452662006425 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 452662006426 Major Facilitator Superfamily; Region: MFS_1; pfam07690 452662006427 putative substrate translocation pore; other site 452662006428 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 452662006429 active site 452662006430 metal binding site [ion binding]; metal-binding site 452662006431 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 452662006432 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662006433 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 452662006434 N-terminal plug; other site 452662006435 ligand-binding site [chemical binding]; other site 452662006436 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 452662006437 active site 452662006438 Transcriptional regulators [Transcription]; Region: GntR; COG1802 452662006439 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 452662006440 DNA-binding site [nucleotide binding]; DNA binding site 452662006441 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 452662006442 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 452662006443 Uncharacterized protein conserved in bacteria (DUF2171); Region: DUF2171; pfam09939 452662006444 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 452662006445 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal...; Region: FkbR2; cd03451 452662006446 putative active site [active] 452662006447 putative catalytic site [active] 452662006448 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 452662006449 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 452662006450 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 452662006451 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 452662006452 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 452662006453 carboxyltransferase (CT) interaction site; other site 452662006454 biotinylation site [posttranslational modification]; other site 452662006455 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 452662006456 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 452662006457 Protein of unknown function, DUF486; Region: DUF486; cl01236 452662006458 isovaleryl-CoA dehydrogenase; Region: PLN02519 452662006459 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 452662006460 substrate binding site [chemical binding]; other site 452662006461 FAD binding site [chemical binding]; other site 452662006462 catalytic base [active] 452662006463 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662006464 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662006465 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 452662006466 dimerization interface [polypeptide binding]; other site 452662006467 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 452662006468 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 452662006469 S-adenosylmethionine binding site [chemical binding]; other site 452662006470 Predicted membrane protein [Function unknown]; Region: COG2311 452662006471 Protein of unknown function (DUF418); Region: DUF418; cl12135 452662006472 Protein of unknown function (DUF418); Region: DUF418; pfam04235 452662006473 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 452662006474 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 452662006475 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 452662006476 heme binding site [chemical binding]; other site 452662006477 ferroxidase pore; other site 452662006478 ferroxidase diiron center [ion binding]; other site 452662006479 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 452662006480 active site 452662006481 8-oxo-dGMP binding site [chemical binding]; other site 452662006482 nudix motif; other site 452662006483 metal binding site [ion binding]; metal-binding site 452662006484 Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion]; Region: Flp; COG3847 452662006485 Flp/Fap pilin component; Region: Flp_Fap; cl01585 452662006486 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 452662006487 Peptidase family M48; Region: Peptidase_M48; pfam01435 452662006488 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 452662006489 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 452662006490 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 452662006491 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 452662006492 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 452662006493 active site 452662006494 DNA binding site [nucleotide binding] 452662006495 Int/Topo IB signature motif; other site 452662006496 shikimate kinase; Provisional; Region: PRK13946 452662006497 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 452662006498 ADP binding site [chemical binding]; other site 452662006499 magnesium binding site [ion binding]; other site 452662006500 putative shikimate binding site; other site 452662006501 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 452662006502 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 452662006503 active site 452662006504 dimer interface [polypeptide binding]; other site 452662006505 metal binding site [ion binding]; metal-binding site 452662006506 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00528 452662006507 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 452662006508 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 452662006509 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 452662006510 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 452662006511 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 452662006512 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 452662006513 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 452662006514 Surface antigen; Region: Bac_surface_Ag; pfam01103 452662006515 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 452662006516 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 452662006517 active site 452662006518 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 452662006519 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 452662006520 putative substrate binding region [chemical binding]; other site 452662006521 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 452662006522 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 452662006523 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 452662006524 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 452662006525 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 452662006526 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 452662006527 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 452662006528 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 452662006529 catalytic residue [active] 452662006530 putative FPP diphosphate binding site; other site 452662006531 putative FPP binding hydrophobic cleft; other site 452662006532 dimer interface [polypeptide binding]; other site 452662006533 putative IPP diphosphate binding site; other site 452662006534 ribosome recycling factor; Reviewed; Region: frr; PRK00083 452662006535 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 452662006536 hinge region; other site 452662006537 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 452662006538 putative nucleotide binding site [chemical binding]; other site 452662006539 uridine monophosphate binding site [chemical binding]; other site 452662006540 homohexameric interface [polypeptide binding]; other site 452662006541 elongation factor Ts; Provisional; Region: tsf; PRK09377 452662006542 UBA/TS-N domain; Region: UBA; pfam00627 452662006543 Elongation factor TS; Region: EF_TS; pfam00889 452662006544 Elongation factor TS; Region: EF_TS; pfam00889 452662006545 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 452662006546 rRNA interaction site [nucleotide binding]; other site 452662006547 S8 interaction site; other site 452662006548 putative laminin-1 binding site; other site 452662006549 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 452662006550 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 452662006551 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 452662006552 isocitrate dehydrogenase; Validated; Region: PRK08299 452662006553 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 452662006554 Coenzyme A binding pocket [chemical binding]; other site 452662006555 Predicted amidohydrolase [General function prediction only]; Region: COG0388 452662006556 Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases); Region: nitrilase_Rim1_like; cd07574 452662006557 putative active site [active] 452662006558 catalytic triad [active] 452662006559 putative dimer interface [polypeptide binding]; other site 452662006560 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 452662006561 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 452662006562 glutaminase active site [active] 452662006563 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 452662006564 dimer interface [polypeptide binding]; other site 452662006565 active site 452662006566 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 452662006567 dimer interface [polypeptide binding]; other site 452662006568 active site 452662006569 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 452662006570 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 452662006571 putative active site [active] 452662006572 putative metal binding site [ion binding]; other site 452662006573 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14353 452662006574 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 452662006575 Substrate binding site; other site 452662006576 Mg++ binding site; other site 452662006577 N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two...; Region: LbH_GlmU_C; cd03353 452662006578 active site 452662006579 substrate binding site [chemical binding]; other site 452662006580 CoA binding site [chemical binding]; other site 452662006581 phosphoglycolate phosphatase; Provisional; Region: PRK13222 452662006582 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 452662006583 motif II; other site 452662006584 enoyl-CoA hydratase; Provisional; Region: PRK06127 452662006585 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662006586 substrate binding site [chemical binding]; other site 452662006587 oxyanion hole (OAH) forming residues; other site 452662006588 trimer interface [polypeptide binding]; other site 452662006589 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662006590 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662006591 metal binding site [ion binding]; metal-binding site 452662006592 active site 452662006593 I-site; other site 452662006594 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 452662006595 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 452662006596 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 452662006597 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 452662006598 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 452662006599 putative active site [active] 452662006600 GIY-YIG motif/motif A; other site 452662006601 putative metal binding site [ion binding]; other site 452662006602 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 452662006603 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 452662006604 E3 interaction surface; other site 452662006605 lipoyl attachment site [posttranslational modification]; other site 452662006606 e3 binding domain; Region: E3_binding; pfam02817 452662006607 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 452662006608 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 452662006609 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 452662006610 TPP-binding site [chemical binding]; other site 452662006611 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 452662006612 dimer interface [polypeptide binding]; other site 452662006613 PYR/PP interface [polypeptide binding]; other site 452662006614 TPP binding site [chemical binding]; other site 452662006615 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 452662006616 CoA binding domain; Region: CoA_binding; smart00881 452662006617 CoA-ligase; Region: Ligase_CoA; pfam00549 452662006618 malate dehydrogenase; Reviewed; Region: PRK06223 452662006619 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 452662006620 NAD(P) binding site [chemical binding]; other site 452662006621 dimer interface [polypeptide binding]; other site 452662006622 tetramer (dimer of dimers) interface [polypeptide binding]; other site 452662006623 substrate binding site [chemical binding]; other site 452662006624 Predicted ATPase [General function prediction only]; Region: COG1485 452662006625 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 452662006626 CoenzymeA binding site [chemical binding]; other site 452662006627 subunit interaction site [polypeptide binding]; other site 452662006628 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 452662006629 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 452662006630 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662006631 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 452662006632 putative ADP-binding pocket [chemical binding]; other site 452662006633 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 452662006634 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 452662006635 nucleotide binding site/active site [active] 452662006636 HIT family signature motif; other site 452662006637 catalytic residue [active] 452662006638 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 452662006639 Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline; Region: PC_cytidylyltransferase; cd02523 452662006640 active site 452662006641 metal-binding site 452662006642 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 452662006643 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 452662006644 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 452662006645 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 452662006646 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 452662006647 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 452662006648 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 452662006649 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 452662006650 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 452662006651 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 452662006652 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 452662006653 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 452662006654 Type IV pili component [Cell motility and secretion]; Region: COG5461 452662006655 Pilus biogenesis CpaD protein (pilus_cpaD); Region: Pilus_CpaD; pfam09476 452662006656 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 452662006657 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 452662006658 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 452662006659 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 452662006660 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 452662006661 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 452662006662 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 452662006663 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 452662006664 active site 452662006665 catalytic residues [active] 452662006666 metal binding site [ion binding]; metal-binding site 452662006667 recombination protein RecR; Reviewed; Region: recR; PRK00076 452662006668 RecR protein; Region: RecR; pfam02132 452662006669 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 452662006670 putative active site [active] 452662006671 putative metal-binding site [ion binding]; other site 452662006672 tetramer interface [polypeptide binding]; other site 452662006673 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 452662006674 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 452662006675 putative active site [active] 452662006676 substrate binding site [chemical binding]; other site 452662006677 putative cosubstrate binding site; other site 452662006678 catalytic site [active] 452662006679 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 452662006680 substrate binding site [chemical binding]; other site 452662006681 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 452662006682 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 452662006683 dimerization interface 3.5A [polypeptide binding]; other site 452662006684 active site 452662006685 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 452662006686 Acyltransferase family; Region: Acyl_transf_3; pfam01757 452662006687 Predicted metalloprotease [General function prediction only]; Region: COG2321 452662006688 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 452662006689 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 452662006690 nucleophile elbow; other site 452662006691 Patatin phospholipase; Region: DUF3734; pfam12536 452662006692 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662006693 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 452662006694 NAD(P) binding site [chemical binding]; other site 452662006695 active site 452662006696 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 452662006697 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like6; cd05664 452662006698 metal binding site [ion binding]; metal-binding site 452662006699 putative dimer interface [polypeptide binding]; other site 452662006700 FtsH Extracellular; Region: FtsH_ext; pfam06480 452662006701 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 452662006702 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 452662006703 Walker A motif; other site 452662006704 ATP binding site [chemical binding]; other site 452662006705 Walker B motif; other site 452662006706 arginine finger; other site 452662006707 Peptidase family M41; Region: Peptidase_M41; pfam01434 452662006708 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 452662006709 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 452662006710 Ligand Binding Site [chemical binding]; other site 452662006711 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 452662006712 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 452662006713 non-specific DNA binding site [nucleotide binding]; other site 452662006714 salt bridge; other site 452662006715 sequence-specific DNA binding site [nucleotide binding]; other site 452662006716 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 452662006717 Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; Region: PtsP; COG3605 452662006718 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 452662006719 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 452662006720 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 452662006721 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 452662006722 putative aminotransferase; Provisional; Region: PRK09105 452662006723 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 452662006724 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662006725 homodimer interface [polypeptide binding]; other site 452662006726 catalytic residue [active] 452662006727 putative aminotransferase; Provisional; Region: PRK09105 452662006728 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 452662006729 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662006730 homodimer interface [polypeptide binding]; other site 452662006731 catalytic residue [active] 452662006732 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 452662006733 hydrophobic ligand binding site; other site 452662006734 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662006735 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 452662006736 dimer interface [polypeptide binding]; other site 452662006737 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662006738 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 452662006739 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 452662006740 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662006741 Protein of unknown function (DUF1428); Region: DUF1428; pfam07237 452662006742 Short-chain dehydrogenase involved in D-alanine esterification of lipoteichoic acid and wall teichoic acid (D-alanine transfer protein) [Cell envelope biogenesis, outer membrane]; Region: DltE; COG3967 452662006743 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662006744 NAD(P) binding site [chemical binding]; other site 452662006745 active site 452662006746 Predicted transcriptional regulators [Transcription]; Region: COG1733 452662006747 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 452662006748 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 452662006749 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 452662006750 FMN binding site [chemical binding]; other site 452662006751 substrate binding site [chemical binding]; other site 452662006752 putative catalytic residue [active] 452662006753 aspartate kinase; Reviewed; Region: PRK06635 452662006754 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 452662006755 putative nucleotide binding site [chemical binding]; other site 452662006756 putative catalytic residues [active] 452662006757 putative Mg ion binding site [ion binding]; other site 452662006758 putative aspartate binding site [chemical binding]; other site 452662006759 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 452662006760 putative allosteric regulatory site; other site 452662006761 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 452662006762 putative allosteric regulatory residue; other site 452662006763 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 452662006764 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 452662006765 S-adenosylmethionine binding site [chemical binding]; other site 452662006766 Domain of unknown function (DU1801); Region: DUF1801; pfam08818 452662006767 Bacteriocin-protection, YdeI or OmpD-Associated; Region: OmdA; pfam13376 452662006768 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 452662006769 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE; Provisional; Region: PRK15051 452662006770 peroxiredoxin, OsmC subfamily; Region: osmo_induc_OsmC; TIGR03562 452662006771 PRC-barrel domain; Region: PRC; pfam05239 452662006772 Serine hydrolase; Region: Ser_hydrolase; pfam06821 452662006773 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 452662006774 Uncharacterized small protein (DUF2292); Region: DUF2292; pfam10055 452662006775 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662006776 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 452662006777 N-terminal plug; other site 452662006778 ligand-binding site [chemical binding]; other site 452662006779 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 452662006780 oligomerization interface [polypeptide binding]; other site 452662006781 active site 452662006782 metal binding site [ion binding]; metal-binding site 452662006783 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4649 452662006784 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 452662006785 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 452662006786 Trp docking motif [polypeptide binding]; other site 452662006787 active site 452662006788 PQQ-like domain; Region: PQQ_2; pfam13360 452662006789 GTP-binding protein Der; Reviewed; Region: PRK00093 452662006790 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 452662006791 G1 box; other site 452662006792 GTP/Mg2+ binding site [chemical binding]; other site 452662006793 Switch I region; other site 452662006794 G2 box; other site 452662006795 Switch II region; other site 452662006796 G3 box; other site 452662006797 G4 box; other site 452662006798 G5 box; other site 452662006799 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 452662006800 G1 box; other site 452662006801 GTP/Mg2+ binding site [chemical binding]; other site 452662006802 Switch I region; other site 452662006803 G2 box; other site 452662006804 G3 box; other site 452662006805 Switch II region; other site 452662006806 G4 box; other site 452662006807 G5 box; other site 452662006808 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 452662006809 CPxP motif; other site 452662006810 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 452662006811 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 452662006812 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 452662006813 Acyltransferase family; Region: Acyl_transf_3; pfam01757 452662006814 Domain of unknown function DUF87; Region: DUF87; pfam01935 452662006815 AAA-like domain; Region: AAA_10; pfam12846 452662006816 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 452662006817 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 452662006818 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 452662006819 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 452662006820 active site 452662006821 HIGH motif; other site 452662006822 nucleotide binding site [chemical binding]; other site 452662006823 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 452662006824 active site 452662006825 KMSKS motif; other site 452662006826 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 452662006827 tRNA binding surface [nucleotide binding]; other site 452662006828 anticodon binding site; other site 452662006829 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 452662006830 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 452662006831 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 452662006832 Protein of unknown function (DUF2497); Region: DUF2497; pfam10691 452662006833 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 452662006834 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 452662006835 Methyltransferase domain; Region: Methyltransf_18; pfam12847 452662006836 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662006837 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 452662006838 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 452662006839 active site 452662006840 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 452662006841 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 452662006842 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662006843 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 452662006844 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 452662006845 TAP-like protein; Region: Abhydrolase_4; pfam08386 452662006846 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 452662006847 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl17208 452662006848 chlorocatechol 1,2-dioxygenase; Region: chlorocat_1_2; TIGR02465 452662006849 active site 452662006850 muconolactone delta-isomerase; Region: muco_delta; TIGR03221 452662006851 Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived...; Region: MLE; cd03318 452662006852 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 452662006853 octamer interface [polypeptide binding]; other site 452662006854 active site 452662006855 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 452662006856 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662006857 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662006858 dimerization interface [polypeptide binding]; other site 452662006859 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 452662006860 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 452662006861 iron-sulfur cluster [ion binding]; other site 452662006862 [2Fe-2S] cluster binding site [ion binding]; other site 452662006863 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 452662006864 putative alpha subunit interface [polypeptide binding]; other site 452662006865 putative active site [active] 452662006866 putative substrate binding site [chemical binding]; other site 452662006867 Fe binding site [ion binding]; other site 452662006868 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 452662006869 inter-subunit interface; other site 452662006870 Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a...; Region: Rieske_RO_ferredoxin; cd03528 452662006871 [2Fe-2S] cluster binding site [ion binding]; other site 452662006872 phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional; Region: PRK09754 452662006873 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 452662006874 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 452662006875 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 452662006876 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 452662006877 catalytic triad [active] 452662006878 dimer interface [polypeptide binding]; other site 452662006879 conserved cis-peptide bond; other site 452662006880 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 452662006881 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 452662006882 Protein of unknown function (DUF1427); Region: DUF1427; pfam07235 452662006883 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 452662006884 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 452662006885 active site 452662006886 DoxX; Region: DoxX; pfam07681 452662006887 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 452662006888 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 452662006889 Protein of unknown function (DUF1211); Region: DUF1211; cl01421 452662006890 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662006891 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662006892 LysR substrate binding domain; Region: LysR_substrate; pfam03466 452662006893 dimerization interface [polypeptide binding]; other site 452662006894 Pirin-related protein [General function prediction only]; Region: COG1741 452662006895 Pirin; Region: Pirin; pfam02678 452662006896 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 452662006897 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 452662006898 N-terminal plug; other site 452662006899 ligand-binding site [chemical binding]; other site 452662006900 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 452662006901 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 452662006902 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 452662006903 dimerization interface [polypeptide binding]; other site 452662006904 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 452662006905 dimer interface [polypeptide binding]; other site 452662006906 phosphorylation site [posttranslational modification] 452662006907 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 452662006908 ATP binding site [chemical binding]; other site 452662006909 Mg2+ binding site [ion binding]; other site 452662006910 G-X-G motif; other site 452662006911 osmolarity response regulator; Provisional; Region: ompR; PRK09468 452662006912 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 452662006913 active site 452662006914 phosphorylation site [posttranslational modification] 452662006915 intermolecular recognition site; other site 452662006916 dimerization interface [polypeptide binding]; other site 452662006917 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 452662006918 DNA binding site [nucleotide binding] 452662006919 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 452662006920 EF-hand domain pair; Region: EF_hand_5; pfam13499 452662006921 Ca2+ binding site [ion binding]; other site 452662006922 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 452662006923 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 452662006924 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 452662006925 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 452662006926 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 452662006927 putative C-terminal domain interface [polypeptide binding]; other site 452662006928 putative GSH binding site (G-site) [chemical binding]; other site 452662006929 putative dimer interface [polypeptide binding]; other site 452662006930 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 452662006931 putative substrate binding pocket (H-site) [chemical binding]; other site 452662006932 putative N-terminal domain interface [polypeptide binding]; other site 452662006933 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 452662006934 active site 452662006935 multimer interface [polypeptide binding]; other site 452662006936 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 452662006937 multifunctional aminopeptidase A; Provisional; Region: PRK00913 452662006938 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 452662006939 interface (dimer of trimers) [polypeptide binding]; other site 452662006940 Substrate-binding/catalytic site; other site 452662006941 Zn-binding sites [ion binding]; other site 452662006942 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 452662006943 OstA-like protein; Region: OstA; cl00844 452662006944 Organic solvent tolerance protein; Region: OstA_C; pfam04453 452662006945 SurA N-terminal domain; Region: SurA_N; pfam09312 452662006946 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 452662006947 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK05312 452662006948 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 452662006949 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 452662006950 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 452662006951 S-adenosylmethionine binding site [chemical binding]; other site 452662006952 Siphovirus protein of unknown function (DUF859); Region: DUF859; pfam05895 452662006953 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 452662006954 binding surface 452662006955 Tetratricopeptide repeat; Region: TPR_16; pfam13432 452662006956 TPR motif; other site 452662006957 NOL1/NOP2/sun family; Region: Nol1_Nop2_Fmu; pfam01189 452662006958 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 452662006959 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 452662006960 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 452662006961 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 452662006962 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 452662006963 active site 452662006964 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 452662006965 aspartate racemase; Region: asp_race; TIGR00035 452662006966 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 452662006967 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 452662006968 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 452662006969 active site 452662006970 phosphorylation site [posttranslational modification] 452662006971 dimerization interface [polypeptide binding]; other site 452662006972 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 452662006973 Walker A motif; other site 452662006974 ATP binding site [chemical binding]; other site 452662006975 Walker B motif; other site 452662006976 arginine finger; other site 452662006977 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 452662006978 Bacterial L-asparaginases and related enzymes; Region: L-asparaginase_like; cl00216 452662006979 active site 452662006980 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 452662006981 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 452662006982 Putative bacterial sensory transduction regulator; Region: YbjN; cl15834 452662006983 Membrane fusogenic activity; Region: BMFP; pfam04380 452662006984 TspO/MBR family; Region: TspO_MBR; pfam03073 452662006985 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 452662006986 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 452662006987 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662006988 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 452662006989 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 452662006990 RNA binding surface [nucleotide binding]; other site 452662006991 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 452662006992 S-adenosylmethionine binding site [chemical binding]; other site 452662006993 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 452662006994 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 452662006995 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 452662006996 DsbD alpha interface [polypeptide binding]; other site 452662006997 catalytic residues [active] 452662006998 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 452662006999 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 452662007000 Penicillinase repressor; Region: Pencillinase_R; cl17580 452662007001 serine O-acetyltransferase; Region: cysE; TIGR01172 452662007002 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 452662007003 trimer interface [polypeptide binding]; other site 452662007004 active site 452662007005 substrate binding site [chemical binding]; other site 452662007006 CoA binding site [chemical binding]; other site 452662007007 HAMP domain; Region: HAMP; pfam00672 452662007008 dimerization interface [polypeptide binding]; other site 452662007009 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 452662007010 dimer interface [polypeptide binding]; other site 452662007011 phosphorylation site [posttranslational modification] 452662007012 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 452662007013 ATP binding site [chemical binding]; other site 452662007014 Mg2+ binding site [ion binding]; other site 452662007015 G-X-G motif; other site 452662007016 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 452662007017 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 452662007018 active site 452662007019 phosphorylation site [posttranslational modification] 452662007020 intermolecular recognition site; other site 452662007021 dimerization interface [polypeptide binding]; other site 452662007022 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 452662007023 DNA binding site [nucleotide binding] 452662007024 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 452662007025 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 452662007026 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 452662007027 Sulfate transporter family; Region: Sulfate_transp; pfam00916 452662007028 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 452662007029 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 452662007030 active site clefts [active] 452662007031 zinc binding site [ion binding]; other site 452662007032 dimer interface [polypeptide binding]; other site 452662007033 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 452662007034 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 452662007035 active site 452662007036 phosphorylation site [posttranslational modification] 452662007037 intermolecular recognition site; other site 452662007038 dimerization interface [polypeptide binding]; other site 452662007039 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 452662007040 DNA binding site [nucleotide binding] 452662007041 This family is most closely related to the GT1 family of glycosyltransferases. aviGT4 in Streptomyces viridochromogenes has been shown to be involved in biosynthesis of oligosaccharide antibiotic avilamycin A. Inactivation of aviGT4 resulted in a mutant...; Region: GT1_AviGT4_like; cd03802 452662007042 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662007043 putative ADP-binding pocket [chemical binding]; other site 452662007044 Glycogen debranching enzyme [Carbohydrate transport and metabolism]; Region: GDB1; COG3408 452662007045 Amylo-alpha-1,6-glucosidase; Region: GDE_C; pfam06202 452662007046 malonic semialdehyde reductase; Provisional; Region: PRK10538 452662007047 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662007048 NAD(P) binding site [chemical binding]; other site 452662007049 active site 452662007050 CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases; Region: CYTH-like_Pase; cl11964 452662007051 putative metal binding residues [ion binding]; other site 452662007052 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 452662007053 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 452662007054 Beta-Casp domain; Region: Beta-Casp; smart01027 452662007055 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 452662007056 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 452662007057 thymidine phosphorylase; Provisional; Region: PRK04350 452662007058 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 452662007059 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 452662007060 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 452662007061 phosphoribosylpyrophosphate synthetase; Provisional; Region: PRK07199 452662007062 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 452662007063 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 452662007064 active site 452662007065 Uncharacterized conserved protein [Function unknown]; Region: HdeD; COG3247 452662007066 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 452662007067 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 452662007068 putative dimer interface [polypeptide binding]; other site 452662007069 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 452662007070 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662007071 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 452662007072 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 452662007073 FtsX-like permease family; Region: FtsX; pfam02687 452662007074 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 452662007075 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 452662007076 Walker A/P-loop; other site 452662007077 ATP binding site [chemical binding]; other site 452662007078 Q-loop/lid; other site 452662007079 ABC transporter signature motif; other site 452662007080 Walker B; other site 452662007081 D-loop; other site 452662007082 H-loop/switch region; other site 452662007083 Predicted membrane protein [Function unknown]; Region: COG3174 452662007084 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 452662007085 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 452662007086 Predicted transporter component [General function prediction only]; Region: COG2391 452662007087 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 452662007088 Ion channel; Region: Ion_trans_2; pfam07885 452662007089 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; cl00447 452662007090 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 452662007091 ParB-like nuclease domain; Region: ParBc; pfam02195 452662007092 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 452662007093 DNA methylase; Region: N6_N4_Mtase; pfam01555 452662007094 Lamin Tail Domain; Region: LTD; pfam00932 452662007095 Uncharacterized conserved protein (DUF2235); Region: DUF2235; pfam09994 452662007096 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662007097 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 452662007098 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 452662007099 Excalibur calcium-binding domain; Region: Excalibur; pfam05901 452662007100 Hypothetical protein (DUF2513); Region: DUF2513; pfam10711 452662007101 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 452662007102 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662007103 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 452662007104 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662007105 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 452662007106 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 452662007107 DNA binding residues [nucleotide binding] 452662007108 dimerization interface [polypeptide binding]; other site 452662007109 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 452662007110 MPN+ (JAMM) motif; other site 452662007111 Zinc-binding site [ion binding]; other site 452662007112 Cyanate lyase [Inorganic ion transport and metabolism]; Region: CynS; COG1513 452662007113 Predicted transcriptional regulator [Transcription]; Region: COG2932 452662007114 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 452662007115 Catalytic site [active] 452662007116 Bacteriophage abortive infection AbiH; Region: AbiH; pfam14253 452662007117 Bacteriophage abortive infection AbiH; Region: AbiH; pfam14253 452662007118 Protein of unknown function (DUF2813); Region: DUF2813; pfam11398 452662007119 AAA domain; Region: AAA_23; pfam13476 452662007120 Family description; Region: UvrD_C_2; pfam13538 452662007121 Protein of unknown function (DUF3489); Region: DUF3489; pfam11994 452662007122 Protein of unknown function (DUF2924); Region: DUF2924; pfam11149 452662007123 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 452662007124 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 452662007125 catalytic residues [active] 452662007126 catalytic nucleophile [active] 452662007127 Presynaptic Site I dimer interface [polypeptide binding]; other site 452662007128 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 452662007129 Synaptic Flat tetramer interface [polypeptide binding]; other site 452662007130 Synaptic Site I dimer interface [polypeptide binding]; other site 452662007131 DNA binding site [nucleotide binding] 452662007132 Recombinase; Region: Recombinase; pfam07508 452662007133 Protein of unknown function (DUF1178); Region: DUF1178; pfam06676 452662007134 nitrilase; Region: PLN02798 452662007135 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 452662007136 putative active site [active] 452662007137 catalytic triad [active] 452662007138 dimer interface [polypeptide binding]; other site 452662007139 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 452662007140 GSH binding site [chemical binding]; other site 452662007141 catalytic residues [active] 452662007142 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 452662007143 Methyltransferase domain; Region: Methyltransf_23; pfam13489 452662007144 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 452662007145 S-adenosylmethionine binding site [chemical binding]; other site 452662007146 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 452662007147 classical (c) SDRs; Region: SDR_c; cd05233 452662007148 NAD(P) binding site [chemical binding]; other site 452662007149 active site 452662007150 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1; Region: FDH_like_1; cd08283 452662007151 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 452662007152 NAD binding site [chemical binding]; other site 452662007153 catalytic Zn binding site [ion binding]; other site 452662007154 structural Zn binding site [ion binding]; other site 452662007155 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_8; cd07817 452662007156 putative hydrophobic ligand binding site [chemical binding]; other site 452662007157 Hemerythrin-like domain; Region: Hr-like; cd12108 452662007158 Fe binding site [ion binding]; other site 452662007159 heat shock protein 90; Provisional; Region: PRK05218 452662007160 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 452662007161 ATP binding site [chemical binding]; other site 452662007162 Mg2+ binding site [ion binding]; other site 452662007163 G-X-G motif; other site 452662007164 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 452662007165 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 452662007166 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 452662007167 2'-5' RNA ligase superfamily; Region: 2_5_RNA_ligase2; pfam13563 452662007168 homoserine O-succinyltransferase; Provisional; Region: PRK05368 452662007169 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 452662007170 proposed active site lysine [active] 452662007171 conserved cys residue [active] 452662007172 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 452662007173 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; pfam09912 452662007174 Predicted permeases [General function prediction only]; Region: COG0795 452662007175 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 452662007176 Predicted permeases [General function prediction only]; Region: COG0795 452662007177 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 452662007178 Fatty acid desaturase; Region: FA_desaturase; pfam00487 452662007179 The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the...; Region: Membrane-FADS-like; cl00615 452662007180 type II secretion system protein F; Region: GspF; TIGR02120 452662007181 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 452662007182 putative lipid kinase; Reviewed; Region: PRK13057 452662007183 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 452662007184 Bacillus subtilis YydB and related proteins, metallophosphatase domain; Region: MPP_YydB; cd07400 452662007185 putative active site [active] 452662007186 putative metal binding site [ion binding]; other site 452662007187 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 452662007188 putative catalytic site [active] 452662007189 putative phosphate binding site [ion binding]; other site 452662007190 active site 452662007191 metal binding site A [ion binding]; metal-binding site 452662007192 DNA binding site [nucleotide binding] 452662007193 putative AP binding site [nucleotide binding]; other site 452662007194 putative metal binding site B [ion binding]; other site 452662007195 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 452662007196 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 452662007197 Peptidase family M23; Region: Peptidase_M23; pfam01551 452662007198 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 452662007199 dinuclear metal binding motif [ion binding]; other site 452662007200 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 452662007201 catalytic triad [active] 452662007202 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 452662007203 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 452662007204 metal binding triad; other site 452662007205 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 452662007206 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 452662007207 metal binding triad; other site 452662007208 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 452662007209 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 452662007210 active site 452662007211 intersubunit interactions; other site 452662007212 catalytic residue [active] 452662007213 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 452662007214 primosome assembly protein PriA; Validated; Region: PRK05580 452662007215 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 452662007216 ATP binding site [chemical binding]; other site 452662007217 putative Mg++ binding site [ion binding]; other site 452662007218 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 452662007219 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 452662007220 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 452662007221 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 452662007222 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 452662007223 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 452662007224 DNA binding site [nucleotide binding] 452662007225 active site 452662007226 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 452662007227 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 452662007228 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 452662007229 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 452662007230 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 452662007231 F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to...; Region: F1_ATPase_alpha; cd01132 452662007232 beta subunit interaction interface [polypeptide binding]; other site 452662007233 Walker A motif; other site 452662007234 ATP binding site [chemical binding]; other site 452662007235 Walker B motif; other site 452662007236 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 452662007237 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 452662007238 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 452662007239 core domain interface [polypeptide binding]; other site 452662007240 delta subunit interface [polypeptide binding]; other site 452662007241 epsilon subunit interface [polypeptide binding]; other site 452662007242 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 452662007243 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 452662007244 F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a...; Region: F1-ATPase_beta; cd01133 452662007245 alpha subunit interaction interface [polypeptide binding]; other site 452662007246 Walker A motif; other site 452662007247 ATP binding site [chemical binding]; other site 452662007248 Walker B motif; other site 452662007249 inhibitor binding site; inhibition site 452662007250 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 452662007251 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 452662007252 gamma subunit interface [polypeptide binding]; other site 452662007253 epsilon subunit interface [polypeptide binding]; other site 452662007254 LBP interface [polypeptide binding]; other site 452662007255 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 452662007256 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 452662007257 ATP binding site [chemical binding]; other site 452662007258 Walker A motif; other site 452662007259 hexamer interface [polypeptide binding]; other site 452662007260 Walker B motif; other site 452662007261 Predicted methyltransferase [General function prediction only]; Region: COG4798 452662007262 Methyltransferase domain; Region: Methyltransf_23; pfam13489 452662007263 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 452662007264 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 452662007265 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 452662007266 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 452662007267 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662007268 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662007269 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 452662007270 dimerization interface [polypeptide binding]; other site 452662007271 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily 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: ACAD10_11_like; cd05154 452662007272 putative active site [active] 452662007273 putative substrate binding site [chemical binding]; other site 452662007274 ATP binding site [chemical binding]; other site 452662007275 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662007276 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 452662007277 active site 452662007278 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662007279 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662007280 NAD(P) binding site [chemical binding]; other site 452662007281 active site 452662007282 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 452662007283 classical (c) SDRs; Region: SDR_c; cd05233 452662007284 NAD(P) binding site [chemical binding]; other site 452662007285 active site 452662007286 Outer membrane efflux protein; Region: OEP; pfam02321 452662007287 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 452662007288 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 452662007289 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 452662007290 putative substrate translocation pore; other site 452662007291 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 452662007292 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 452662007293 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662007294 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662007295 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662007296 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 452662007297 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 452662007298 MarR family; Region: MarR_2; pfam12802 452662007299 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 452662007300 EamA-like transporter family; Region: EamA; pfam00892 452662007301 enoyl-CoA hydratase; Provisional; Region: PRK06688 452662007302 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662007303 substrate binding site [chemical binding]; other site 452662007304 oxyanion hole (OAH) forming residues; other site 452662007305 trimer interface [polypeptide binding]; other site 452662007306 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 452662007307 SBF-like CPA transporter family (DUF4137); Region: DUF4137; pfam13593 452662007308 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 452662007309 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 452662007310 [2Fe-2S] cluster binding site [ion binding]; other site 452662007311 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 452662007312 alpha subunit interface [polypeptide binding]; other site 452662007313 active site 452662007314 substrate binding site [chemical binding]; other site 452662007315 Fe binding site [ion binding]; other site 452662007316 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 452662007317 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 452662007318 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 452662007319 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 452662007320 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 452662007321 dihydroorotase; Validated; Region: pyrC; PRK09357 452662007322 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 452662007323 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 452662007324 active site 452662007325 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 452662007326 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 452662007327 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 452662007328 putative homodimer interface [polypeptide binding]; other site 452662007329 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 452662007330 heterodimer interface [polypeptide binding]; other site 452662007331 homodimer interface [polypeptide binding]; other site 452662007332 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 452662007333 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 452662007334 23S rRNA interface [nucleotide binding]; other site 452662007335 L7/L12 interface [polypeptide binding]; other site 452662007336 putative thiostrepton binding site; other site 452662007337 L25 interface [polypeptide binding]; other site 452662007338 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 452662007339 mRNA/rRNA interface [nucleotide binding]; other site 452662007340 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 452662007341 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 452662007342 ATP binding site [chemical binding]; other site 452662007343 Mg++ binding site [ion binding]; other site 452662007344 motif III; other site 452662007345 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 452662007346 nucleotide binding region [chemical binding]; other site 452662007347 ATP-binding site [chemical binding]; other site 452662007348 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 452662007349 RNA binding site [nucleotide binding]; other site 452662007350 putative cation:proton antiport protein; Provisional; Region: PRK10669 452662007351 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 452662007352 TrkA-N domain; Region: TrkA_N; pfam02254 452662007353 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 452662007354 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 452662007355 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 452662007356 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 452662007357 GTPase CgtA; Reviewed; Region: obgE; PRK12299 452662007358 GTP1/OBG; Region: GTP1_OBG; pfam01018 452662007359 Obg GTPase; Region: Obg; cd01898 452662007360 G1 box; other site 452662007361 GTP/Mg2+ binding site [chemical binding]; other site 452662007362 Switch I region; other site 452662007363 G2 box; other site 452662007364 G3 box; other site 452662007365 Switch II region; other site 452662007366 G4 box; other site 452662007367 G5 box; other site 452662007368 gamma-glutamyl kinase; Provisional; Region: PRK05429 452662007369 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 452662007370 nucleotide binding site [chemical binding]; other site 452662007371 homotetrameric interface [polypeptide binding]; other site 452662007372 putative phosphate binding site [ion binding]; other site 452662007373 putative allosteric binding site; other site 452662007374 PUA domain; Region: PUA; pfam01472 452662007375 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 452662007376 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662007377 NAD(P) binding site [chemical binding]; other site 452662007378 active site 452662007379 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 452662007380 dihydropteroate synthase; Region: DHPS; TIGR01496 452662007381 substrate binding pocket [chemical binding]; other site 452662007382 dimer interface [polypeptide binding]; other site 452662007383 inhibitor binding site; inhibition site 452662007384 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 452662007385 DNA methylase; Region: N6_N4_Mtase; pfam01555 452662007386 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 452662007387 dimerization interface [polypeptide binding]; other site 452662007388 putative DNA binding site [nucleotide binding]; other site 452662007389 putative Zn2+ binding site [ion binding]; other site 452662007390 MobA-like NTP transferase domain; Region: NTP_transf_3; pfam12804 452662007391 active site 452662007392 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 452662007393 Peptidase family M23; Region: Peptidase_M23; pfam01551 452662007394 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 452662007395 nucleotide binding region [chemical binding]; other site 452662007396 ATP-binding site [chemical binding]; other site 452662007397 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 452662007398 RNA binding surface [nucleotide binding]; other site 452662007399 Ferredoxin [Energy production and conversion]; Region: COG1146 452662007400 4Fe-4S binding domain; Region: Fer4; cl02805 452662007401 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 452662007402 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 452662007403 D-aminopeptidase; Reviewed; Region: PRK13128 452662007404 transcriptional repressor BetI; Region: betaine_BetI; TIGR03384 452662007405 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662007406 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 452662007407 peroxiredoxin; Region: AhpC; TIGR03137 452662007408 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 452662007409 dimer interface [polypeptide binding]; other site 452662007410 decamer (pentamer of dimers) interface [polypeptide binding]; other site 452662007411 catalytic triad [active] 452662007412 peroxidatic and resolving cysteines [active] 452662007413 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 452662007414 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 452662007415 catalytic residue [active] 452662007416 TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then...; Region: AhpF_NTD_C; cd03026 452662007417 catalytic residues [active] 452662007418 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 452662007419 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 452662007420 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 452662007421 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 452662007422 RNA/DNA hybrid binding site [nucleotide binding]; other site 452662007423 active site 452662007424 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 452662007425 dimer interface [polypeptide binding]; other site 452662007426 substrate binding site [chemical binding]; other site 452662007427 ATP binding site [chemical binding]; other site 452662007428 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3813 452662007429 Protein of unknown function (DUF1272); Region: DUF1272; pfam06906 452662007430 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14315 452662007431 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 452662007432 active site 452662007433 substrate binding site [chemical binding]; other site 452662007434 metal binding site [ion binding]; metal-binding site 452662007435 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 452662007436 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 452662007437 amino acid transporter; Region: 2A0306; TIGR00909 452662007438 C-terminus of AA_permease; Region: AA_permease_C; pfam13906 452662007439 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 452662007440 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 452662007441 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 452662007442 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 452662007443 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 452662007444 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 452662007445 FeS/SAM binding site; other site 452662007446 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 452662007447 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 452662007448 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 452662007449 P loop; other site 452662007450 GTP binding site [chemical binding]; other site 452662007451 Intracellular septation protein A; Region: IspA; pfam04279 452662007452 Predicted membrane protein [Function unknown]; Region: COG3748 452662007453 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 452662007454 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 452662007455 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 452662007456 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 452662007457 Protein of unknown function (DUF1636); Region: DUF1636; cl17843 452662007458 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 452662007459 HSP70 interaction site [polypeptide binding]; other site 452662007460 patatin-related protein; Region: TIGR03607 452662007461 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_b; cd00914 452662007462 aromatic arch; other site 452662007463 DCoH dimer interaction site [polypeptide binding]; other site 452662007464 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 452662007465 DCoH tetramer interaction site [polypeptide binding]; other site 452662007466 substrate binding site [chemical binding]; other site 452662007467 Minimal MMP-like domain found in Acidothermus cellulolyticus hypothetical protein ACEL2062 and similar protein; Region: MMP_ACEL2062; cd12952 452662007468 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662007469 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13539 452662007470 Walker A/P-loop; other site 452662007471 ATP binding site [chemical binding]; other site 452662007472 Q-loop/lid; other site 452662007473 ABC transporter signature motif; other site 452662007474 Walker B; other site 452662007475 D-loop; other site 452662007476 H-loop/switch region; other site 452662007477 CcmB protein; Region: CcmB; cl17444 452662007478 chorismate mutase; Provisional; Region: PRK09239 452662007479 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 452662007480 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 452662007481 substrate binding pocket [chemical binding]; other site 452662007482 chain length determination region; other site 452662007483 substrate-Mg2+ binding site; other site 452662007484 catalytic residues [active] 452662007485 aspartate-rich region 1; other site 452662007486 active site lid residues [active] 452662007487 aspartate-rich region 2; other site 452662007488 hypothetical protein; Provisional; Region: PRK10621 452662007489 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 452662007490 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 452662007491 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 452662007492 ATP binding site [chemical binding]; other site 452662007493 putative Mg++ binding site [ion binding]; other site 452662007494 nucleotide binding region [chemical binding]; other site 452662007495 helicase superfamily c-terminal domain; Region: HELICc; smart00490 452662007496 Helicase associated domain (HA2) Add an annotation; Region: HA2; smart00847 452662007497 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 452662007498 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 452662007499 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 452662007500 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 452662007501 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 452662007502 substrate-cofactor binding pocket; other site 452662007503 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662007504 catalytic residue [active] 452662007505 CHASE3 domain; Region: CHASE3; pfam05227 452662007506 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662007507 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 452662007508 ATP binding site [chemical binding]; other site 452662007509 Mg2+ binding site [ion binding]; other site 452662007510 G-X-G motif; other site 452662007511 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 452662007512 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 452662007513 active site 452662007514 phosphorylation site [posttranslational modification] 452662007515 intermolecular recognition site; other site 452662007516 dimerization interface [polypeptide binding]; other site 452662007517 Protein of unknown function (DUF938); Region: DUF938; pfam06080 452662007518 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 452662007519 tetramer interface [polypeptide binding]; other site 452662007520 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662007521 catalytic residue [active] 452662007522 glycine dehydrogenase subunit 1; Validated; Region: PRK00451 452662007523 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 452662007524 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 452662007525 catalytic residue [active] 452662007526 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 452662007527 lipoyl attachment site [posttranslational modification]; other site 452662007528 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 452662007529 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 452662007530 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 452662007531 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 452662007532 Zn2+ binding site [ion binding]; other site 452662007533 Mg2+ binding site [ion binding]; other site 452662007534 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 452662007535 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 452662007536 binding surface 452662007537 TPR motif; other site 452662007538 Sporulation related domain; Region: SPOR; pfam05036 452662007539 cell division protein FtsZ; Validated; Region: PRK09330 452662007540 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 452662007541 nucleotide binding site [chemical binding]; other site 452662007542 SulA interaction site; other site 452662007543 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 452662007544 Cell division protein FtsA; Region: FtsA; smart00842 452662007545 Cell division protein FtsA; Region: FtsA; pfam14450 452662007546 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 452662007547 Cell division protein FtsQ; Region: FtsQ; pfam03799 452662007548 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 452662007549 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 452662007550 ATP-grasp domain; Region: ATP-grasp_4; cl17255 452662007551 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 452662007552 FAD binding domain; Region: FAD_binding_4; pfam01565 452662007553 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 452662007554 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 452662007555 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 452662007556 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 452662007557 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 452662007558 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 452662007559 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 452662007560 homodimer interface [polypeptide binding]; other site 452662007561 active site 452662007562 cell division protein FtsW; Region: ftsW; TIGR02614 452662007563 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01390 452662007564 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 452662007565 NAD(P) binding pocket [chemical binding]; other site 452662007566 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 452662007567 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 452662007568 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 452662007569 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 452662007570 Mg++ binding site [ion binding]; other site 452662007571 putative catalytic motif [active] 452662007572 putative substrate binding site [chemical binding]; other site 452662007573 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional; Region: PRK14093 452662007574 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 452662007575 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 452662007576 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 452662007577 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 452662007578 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 452662007579 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 452662007580 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 452662007581 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 452662007582 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 452662007583 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 452662007584 MraW methylase family; Region: Methyltransf_5; cl17771 452662007585 cell division protein MraZ; Reviewed; Region: PRK00326 452662007586 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 452662007587 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 452662007588 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 452662007589 dimer interface [polypeptide binding]; other site 452662007590 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662007591 catalytic residue [active] 452662007592 Cell wall hydrolyses involved in spore germination [Cell envelope biogenesis, outer membrane]; Region: SleB; COG3773 452662007593 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 452662007594 Predicted small secreted protein [Function unknown]; Region: COG5510 452662007595 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 452662007596 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 452662007597 twin arginine translocase protein A; Provisional; Region: tatA; PRK00720 452662007598 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 452662007599 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 452662007600 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 452662007601 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 452662007602 Sporulation related domain; Region: SPOR; pfam05036 452662007603 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 452662007604 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 452662007605 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 452662007606 active site 452662007607 HIGH motif; other site 452662007608 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 452662007609 KMSK motif region; other site 452662007610 tRNA binding surface [nucleotide binding]; other site 452662007611 DALR anticodon binding domain; Region: DALR_1; smart00836 452662007612 anticodon binding site; other site 452662007613 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 452662007614 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 452662007615 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 452662007616 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 452662007617 putative active site [active] 452662007618 putative substrate binding site [chemical binding]; other site 452662007619 ATP binding site [chemical binding]; other site 452662007620 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 452662007621 RNA/DNA hybrid binding site [nucleotide binding]; other site 452662007622 active site 452662007623 SCP: SCP-like extracellular protein domain, found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in...; Region: SCP; cl00133 452662007624 coproporphyrinogen III oxidase; Provisional; Region: PRK09057 452662007625 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 452662007626 FeS/SAM binding site; other site 452662007627 HemN C-terminal domain; Region: HemN_C; pfam06969 452662007628 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 452662007629 Penicillinase repressor; Region: Pencillinase_R; pfam03965 452662007630 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 452662007631 putative GSH binding site [chemical binding]; other site 452662007632 catalytic residues [active] 452662007633 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 452662007634 Domain of unknown function (DUF1476); Region: DUF1476; pfam07345 452662007635 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 452662007636 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 452662007637 substrate binding site [chemical binding]; other site 452662007638 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 452662007639 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 452662007640 substrate binding site [chemical binding]; other site 452662007641 ligand binding site [chemical binding]; other site 452662007642 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 452662007643 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 452662007644 putative C-terminal domain interface [polypeptide binding]; other site 452662007645 putative GSH binding site (G-site) [chemical binding]; other site 452662007646 putative dimer interface [polypeptide binding]; other site 452662007647 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 452662007648 putative N-terminal domain interface [polypeptide binding]; other site 452662007649 putative dimer interface [polypeptide binding]; other site 452662007650 putative substrate binding pocket (H-site) [chemical binding]; other site 452662007651 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 452662007652 tetramer interface [polypeptide binding]; other site 452662007653 active site 452662007654 Mg2+/Mn2+ binding site [ion binding]; other site 452662007655 Members of the ICL/PEPM_KPHMT enzyme superfamily catalyze the formation and cleavage of either P-C or C-C bonds. Typical members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate...; Region: ICL_KPHMT; cl00435 452662007656 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 452662007657 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 452662007658 sequence-specific DNA binding site [nucleotide binding]; other site 452662007659 salt bridge; other site 452662007660 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 452662007661 Domain of unknown function (DUF955); Region: DUF955; pfam06114 452662007662 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 452662007663 Right handed beta helix region; Region: Beta_helix; pfam13229 452662007664 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 452662007665 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 452662007666 Domain of unknown function (DUF4112); Region: DUF4112; pfam13430 452662007667 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 452662007668 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 452662007669 dimerization interface [polypeptide binding]; other site 452662007670 active site 452662007671 quinolinate synthetase; Provisional; Region: PRK09375 452662007672 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 452662007673 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 452662007674 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 452662007675 active site 452662007676 DNA binding site [nucleotide binding] 452662007677 Int/Topo IB signature motif; other site 452662007678 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 452662007679 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 452662007680 glutathione synthetase; Provisional; Region: PRK05246 452662007681 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 452662007682 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 452662007683 hypothetical protein; Reviewed; Region: PRK12497 452662007684 Predicted methyltransferases [General function prediction only]; Region: COG0313 452662007685 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 452662007686 putative SAM binding site [chemical binding]; other site 452662007687 putative homodimer interface [polypeptide binding]; other site 452662007688 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 452662007689 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 452662007690 putative ligand binding site [chemical binding]; other site 452662007691 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 452662007692 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 452662007693 Walker A/P-loop; other site 452662007694 ATP binding site [chemical binding]; other site 452662007695 Q-loop/lid; other site 452662007696 ABC transporter signature motif; other site 452662007697 Walker B; other site 452662007698 D-loop; other site 452662007699 H-loop/switch region; other site 452662007700 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 452662007701 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 452662007702 ABC-ATPase subunit interface; other site 452662007703 dimer interface [polypeptide binding]; other site 452662007704 putative PBP binding regions; other site 452662007705 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 452662007706 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 452662007707 intersubunit interface [polypeptide binding]; other site 452662007708 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 452662007709 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 452662007710 N-terminal plug; other site 452662007711 ligand-binding site [chemical binding]; other site 452662007712 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 452662007713 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 452662007714 GTP binding site; other site 452662007715 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 452662007716 active site 452662007717 SAM binding site [chemical binding]; other site 452662007718 homodimer interface [polypeptide binding]; other site 452662007719 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 452662007720 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 452662007721 [4Fe-4S] binding site [ion binding]; other site 452662007722 molybdopterin cofactor binding site; other site 452662007723 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 452662007724 molybdopterin cofactor binding site; other site 452662007725 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 452662007726 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 452662007727 [2Fe-2S] cluster binding site [ion binding]; other site 452662007728 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 452662007729 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 452662007730 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 452662007731 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 452662007732 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 452662007733 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 452662007734 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 452662007735 putative substrate translocation pore; other site 452662007736 NMT1-like family; Region: NMT1_2; pfam13379 452662007737 NMT1/THI5 like; Region: NMT1; pfam09084 452662007738 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 452662007739 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 452662007740 active site 452662007741 phosphorylation site [posttranslational modification] 452662007742 intermolecular recognition site; other site 452662007743 ANTAR domain; Region: ANTAR; pfam03861 452662007744 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 452662007745 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 452662007746 putative substrate translocation pore; other site 452662007747 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 452662007748 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 452662007749 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662007750 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 452662007751 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662007752 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662007753 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 452662007754 Response regulator receiver domain; Region: Response_reg; pfam00072 452662007755 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 452662007756 active site 452662007757 phosphorylation site [posttranslational modification] 452662007758 intermolecular recognition site; other site 452662007759 dimerization interface [polypeptide binding]; other site 452662007760 Salmonella typhimurium Zn2+ transporter ZntB-like subgroup; Region: ZntB-like_1; cd12833 452662007761 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 452662007762 Cl binding site [ion binding]; other site 452662007763 oligomer interface [polypeptide binding]; other site 452662007764 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 452662007765 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 452662007766 diaminopimelate decarboxylase; Region: lysA; TIGR01048 452662007767 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 452662007768 active site 452662007769 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 452662007770 substrate binding site [chemical binding]; other site 452662007771 catalytic residues [active] 452662007772 dimer interface [polypeptide binding]; other site 452662007773 argininosuccinate lyase; Provisional; Region: PRK00855 452662007774 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 452662007775 active sites [active] 452662007776 tetramer interface [polypeptide binding]; other site 452662007777 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 452662007778 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 452662007779 catalytic residues [active] 452662007780 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662007781 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 452662007782 N-terminal plug; other site 452662007783 ligand-binding site [chemical binding]; other site 452662007784 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 452662007785 homotrimer interaction site [polypeptide binding]; other site 452662007786 putative active site [active] 452662007787 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 452662007788 diiron binding motif [ion binding]; other site 452662007789 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 452662007790 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 452662007791 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 452662007792 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 452662007793 protein binding site [polypeptide binding]; other site 452662007794 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 452662007795 Catalytic dyad [active] 452662007796 HprK-related kinase A; Region: HprK_rel_A; TIGR04352 452662007797 PqqD family protein, HPr-rel-A system; Region: PqqD_rel_X; TIGR04353 452662007798 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 452662007799 putative ADP-binding pocket [chemical binding]; other site 452662007800 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662007801 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 452662007802 PAS domain; Region: PAS_8; pfam13188 452662007803 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 452662007804 dimer interface [polypeptide binding]; other site 452662007805 phosphorylation site [posttranslational modification] 452662007806 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 452662007807 ATP binding site [chemical binding]; other site 452662007808 Mg2+ binding site [ion binding]; other site 452662007809 G-X-G motif; other site 452662007810 ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: PstS; COG0226 452662007811 Phosphate ATP-binding cassette transporter; Region: DUF3708; pfam12501 452662007812 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 452662007813 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 452662007814 dimer interface [polypeptide binding]; other site 452662007815 conserved gate region; other site 452662007816 putative PBP binding loops; other site 452662007817 ABC-ATPase subunit interface; other site 452662007818 Domain of unknown function (DUF3333); Region: DUF3333; pfam11812 452662007819 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 452662007820 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 452662007821 dimer interface [polypeptide binding]; other site 452662007822 conserved gate region; other site 452662007823 putative PBP binding loops; other site 452662007824 ABC-ATPase subunit interface; other site 452662007825 phosphate transporter ATP-binding protein; Provisional; Region: PRK14235 452662007826 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 452662007827 Walker A/P-loop; other site 452662007828 ATP binding site [chemical binding]; other site 452662007829 Q-loop/lid; other site 452662007830 ABC transporter signature motif; other site 452662007831 Walker B; other site 452662007832 D-loop; other site 452662007833 H-loop/switch region; other site 452662007834 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 452662007835 PhoU domain; Region: PhoU; pfam01895 452662007836 PhoU domain; Region: PhoU; pfam01895 452662007837 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 452662007838 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 452662007839 active site 452662007840 phosphorylation site [posttranslational modification] 452662007841 intermolecular recognition site; other site 452662007842 dimerization interface [polypeptide binding]; other site 452662007843 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 452662007844 DNA binding site [nucleotide binding] 452662007845 Uncharacterized conserved protein [Function unknown]; Region: COG2835 452662007846 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 452662007847 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 452662007848 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 452662007849 catalytic residues [active] 452662007850 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; pfam09912 452662007851 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 452662007852 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 452662007853 prephenate dehydratase; Provisional; Region: PRK11899 452662007854 Prephenate dehydratase; Region: PDT; pfam00800 452662007855 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 452662007856 putative L-Phe binding site [chemical binding]; other site 452662007857 Cytochrome c2 [Energy production and conversion]; Region: COG3474 452662007858 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 452662007859 active site 452662007860 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 452662007861 Domain of unknown function DUF21; Region: DUF21; pfam01595 452662007862 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 452662007863 Transporter associated domain; Region: CorC_HlyC; smart01091 452662007864 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 452662007865 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 452662007866 ligand binding site [chemical binding]; other site 452662007867 exopolyphosphatase; Region: exo_poly_only; TIGR03706 452662007868 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 452662007869 potential frameshift: common BLAST hit: gi|85373477|ref|YP_457539.1| polyphosphate kinase 452662007870 polyphosphate kinase; Provisional; Region: PRK05443 452662007871 polyphosphate kinase; Provisional; Region: PRK05443 452662007872 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 452662007873 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 452662007874 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 452662007875 putative domain interface [polypeptide binding]; other site 452662007876 putative active site [active] 452662007877 catalytic site [active] 452662007878 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 452662007879 putative active site [active] 452662007880 catalytic site [active] 452662007881 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 452662007882 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 452662007883 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 452662007884 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 452662007885 dimerization interface [polypeptide binding]; other site 452662007886 putative ATP binding site [chemical binding]; other site 452662007887 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 452662007888 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 452662007889 active site 452662007890 substrate binding site [chemical binding]; other site 452662007891 cosubstrate binding site; other site 452662007892 catalytic site [active] 452662007893 Protein of unknown function (DUF419); Region: DUF419; pfam04237 452662007894 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 452662007895 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662007896 Walker A/P-loop; other site 452662007897 ATP binding site [chemical binding]; other site 452662007898 Q-loop/lid; other site 452662007899 ABC transporter signature motif; other site 452662007900 Walker B; other site 452662007901 D-loop; other site 452662007902 H-loop/switch region; other site 452662007903 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 452662007904 putative active site [active] 452662007905 L-aspartate oxidase; Provisional; Region: PRK09077 452662007906 L-aspartate oxidase; Provisional; Region: PRK06175 452662007907 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 452662007908 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 452662007909 Beta-lactamase enzyme family; Region: Beta-lactamase2; pfam13354 452662007910 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Region: MetH; COG1410 452662007911 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 452662007912 substrate binding pocket [chemical binding]; other site 452662007913 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 452662007914 B12 binding site [chemical binding]; other site 452662007915 cobalt ligand [ion binding]; other site 452662007916 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 452662007917 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 452662007918 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 452662007919 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 452662007920 FAD binding site [chemical binding]; other site 452662007921 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 452662007922 dimerization interface [polypeptide binding]; other site 452662007923 putative DNA binding site [nucleotide binding]; other site 452662007924 putative Zn2+ binding site [ion binding]; other site 452662007925 Methyltransferase domain; Region: Methyltransf_31; pfam13847 452662007926 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 452662007927 S-adenosylmethionine binding site [chemical binding]; other site 452662007928 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4246 452662007929 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 452662007930 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 452662007931 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 452662007932 nucleoside/Zn binding site; other site 452662007933 dimer interface [polypeptide binding]; other site 452662007934 catalytic motif [active] 452662007935 Predicted membrane protein [Function unknown]; Region: COG2246 452662007936 GtrA-like protein; Region: GtrA; pfam04138 452662007937 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 452662007938 GIY-YIG motif/motif A; other site 452662007939 putative active site [active] 452662007940 putative metal binding site [ion binding]; other site 452662007941 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 452662007942 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 452662007943 active site 452662007944 phosphorylation site [posttranslational modification] 452662007945 intermolecular recognition site; other site 452662007946 dimerization interface [polypeptide binding]; other site 452662007947 LytTr DNA-binding domain; Region: LytTR; smart00850 452662007948 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662007949 Histidine kinase; Region: His_kinase; pfam06580 452662007950 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 452662007951 ATP binding site [chemical binding]; other site 452662007952 Mg2+ binding site [ion binding]; other site 452662007953 G-X-G motif; other site 452662007954 Predicted transcriptional regulators [Transcription]; Region: COG1733 452662007955 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 452662007956 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 452662007957 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 452662007958 Zn2+ binding site [ion binding]; other site 452662007959 Mg2+ binding site [ion binding]; other site 452662007960 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 452662007961 synthetase active site [active] 452662007962 NTP binding site [chemical binding]; other site 452662007963 metal binding site [ion binding]; metal-binding site 452662007964 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 452662007965 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 452662007966 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 452662007967 catalytic site [active] 452662007968 metal binding site [ion binding]; metal-binding site 452662007969 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 452662007970 23S rRNA interface [nucleotide binding]; other site 452662007971 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 452662007972 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 452662007973 L11 interface [polypeptide binding]; other site 452662007974 putative EF-Tu interaction site [polypeptide binding]; other site 452662007975 putative EF-G interaction site [polypeptide binding]; other site 452662007976 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 452662007977 Response regulator receiver domain; Region: Response_reg; pfam00072 452662007978 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 452662007979 active site 452662007980 phosphorylation site [posttranslational modification] 452662007981 intermolecular recognition site; other site 452662007982 dimerization interface [polypeptide binding]; other site 452662007983 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK01663 452662007984 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 452662007985 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 452662007986 active site 452662007987 DNA binding site [nucleotide binding] 452662007988 Int/Topo IB signature motif; other site 452662007989 Uncharacterized protein conserved in bacteria (DUF2191); Region: DUF2191; pfam09957 452662007990 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; Region: VapC; COG1487 452662007991 HipA N-terminal domain; Region: Couple_hipA; cl11853 452662007992 HipA-like N-terminal domain; Region: HipA_N; pfam07805 452662007993 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 452662007994 HipA-like C-terminal domain; Region: HipA_C; pfam07804 452662007995 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 452662007996 DNA binding site [nucleotide binding] 452662007997 active site 452662007998 Int/Topo IB signature motif; other site 452662007999 Fic/DOC family; Region: Fic; cl00960 452662008000 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 452662008001 DNA binding site [nucleotide binding] 452662008002 Int/Topo IB signature motif; other site 452662008003 active site 452662008004 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 452662008005 Transposase; Region: DEDD_Tnp_IS110; pfam01548 452662008006 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 452662008007 Fic family protein [Function unknown]; Region: COG3177 452662008008 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 452662008009 Fic/DOC family; Region: Fic; pfam02661 452662008010 NLI interacting factor-like phosphatase; Region: NIF; pfam03031 452662008011 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 452662008012 putative active site [active] 452662008013 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 452662008014 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 452662008015 Ligand binding site; other site 452662008016 Putative Catalytic site; other site 452662008017 DXD motif; other site 452662008018 Methyltransferase domain; Region: Methyltransf_23; pfam13489 452662008019 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 452662008020 S-adenosylmethionine binding site [chemical binding]; other site 452662008021 Predicted membrane protein [Function unknown]; Region: COG2246 452662008022 GtrA-like protein; Region: GtrA; pfam04138 452662008023 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 452662008024 Protein of unknown function (DUF2274); Region: DUF2274; pfam10038 452662008025 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 452662008026 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 452662008027 VirB7 interaction site; other site 452662008028 conjugal transfer protein TrbF; Provisional; Region: PRK13872 452662008029 conjugal transfer protein TrbL; Provisional; Region: PRK13875 452662008030 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 452662008031 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 452662008032 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 452662008033 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 452662008034 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662008035 Walker B; other site 452662008036 D-loop; other site 452662008037 H-loop/switch region; other site 452662008038 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 452662008039 TrbC/VIRB2 family; Region: TrbC; cl01583 452662008040 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 452662008041 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 452662008042 ATP binding site [chemical binding]; other site 452662008043 Walker A motif; other site 452662008044 hexamer interface [polypeptide binding]; other site 452662008045 Walker B motif; other site 452662008046 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 452662008047 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 452662008048 Walker A motif; other site 452662008049 ATP binding site [chemical binding]; other site 452662008050 Walker B motif; other site 452662008051 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 452662008052 active site 452662008053 NTP binding site [chemical binding]; other site 452662008054 metal binding triad [ion binding]; metal-binding site 452662008055 antibiotic binding site [chemical binding]; other site 452662008056 Higher Eukarytoes and Prokaryotes Nucleotide-binding domain; Region: HEPN; smart00748 452662008057 Predicted transcriptional regulator [Transcription]; Region: COG3905 452662008058 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 452662008059 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 452662008060 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 452662008061 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 452662008062 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 452662008063 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 452662008064 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 452662008065 N-acetyl-D-glucosamine binding site [chemical binding]; other site 452662008066 catalytic residue [active] 452662008067 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 452662008068 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 452662008069 Helix-turn-helix domain; Region: HTH_17; pfam12728 452662008070 Protein of unknown function (DUF736); Region: DUF736; pfam05284 452662008071 toxin MazF; Provisional; Region: PRK09907 452662008072 Growth regulator [Signal transduction mechanisms]; Region: MazE; COG2336 452662008073 ParB-like nuclease domain; Region: ParB; smart00470 452662008074 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 452662008075 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 452662008076 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 452662008077 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 452662008078 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; pfam02899 452662008079 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 452662008080 active site 452662008081 DNA binding site [nucleotide binding] 452662008082 Int/Topo IB signature motif; other site 452662008083 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 452662008084 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 452662008085 Autoinducer binding domain; Region: Autoind_bind; pfam03472 452662008086 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 452662008087 DNA binding residues [nucleotide binding] 452662008088 dimerization interface [polypeptide binding]; other site 452662008089 Autoinducer synthetase; Region: Autoind_synth; cl17404 452662008090 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 452662008091 Transcriptional regulators [Transcription]; Region: GntR; COG1802 452662008092 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 452662008093 DNA-binding site [nucleotide binding]; DNA binding site 452662008094 Transglutaminase-like superfamily; Region: Transglut_core3; pfam13471 452662008095 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 452662008096 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 452662008097 Ligand Binding Site [chemical binding]; other site 452662008098 Molecular Tunnel; other site 452662008099 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 452662008100 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 452662008101 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 452662008102 Secretin and TonB N terminus short domain; Region: STN; smart00965 452662008103 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 452662008104 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 452662008105 N-terminal plug; other site 452662008106 ligand-binding site [chemical binding]; other site 452662008107 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 452662008108 FecR protein; Region: FecR; pfam04773 452662008109 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 452662008110 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 452662008111 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 452662008112 DNA binding residues [nucleotide binding] 452662008113 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 452662008114 active site 452662008115 DNA binding site [nucleotide binding] 452662008116 Int/Topo IB signature motif; other site 452662008117 Alpha-Mannosidase Binding Domain of Atg19/34; Region: ABD; cl15429 452662008118 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 452662008119 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 452662008120 ManB is a bacterial phosphomannomutase (PMM) that catalyzes the conversion of mannose 6-phosphate to mannose-1-phosphate in the second of three steps in the GDP-mannose pathway, in which GDP-D-mannose is synthesized from fructose-6-phosphate. In...; Region: ManB; cd03088 452662008121 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 452662008122 active site 452662008123 substrate binding site [chemical binding]; other site 452662008124 metal binding site [ion binding]; metal-binding site 452662008125 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 452662008126 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662008127 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 452662008128 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 452662008129 polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family; Region: BexC_CtrB_KpsE; TIGR01010 452662008130 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 452662008131 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 452662008132 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 452662008133 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 452662008134 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 452662008135 putative trimer interface [polypeptide binding]; other site 452662008136 putative CoA binding site [chemical binding]; other site 452662008137 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662008138 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 452662008139 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662008140 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 452662008141 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 452662008142 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662008143 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 452662008144 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 452662008145 inhibitor-cofactor binding pocket; inhibition site 452662008146 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662008147 catalytic residue [active] 452662008148 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 452662008149 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 452662008150 NADP-binding site; other site 452662008151 homotetramer interface [polypeptide binding]; other site 452662008152 substrate binding site [chemical binding]; other site 452662008153 homodimer interface [polypeptide binding]; other site 452662008154 active site 452662008155 Transposase domain (DUF772); Region: DUF772; pfam05598 452662008156 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662008157 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 452662008158 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 452662008159 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 452662008160 NADP-binding site; other site 452662008161 homotetramer interface [polypeptide binding]; other site 452662008162 substrate binding site [chemical binding]; other site 452662008163 homodimer interface [polypeptide binding]; other site 452662008164 active site 452662008165 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 452662008166 Helix-turn-helix domain; Region: HTH_38; pfam13936 452662008167 Integrase core domain; Region: rve; pfam00665 452662008168 transposase/IS protein; Provisional; Region: PRK09183 452662008169 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 452662008170 Walker A motif; other site 452662008171 ATP binding site [chemical binding]; other site 452662008172 Walker B motif; other site 452662008173 Transposase domain (DUF772); Region: DUF772; pfam05598 452662008174 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662008175 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 452662008176 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 452662008177 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662008178 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662008179 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 452662008180 recognition site for restriction enzyme PmeI 452662008181 Transposase, Mutator family; Region: Transposase_mut; pfam00872 452662008182 Transposase, Mutator family; Region: Transposase_mut; pfam00872 452662008183 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 452662008184 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; pfam07971 452662008185 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 452662008186 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 452662008187 Alpha-Mannosidase Binding Domain of Atg19/34; Region: ABD; cl15429 452662008188 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK06026 452662008189 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase, putative; Region: MTA/SAH-nuc-hyp; TIGR01705 452662008190 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 452662008191 active site 452662008192 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 452662008193 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 452662008194 cytochrome b; Provisional; Region: CYTB; MTH00191 452662008195 interchain domain interface [polypeptide binding]; other site 452662008196 intrachain domain interface; other site 452662008197 heme bH binding site [chemical binding]; other site 452662008198 Qi binding site; other site 452662008199 heme bL binding site [chemical binding]; other site 452662008200 Qo binding site; other site 452662008201 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cd00290 452662008202 interchain domain interface [polypeptide binding]; other site 452662008203 intrachain domain interface; other site 452662008204 Qi binding site; other site 452662008205 Qo binding site; other site 452662008206 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 452662008207 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 452662008208 [2Fe-2S] cluster binding site [ion binding]; other site 452662008209 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 452662008210 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 452662008211 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl17752 452662008212 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 452662008213 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 452662008214 Coenzyme A binding pocket [chemical binding]; other site 452662008215 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 452662008216 lipoate-protein ligase B; Provisional; Region: PRK14341 452662008217 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 452662008218 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 452662008219 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 452662008220 Ligand Binding Site [chemical binding]; other site 452662008221 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 452662008222 dimerization interface [polypeptide binding]; other site 452662008223 domain crossover interface; other site 452662008224 redox-dependent activation switch; other site 452662008225 ornithine carbamoyltransferase; Provisional; Region: PRK00779 452662008226 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 452662008227 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 452662008228 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 452662008229 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 452662008230 inhibitor-cofactor binding pocket; inhibition site 452662008231 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662008232 catalytic residue [active] 452662008233 Flagellar protein FliS; Region: FliS; cl00654 452662008234 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 452662008235 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 452662008236 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 452662008237 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 452662008238 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 452662008239 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 452662008240 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 452662008241 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 452662008242 flagellar biosynthetic protein FliO; Region: FliO_TIGR; TIGR03500 452662008243 flagellar motor switch protein FliN; Region: fliN; TIGR02480 452662008244 Flagellar motor switch protein FliM; Region: FliM; pfam02154 452662008245 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 452662008246 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 452662008247 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 452662008248 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 452662008249 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 452662008250 Walker A motif; other site 452662008251 ATP binding site [chemical binding]; other site 452662008252 Walker B motif; other site 452662008253 Flagellar assembly protein FliH; Region: FliH; pfam02108 452662008254 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 452662008255 MgtE intracellular N domain; Region: MgtE_N; smart00924 452662008256 FliG C-terminal domain; Region: FliG_C; pfam01706 452662008257 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 452662008258 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 452662008259 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 452662008260 Flagellar hook-basal body complex protein FliE; Region: FliE; pfam02049 452662008261 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 452662008262 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 452662008263 Walker A motif; other site 452662008264 ATP binding site [chemical binding]; other site 452662008265 Walker B motif; other site 452662008266 arginine finger; other site 452662008267 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 452662008268 flagellin; Provisional; Region: PRK12802 452662008269 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 452662008270 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 452662008271 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 452662008272 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 452662008273 glucosyltransferase MdoH; Provisional; Region: PRK05454 452662008274 active site 452662008275 Glycosyl transferase family 21; Region: Glyco_transf_21; pfam13506 452662008276 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 452662008277 RNA polymerase sigma factor, FliA/WhiG family; Region: FliA_WhiG; TIGR02479 452662008278 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 452662008279 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 452662008280 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 452662008281 DNA binding residues [nucleotide binding] 452662008282 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 452662008283 FHIPEP family; Region: FHIPEP; pfam00771 452662008284 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 452662008285 catalytic residue [active] 452662008286 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 452662008287 Anti-sigma-28 factor, FlgM; Region: FlgM; pfam04316 452662008288 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 452662008289 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 452662008290 OmpA family; Region: OmpA; pfam00691 452662008291 ligand binding site [chemical binding]; other site 452662008292 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 452662008293 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 452662008294 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 452662008295 flagellar basal-body rod protein FlgC; Region: FlgC; TIGR01395 452662008296 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 452662008297 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 452662008298 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 452662008299 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 452662008300 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 452662008301 flagellar hook-basal body protein; Region: FlgEFG_subfam; TIGR03506 452662008302 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 452662008303 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 452662008304 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 452662008305 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 452662008306 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12691 452662008307 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 452662008308 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 452662008309 Flagellar L-ring protein; Region: FlgH; pfam02107 452662008310 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 452662008311 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 452662008312 Rod binding protein; Region: Rod-binding; cl01626 452662008313 flagellar hook-associated protein FlgK; Region: flgK_ends; TIGR02492 452662008314 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 452662008315 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 452662008316 flagellar hook-associated protein 3; Region: flagell_flgL; TIGR02550 452662008317 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 452662008318 flagellar motor protein MotA; Validated; Region: PRK09110 452662008319 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 452662008320 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 452662008321 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 452662008322 ligand binding site [chemical binding]; other site 452662008323 HAMP domain; Region: HAMP; pfam00672 452662008324 dimerization interface [polypeptide binding]; other site 452662008325 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 452662008326 dimer interface [polypeptide binding]; other site 452662008327 phosphorylation site [posttranslational modification] 452662008328 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 452662008329 ATP binding site [chemical binding]; other site 452662008330 Mg2+ binding site [ion binding]; other site 452662008331 G-X-G motif; other site 452662008332 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 452662008333 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 452662008334 active site 452662008335 phosphorylation site [posttranslational modification] 452662008336 intermolecular recognition site; other site 452662008337 dimerization interface [polypeptide binding]; other site 452662008338 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 452662008339 DNA binding site [nucleotide binding] 452662008340 EF-hand domain pair; Region: EF_hand_5; pfam13499 452662008341 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 452662008342 Ca2+ binding site [ion binding]; other site 452662008343 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 452662008344 argininosuccinate synthase; Provisional; Region: PRK13820 452662008345 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 452662008346 ANP binding site [chemical binding]; other site 452662008347 Substrate Binding Site II [chemical binding]; other site 452662008348 Substrate Binding Site I [chemical binding]; other site 452662008349 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662008350 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662008351 LysR substrate binding domain; Region: LysR_substrate; pfam03466 452662008352 dimerization interface [polypeptide binding]; other site 452662008353 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 452662008354 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 452662008355 N-terminal plug; other site 452662008356 ligand-binding site [chemical binding]; other site 452662008357 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_9; cd04666 452662008358 nudix motif; other site 452662008359 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 452662008360 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 452662008361 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 452662008362 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 452662008363 non-specific DNA binding site [nucleotide binding]; other site 452662008364 salt bridge; other site 452662008365 sequence-specific DNA binding site [nucleotide binding]; other site 452662008366 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 452662008367 Domain of unknown function (DUF955); Region: DUF955; pfam06114 452662008368 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 452662008369 recognition site for restriction enzyme SwaI 452662008370 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 452662008371 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 452662008372 P-loop; other site 452662008373 Magnesium ion binding site [ion binding]; other site 452662008374 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 452662008375 Magnesium ion binding site [ion binding]; other site 452662008376 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 452662008377 DNA-binding site [nucleotide binding]; DNA binding site 452662008378 RNA-binding motif; other site 452662008379 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 452662008380 DNA-binding site [nucleotide binding]; DNA binding site 452662008381 RNA-binding motif; other site 452662008382 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 452662008383 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 452662008384 catalytic site [active] 452662008385 putative active site [active] 452662008386 putative substrate binding site [chemical binding]; other site 452662008387 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 452662008388 OstA-like protein; Region: OstA; pfam03968 452662008389 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 452662008390 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 452662008391 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 452662008392 active site 452662008393 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 452662008394 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 452662008395 putative active site [active] 452662008396 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 452662008397 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 452662008398 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 452662008399 putative NAD(P) binding site [chemical binding]; other site 452662008400 active site 452662008401 putative substrate binding site [chemical binding]; other site 452662008402 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 452662008403 Cupin-like domain; Region: Cupin_8; pfam13621 452662008404 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 452662008405 Protein of unknown function (DUF962); Region: DUF962; pfam06127 452662008406 beta-lactamase TEM; Provisional; Region: PRK15442 452662008407 Beta-lactamase enzyme family; Region: Beta-lactamase2; pfam13354 452662008408 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 452662008409 ligand binding site [chemical binding]; other site 452662008410 active site 452662008411 UGI interface [polypeptide binding]; other site 452662008412 catalytic site [active] 452662008413 Protein of unknown function, DUF488; Region: DUF488; pfam04343 452662008414 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 452662008415 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 452662008416 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 452662008417 Putative amidoligase enzyme (DUF2126); Region: DUF2126; pfam09899 452662008418 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4196 452662008419 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 452662008420 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 452662008421 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 452662008422 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 452662008423 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 452662008424 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 452662008425 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 452662008426 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 452662008427 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 452662008428 hexamer interface [polypeptide binding]; other site 452662008429 ligand binding site [chemical binding]; other site 452662008430 putative active site [active] 452662008431 NAD(P) binding site [chemical binding]; other site 452662008432 Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD; Region: Pro_isomerase; pfam00160 452662008433 active site 452662008434 integrase; Provisional; Region: PRK09692 452662008435 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 452662008436 active site 452662008437 Int/Topo IB signature motif; other site 452662008438 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 452662008439 DNA methylase; Region: N6_N4_Mtase; pfam01555 452662008440 DNA methylase; Region: N6_N4_Mtase; pfam01555 452662008441 Restriction endonuclease; Region: Mrr_cat; pfam04471 452662008442 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 452662008443 non-specific DNA binding site [nucleotide binding]; other site 452662008444 salt bridge; other site 452662008445 sequence-specific DNA binding site [nucleotide binding]; other site 452662008446 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 452662008447 Protein of unknown function (DUF3631); Region: DUF3631; pfam12307 452662008448 Helix-turn-helix domain; Region: HTH_17; pfam12728 452662008449 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662008450 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 452662008451 active site 452662008452 metal binding site [ion binding]; metal-binding site 452662008453 Epoxide hydrolase N terminus; Region: EHN; pfam06441 452662008454 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 452662008455 short chain dehydrogenase; Provisional; Region: PRK06180 452662008456 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 452662008457 NADP binding site [chemical binding]; other site 452662008458 active site 452662008459 steroid binding site; other site 452662008460 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662008461 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662008462 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 452662008463 dimerization interface [polypeptide binding]; other site 452662008464 Protein of unknown function (DUF1109); Region: DUF1109; cl02071 452662008465 RNA polymerase sigma factor; Provisional; Region: PRK12539 452662008466 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 452662008467 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 452662008468 DNA binding residues [nucleotide binding] 452662008469 short chain dehydrogenase; Provisional; Region: PRK06523 452662008470 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662008471 NAD(P) binding site [chemical binding]; other site 452662008472 active site 452662008473 SnoaL-like domain; Region: SnoaL_2; pfam12680 452662008474 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662008475 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662008476 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 452662008477 putative effector binding pocket; other site 452662008478 putative dimerization interface [polypeptide binding]; other site 452662008479 A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine...; Region: Peptidase_C39_likeA; cd02417 452662008480 type I secretion system ABC transporter, HlyB family; Region: type_I_sec_HlyB; TIGR01846 452662008481 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 452662008482 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662008483 Walker A/P-loop; other site 452662008484 ATP binding site [chemical binding]; other site 452662008485 Q-loop/lid; other site 452662008486 ABC transporter signature motif; other site 452662008487 Walker B; other site 452662008488 D-loop; other site 452662008489 H-loop/switch region; other site 452662008490 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 452662008491 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 452662008492 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662008493 RTX toxin acyltransferase family; Region: HlyC; pfam02794 452662008494 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 452662008495 Sel1-like repeats; Region: SEL1; smart00671 452662008496 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008497 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008498 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008499 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008500 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008501 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008502 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008503 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008504 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 452662008505 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008506 Src Homology 3 domain superfamily; Region: SH3; cl17036 452662008507 peptide ligand binding site [polypeptide binding]; other site 452662008508 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008509 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008510 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008511 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008512 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 452662008513 choice-of-anchor C domain; Region: choice_anch_C; TIGR04362 452662008514 choice-of-anchor C domain; Region: choice_anch_C; TIGR04362 452662008515 conjugal transfer relaxase TraA; Provisional; Region: PRK13889 452662008516 MobA/MobL family; Region: MobA_MobL; pfam03389 452662008517 AAA domain; Region: AAA_30; pfam13604 452662008518 Family description; Region: UvrD_C_2; pfam13538 452662008519 Conjugal transfer protein TraD; Region: TraD; cl05753 452662008520 Conjugal transfer protein TraD; Region: TraD; cl05753 452662008521 Higher Eukarytoes and Prokaryotes Nucleotide-binding domain; Region: HEPN; smart00748 452662008522 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 452662008523 ParB-like nuclease domain; Region: ParB; smart00470 452662008524 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 452662008525 TIR domain; Region: TIR_2; pfam13676 452662008526 radical SAM/SPASM domain, FxsB family; Region: SAM_SPASM_FxsB; TIGR04269 452662008527 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 452662008528 FeS/SAM binding site; other site 452662008529 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 452662008530 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 452662008531 HEXXH motif domain; Region: mod_HExxH; TIGR04267 452662008532 TIGR02646 family protein; Region: TIGR02646 452662008533 AAA domain; Region: AAA_23; pfam13476 452662008534 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662008535 AAA domain; Region: AAA_21; pfam13304 452662008536 Walker A/P-loop; other site 452662008537 ATP binding site [chemical binding]; other site 452662008538 anti-TRAP (AT) protein specific to Bacilli; Region: anti-TRAP; cd10748 452662008539 dodecamer interface 1 [polypeptide binding]; other site 452662008540 dodecamer interface 2 [polypeptide binding]; other site 452662008541 TRAP binding interface [polypeptide binding]; other site 452662008542 trimer interface [polypeptide binding]; other site 452662008543 Zn binding site [ion binding]; other site 452662008544 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662008545 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662008546 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662008547 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 452662008548 active site 452662008549 metal binding site [ion binding]; metal-binding site 452662008550 Domain of unknown function (DUF1905); Region: DUF1905; pfam08922 452662008551 integrase; Provisional; Region: PRK09692 452662008552 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 452662008553 active site 452662008554 Int/Topo IB signature motif; other site 452662008555 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 452662008556 DHH family; Region: DHH; pfam01368 452662008557 DHHA1 domain; Region: DHHA1; pfam02272 452662008558 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 452662008559 Multicopper oxidase; Region: Cu-oxidase; pfam00394 452662008560 Surface antigen; Region: Bac_surface_Ag; pfam01103 452662008561 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 452662008562 Family of unknown function (DUF490); Region: DUF490; pfam04357 452662008563 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 452662008564 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 452662008565 dimer interface [polypeptide binding]; other site 452662008566 putative CheW interface [polypeptide binding]; other site 452662008567 EamA-like transporter family; Region: EamA; pfam00892 452662008568 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 452662008569 putative active site [active] 452662008570 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 452662008571 Fumarase C-terminus; Region: Fumerase_C; pfam05683 452662008572 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 452662008573 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 452662008574 C-terminal domain interface [polypeptide binding]; other site 452662008575 GSH binding site (G-site) [chemical binding]; other site 452662008576 dimer interface [polypeptide binding]; other site 452662008577 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 452662008578 N-terminal domain interface [polypeptide binding]; other site 452662008579 dimer interface [polypeptide binding]; other site 452662008580 substrate binding pocket (H-site) [chemical binding]; other site 452662008581 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 452662008582 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 452662008583 Class I ribonucleotide reductase; Region: RNR_I; cd01679 452662008584 active site 452662008585 dimer interface [polypeptide binding]; other site 452662008586 catalytic residues [active] 452662008587 effector binding site; other site 452662008588 R2 peptide binding site; other site 452662008589 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 452662008590 putative active site [active] 452662008591 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 452662008592 dimer interface [polypeptide binding]; other site 452662008593 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 452662008594 putative radical transfer pathway; other site 452662008595 diiron center [ion binding]; other site 452662008596 tyrosyl radical; other site 452662008597 Transposase domain (DUF772); Region: DUF772; pfam05598 452662008598 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662008599 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 452662008600 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]; Region: COG1525 452662008601 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 452662008602 Catalytic site; other site 452662008603 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 452662008604 heme-binding site [chemical binding]; other site 452662008605 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_6; cd06154 452662008606 homotrimer interaction site [polypeptide binding]; other site 452662008607 putative active site [active] 452662008608 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 452662008609 ArsC family; Region: ArsC; pfam03960 452662008610 putative catalytic residues [active] 452662008611 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 452662008612 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 452662008613 active site 452662008614 catalytic site [active] 452662008615 Rrf2 family protein; Region: rrf2_super; TIGR00738 452662008616 Transcriptional regulator; Region: Rrf2; pfam02082 452662008617 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 452662008618 MAPEG family; Region: MAPEG; cl09190 452662008619 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 452662008620 putative phosphate acyltransferase; Provisional; Region: PRK05331 452662008621 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 452662008622 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 452662008623 dimer interface [polypeptide binding]; other site 452662008624 active site 452662008625 CoA binding pocket [chemical binding]; other site 452662008626 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 452662008627 IHF dimer interface [polypeptide binding]; other site 452662008628 IHF - DNA interface [nucleotide binding]; other site 452662008629 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 452662008630 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 452662008631 DNA binding residues [nucleotide binding] 452662008632 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; cd07040 452662008633 catalytic core [active] 452662008634 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 452662008635 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated; Region: PRK08074 452662008636 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 452662008637 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 452662008638 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 452662008639 active site 452662008640 nucleotide binding site [chemical binding]; other site 452662008641 HIGH motif; other site 452662008642 KMSKS motif; other site 452662008643 Domain of unknown function (DUF3315); Region: DUF3315; pfam11776 452662008644 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 452662008645 Domain of unknown function (DUF3315); Region: DUF3315; cl02275 452662008646 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]; Region: COG4251 452662008647 GAF domain; Region: GAF; pfam01590 452662008648 Phytochrome region; Region: PHY; pfam00360 452662008649 HWE histidine kinase; Region: HWE_HK; pfam07536 452662008650 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 452662008651 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 452662008652 active site 452662008653 phosphorylation site [posttranslational modification] 452662008654 intermolecular recognition site; other site 452662008655 dimerization interface [polypeptide binding]; other site 452662008656 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 452662008657 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 452662008658 putative active site [active] 452662008659 metal binding site [ion binding]; metal-binding site 452662008660 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 452662008661 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 452662008662 catalytic loop [active] 452662008663 iron binding site [ion binding]; other site 452662008664 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 452662008665 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 452662008666 aminotransferase; Validated; Region: PRK09148 452662008667 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 452662008668 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662008669 homodimer interface [polypeptide binding]; other site 452662008670 catalytic residue [active] 452662008671 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 452662008672 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 452662008673 Phasin protein; Region: Phasin_2; pfam09361 452662008674 Uncharacterized conserved protein [Function unknown]; Region: COG2127 452662008675 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 452662008676 Major Facilitator Superfamily; Region: MFS_1; pfam07690 452662008677 putative substrate translocation pore; other site 452662008678 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 452662008679 Prostaglandin dehydrogenases; Region: PGDH; cd05288 452662008680 NAD(P) binding site [chemical binding]; other site 452662008681 substrate binding site [chemical binding]; other site 452662008682 dimer interface [polypeptide binding]; other site 452662008683 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 452662008684 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 452662008685 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662008686 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662008687 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662008688 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662008689 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 452662008690 dimerization interface [polypeptide binding]; other site 452662008691 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 452662008692 allantoinase; Region: allantoinase; TIGR03178 452662008693 active site 452662008694 allantoate amidohydrolase; Reviewed; Region: PRK09290 452662008695 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 452662008696 active site 452662008697 metal binding site [ion binding]; metal-binding site 452662008698 dimer interface [polypeptide binding]; other site 452662008699 metabolite-proton symporter; Region: 2A0106; TIGR00883 452662008700 urocanate hydratase; Provisional; Region: PRK05414 452662008701 Protein of unknown function (DUF917); Region: DUF917; pfam06032 452662008702 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 452662008703 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 452662008704 FMN binding site [chemical binding]; other site 452662008705 substrate binding site [chemical binding]; other site 452662008706 putative catalytic residue [active] 452662008707 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662008708 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662008709 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 452662008710 N-terminal plug; other site 452662008711 ligand-binding site [chemical binding]; other site 452662008712 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 452662008713 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 452662008714 active site 452662008715 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 452662008716 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 452662008717 DNA/RNA non-specific endonuclease; Region: Endonuclea_NS_2; cl17626 452662008718 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 452662008719 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 452662008720 excinuclease ABC subunit B; Provisional; Region: PRK05298 452662008721 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 452662008722 ATP binding site [chemical binding]; other site 452662008723 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 452662008724 nucleotide binding region [chemical binding]; other site 452662008725 ATP-binding site [chemical binding]; other site 452662008726 Ultra-violet resistance protein B; Region: UvrB; pfam12344 452662008727 UvrB/uvrC motif; Region: UVR; pfam02151 452662008728 recombinase A; Provisional; Region: recA; PRK09354 452662008729 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 452662008730 hexamer interface [polypeptide binding]; other site 452662008731 Walker A motif; other site 452662008732 ATP binding site [chemical binding]; other site 452662008733 Walker B motif; other site 452662008734 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 452662008735 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 452662008736 active site 452662008737 phosphorylation site [posttranslational modification] 452662008738 intermolecular recognition site; other site 452662008739 dimerization interface [polypeptide binding]; other site 452662008740 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 452662008741 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 452662008742 dimer interface [polypeptide binding]; other site 452662008743 phosphorylation site [posttranslational modification] 452662008744 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 452662008745 ATP binding site [chemical binding]; other site 452662008746 Mg2+ binding site [ion binding]; other site 452662008747 G-X-G motif; other site 452662008748 Response regulator receiver domain; Region: Response_reg; pfam00072 452662008749 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 452662008750 active site 452662008751 phosphorylation site [posttranslational modification] 452662008752 intermolecular recognition site; other site 452662008753 dimerization interface [polypeptide binding]; other site 452662008754 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 452662008755 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 452662008756 SmpB-tmRNA interface; other site 452662008757 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 452662008758 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 452662008759 dimer interface [polypeptide binding]; other site 452662008760 active site 452662008761 catalytic residue [active] 452662008762 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 452662008763 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 452662008764 N-acetyl-D-glucosamine binding site [chemical binding]; other site 452662008765 catalytic residue [active] 452662008766 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 452662008767 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 452662008768 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 452662008769 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 452662008770 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 452662008771 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 452662008772 dimer interface [polypeptide binding]; other site 452662008773 anticodon binding site; other site 452662008774 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 452662008775 homodimer interface [polypeptide binding]; other site 452662008776 motif 1; other site 452662008777 active site 452662008778 motif 2; other site 452662008779 GAD domain; Region: GAD; pfam02938 452662008780 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 452662008781 active site 452662008782 motif 3; other site 452662008783 ribonuclease D; Region: rnd; TIGR01388 452662008784 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 452662008785 catalytic site [active] 452662008786 putative active site [active] 452662008787 putative substrate binding site [chemical binding]; other site 452662008788 HRDC domain; Region: HRDC; pfam00570 452662008789 Peptidase inhibitor I78 family; Region: Inhibitor_I78; pfam11720 452662008790 Bacterial PH domain; Region: DUF304; pfam03703 452662008791 putative addiction module antidote; Region: doc_partner; TIGR02609 452662008792 Prophage maintenance system killer protein [General function prediction only]; Region: Doc; COG3654 452662008793 GTP-binding protein LepA; Provisional; Region: PRK05433 452662008794 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 452662008795 G1 box; other site 452662008796 putative GEF interaction site [polypeptide binding]; other site 452662008797 GTP/Mg2+ binding site [chemical binding]; other site 452662008798 Switch I region; other site 452662008799 G2 box; other site 452662008800 G3 box; other site 452662008801 Switch II region; other site 452662008802 G4 box; other site 452662008803 G5 box; other site 452662008804 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 452662008805 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 452662008806 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 452662008807 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 452662008808 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 452662008809 non-specific DNA binding site [nucleotide binding]; other site 452662008810 salt bridge; other site 452662008811 sequence-specific DNA binding site [nucleotide binding]; other site 452662008812 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662008813 This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core; Region: GT1_wlbH_like; cd03798 452662008814 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 452662008815 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662008816 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 452662008817 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 452662008818 molybdopterin cofactor binding site; other site 452662008819 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 452662008820 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 452662008821 Eukaryotic phosphomannomutase; Region: PMM; cl17107 452662008822 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 452662008823 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 452662008824 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 452662008825 putative PBP binding loops; other site 452662008826 ABC-ATPase subunit interface; other site 452662008827 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 452662008828 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662008829 Walker A/P-loop; other site 452662008830 ATP binding site [chemical binding]; other site 452662008831 Q-loop/lid; other site 452662008832 ABC transporter signature motif; other site 452662008833 Walker B; other site 452662008834 D-loop; other site 452662008835 H-loop/switch region; other site 452662008836 Phosphotransferase enzyme family; Region: APH; pfam01636 452662008837 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 452662008838 active site 452662008839 ATP binding site [chemical binding]; other site 452662008840 Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]; Region: KpsS; COG3562 452662008841 Capsule polysaccharide biosynthesis protein; Region: Capsule_synth; pfam05159 452662008842 Capsule polysaccharide biosynthesis protein; Region: Capsule_synth; pfam05159 452662008843 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 452662008844 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662008845 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 452662008846 HIT family signature motif; other site 452662008847 catalytic residue [active] 452662008848 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 452662008849 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 452662008850 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662008851 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662008852 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 452662008853 dimerization interface [polypeptide binding]; other site 452662008854 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional; Region: PRK11840 452662008855 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 452662008856 thiS-thiF/thiG interaction site; other site 452662008857 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 452662008858 ThiS interaction site; other site 452662008859 putative active site [active] 452662008860 tetramer interface [polypeptide binding]; other site 452662008861 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 452662008862 Dehydroquinase class II; Region: DHquinase_II; pfam01220 452662008863 trimer interface [polypeptide binding]; other site 452662008864 active site 452662008865 dimer interface [polypeptide binding]; other site 452662008866 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 452662008867 carboxyltransferase (CT) interaction site; other site 452662008868 biotinylation site [posttranslational modification]; other site 452662008869 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 452662008870 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 452662008871 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 452662008872 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 452662008873 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 452662008874 ArsC family; Region: ArsC; pfam03960 452662008875 catalytic residues [active] 452662008876 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 452662008877 GIY-YIG motif/motif A; other site 452662008878 putative active site [active] 452662008879 putative metal binding site [ion binding]; other site 452662008880 DNA polymerase I; Provisional; Region: PRK05755 452662008881 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 452662008882 active site 452662008883 metal binding site 1 [ion binding]; metal-binding site 452662008884 putative 5' ssDNA interaction site; other site 452662008885 metal binding site 3; metal-binding site 452662008886 metal binding site 2 [ion binding]; metal-binding site 452662008887 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 452662008888 putative DNA binding site [nucleotide binding]; other site 452662008889 putative metal binding site [ion binding]; other site 452662008890 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 452662008891 active site 452662008892 catalytic site [active] 452662008893 substrate binding site [chemical binding]; other site 452662008894 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 452662008895 active site 452662008896 DNA binding site [nucleotide binding] 452662008897 catalytic site [active] 452662008898 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 452662008899 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 452662008900 Substrate binding site; other site 452662008901 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 452662008902 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3809 452662008903 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 452662008904 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 452662008905 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 452662008906 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 452662008907 active site 452662008908 HIGH motif; other site 452662008909 nucleotide binding site [chemical binding]; other site 452662008910 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 452662008911 active site 452662008912 KMSKS motif; other site 452662008913 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 452662008914 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 452662008915 AAA domain; Region: AAA_31; pfam13614 452662008916 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 452662008917 P-loop; other site 452662008918 Magnesium ion binding site [ion binding]; other site 452662008919 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 452662008920 Magnesium ion binding site [ion binding]; other site 452662008921 PAS domain; Region: PAS_9; pfam13426 452662008922 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 452662008923 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662008924 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662008925 metal binding site [ion binding]; metal-binding site 452662008926 active site 452662008927 I-site; other site 452662008928 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 452662008929 acyl-CoA synthetase; Validated; Region: PRK09192 452662008930 Fatty acyl-AMP ligase (FAAL); Region: FAAL; cd05931 452662008931 acyl-activating enzyme (AAE) consensus motif; other site 452662008932 active site 452662008933 RecX family; Region: RecX; pfam02631 452662008934 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 452662008935 NADH dehydrogenase; Validated; Region: PRK08183 452662008936 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 452662008937 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 452662008938 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 452662008939 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 452662008940 active site 452662008941 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 452662008942 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 452662008943 active site 452662008944 (T/H)XGH motif; other site 452662008945 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 452662008946 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 452662008947 substrate binding pocket [chemical binding]; other site 452662008948 chain length determination region; other site 452662008949 substrate-Mg2+ binding site; other site 452662008950 catalytic residues [active] 452662008951 aspartate-rich region 1; other site 452662008952 active site lid residues [active] 452662008953 aspartate-rich region 2; other site 452662008954 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 452662008955 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 452662008956 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 452662008957 dimerization interface [polypeptide binding]; other site 452662008958 ATP binding site [chemical binding]; other site 452662008959 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 452662008960 dimerization interface [polypeptide binding]; other site 452662008961 ATP binding site [chemical binding]; other site 452662008962 Dienelactone hydrolase family; Region: DLH; pfam01738 452662008963 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 452662008964 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 452662008965 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 452662008966 active site 452662008967 Zn binding site [ion binding]; other site 452662008968 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 452662008969 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 452662008970 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 452662008971 motif II; other site 452662008972 pyruvate kinase; Provisional; Region: PRK06247 452662008973 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 452662008974 domain interfaces; other site 452662008975 active site 452662008976 Protein of unknown function (DUF1244); Region: DUF1244; cl01385 452662008977 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; pfam10073 452662008978 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 452662008979 hypothetical protein; Validated; Region: PRK00110 452662008980 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 452662008981 active site 452662008982 putative DNA-binding cleft [nucleotide binding]; other site 452662008983 dimer interface [polypeptide binding]; other site 452662008984 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 452662008985 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 452662008986 HerA helicase [Replication, recombination, and repair]; Region: COG0433 452662008987 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 452662008988 Low molecular weight phosphatase family; Region: LMWPc; cd00115 452662008989 active site 452662008990 S1/P1 nucleases and related enzymes; Region: S1-P1_nuclease; cd11010 452662008991 active site 452662008992 Zn binding site [ion binding]; other site 452662008993 potential frameshift: common BLAST hit: gi|148550571|ref|YP_001260010.1| TonB-dependent receptor 452662008994 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 452662008995 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662008996 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 452662008997 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 452662008998 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 452662008999 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 452662009000 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 452662009001 FAD binding domain in molybdopterin dehydrogenase; Region: FAD_binding_5; pfam00941 452662009002 aldehyde oxidoreductase 2Fe-2S subunit; Provisional; Region: PRK11433 452662009003 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 452662009004 catalytic loop [active] 452662009005 iron binding site [ion binding]; other site 452662009006 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 452662009007 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 452662009008 ThiC-associated domain; Region: ThiC-associated; pfam13667 452662009009 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 452662009010 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 452662009011 acetyl-CoA synthetase; Provisional; Region: PRK00174 452662009012 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 452662009013 active site 452662009014 CoA binding site [chemical binding]; other site 452662009015 acyl-activating enzyme (AAE) consensus motif; other site 452662009016 AMP binding site [chemical binding]; other site 452662009017 acetate binding site [chemical binding]; other site 452662009018 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 452662009019 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 452662009020 C-terminal domain interface [polypeptide binding]; other site 452662009021 GSH binding site (G-site) [chemical binding]; other site 452662009022 dimer interface [polypeptide binding]; other site 452662009023 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 452662009024 N-terminal domain interface [polypeptide binding]; other site 452662009025 dimer interface [polypeptide binding]; other site 452662009026 substrate binding pocket (H-site) [chemical binding]; other site 452662009027 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662009028 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662009029 metal binding site [ion binding]; metal-binding site 452662009030 active site 452662009031 I-site; other site 452662009032 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 452662009033 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662009034 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662009035 dimerization interface [polypeptide binding]; other site 452662009036 AAA family ATPase, CDC48 subfamily; Region: CDC48; TIGR01243 452662009037 Cell division protein 48 (CDC48), N-terminal domain; Region: CDC48_N; pfam02359 452662009038 Cell division protein 48 (CDC48), domain 2; Region: CDC48_2; pfam02933 452662009039 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 452662009040 Walker A motif; other site 452662009041 ATP binding site [chemical binding]; other site 452662009042 Walker B motif; other site 452662009043 arginine finger; other site 452662009044 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 452662009045 Walker A motif; other site 452662009046 ATP binding site [chemical binding]; other site 452662009047 Walker B motif; other site 452662009048 arginine finger; other site 452662009049 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 452662009050 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 452662009051 putative catalytic cysteine [active] 452662009052 DDE superfamily endonuclease; Region: DDE_3; pfam13358 452662009053 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 452662009054 Winged helix-turn helix; Region: HTH_29; pfam13551 452662009055 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 452662009056 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 452662009057 Cytochrome P450; Region: p450; cl12078 452662009058 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 452662009059 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 452662009060 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 452662009061 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 452662009062 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 452662009063 homodimer interface [polypeptide binding]; other site 452662009064 substrate-cofactor binding pocket; other site 452662009065 catalytic residue [active] 452662009066 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 452662009067 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 452662009068 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 452662009069 catalytic residue [active] 452662009070 EamA-like transporter family; Region: EamA; pfam00892 452662009071 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 452662009072 EamA-like transporter family; Region: EamA; pfam00892 452662009073 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 452662009074 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662009075 NAD(P) binding site [chemical binding]; other site 452662009076 active site 452662009077 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 452662009078 FeS assembly SUF system protein; Region: SUF_assoc; TIGR02945 452662009079 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 452662009080 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 452662009081 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 452662009082 catalytic residue [active] 452662009083 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 452662009084 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 452662009085 FeS assembly ATPase SufC; Region: sufC; TIGR01978 452662009086 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 452662009087 Walker A/P-loop; other site 452662009088 ATP binding site [chemical binding]; other site 452662009089 Q-loop/lid; other site 452662009090 ABC transporter signature motif; other site 452662009091 Walker B; other site 452662009092 D-loop; other site 452662009093 H-loop/switch region; other site 452662009094 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 452662009095 putative active site [active] 452662009096 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 452662009097 putative ABC transporter; Region: ycf24; CHL00085 452662009098 Rrf2 family protein; Region: rrf2_super; TIGR00738 452662009099 Transcriptional regulator; Region: Rrf2; pfam02082 452662009100 Helix-turn-helix domain; Region: HTH_18; pfam12833 452662009101 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 452662009102 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 452662009103 quinone interaction residues [chemical binding]; other site 452662009104 active site 452662009105 catalytic residues [active] 452662009106 FMN binding site [chemical binding]; other site 452662009107 substrate binding site [chemical binding]; other site 452662009108 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 452662009109 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 452662009110 Fe-S metabolism associated domain; Region: SufE; cl00951 452662009111 phage shock protein C; Region: phageshock_pspC; TIGR02978 452662009112 PspC domain; Region: PspC; pfam04024 452662009113 Phage shock protein B; Region: PspB; cl05946 452662009114 phage shock protein A; Region: phageshock_pspA; TIGR02977 452662009115 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 452662009116 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 452662009117 Walker A motif; other site 452662009118 ATP binding site [chemical binding]; other site 452662009119 Walker B motif; other site 452662009120 arginine finger; other site 452662009121 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 452662009122 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK07530 452662009123 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 452662009124 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662009125 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 452662009126 active site 452662009127 TolQ protein; Region: tolQ; TIGR02796 452662009128 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 452662009129 TolR protein; Region: tolR; TIGR02801 452662009130 translocation protein TolB; Provisional; Region: tolB; PRK05137 452662009131 TolB amino-terminal domain; Region: TolB_N; pfam04052 452662009132 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 452662009133 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 452662009134 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 452662009135 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 452662009136 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 452662009137 ligand binding site [chemical binding]; other site 452662009138 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 452662009139 HlyD family secretion protein; Region: HlyD; pfam00529 452662009140 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 452662009141 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662009142 Protein of unknown function (DUF1656); Region: DUF1656; pfam07869 452662009143 Fusaric acid resistance protein family; Region: FUSC; pfam04632 452662009144 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 452662009145 may be target duplication site 452662009146 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662009147 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662009148 Integrase core domain; Region: rve; pfam00665 452662009149 may be target duplication site 452662009150 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662009151 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662009152 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662009153 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 452662009154 addiction module antitoxin, RelB/DinJ family; Region: RelB_DinJ; TIGR02384 452662009155 DDE domain; Region: DDE_Tnp_IS240; pfam13610 452662009156 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662009157 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662009158 Integrase core domain; Region: rve; pfam00665 452662009159 MarR family; Region: MarR_2; pfam12802 452662009160 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 452662009161 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 452662009162 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 452662009163 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 452662009164 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 452662009165 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 452662009166 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 452662009167 PA_M28_1_1: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 1. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_1; cd04820 452662009168 PA/protease or protease-like domain interface [polypeptide binding]; other site 452662009169 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_2; cd05661 452662009170 Peptidase family M28; Region: Peptidase_M28; pfam04389 452662009171 metal binding site [ion binding]; metal-binding site 452662009172 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 452662009173 Clp amino terminal domain; Region: Clp_N; pfam02861 452662009174 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 452662009175 Walker A motif; other site 452662009176 ATP binding site [chemical binding]; other site 452662009177 Walker B motif; other site 452662009178 arginine finger; other site 452662009179 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 452662009180 Walker A motif; other site 452662009181 ATP binding site [chemical binding]; other site 452662009182 Walker B motif; other site 452662009183 arginine finger; other site 452662009184 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 452662009185 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 452662009186 binding surface 452662009187 TPR motif; other site 452662009188 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 452662009189 binding surface 452662009190 TPR motif; other site 452662009191 Sulfotransferase family; Region: Sulfotransfer_3; pfam13469 452662009192 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 452662009193 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662009194 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 452662009195 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 452662009196 Peptidase family M23; Region: Peptidase_M23; pfam01551 452662009197 Uncharacterized protein conserved in bacteria (DUF2093); Region: DUF2093; pfam09866 452662009198 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 452662009199 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 452662009200 generic binding surface II; other site 452662009201 generic binding surface I; other site 452662009202 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 452662009203 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 452662009204 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 452662009205 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 452662009206 Uncharacterized conserved protein [Function unknown]; Region: COG3743 452662009207 Fucose 4-O-acetylase and related acetyltransferases [Carbohydrate transport and metabolism]; Region: NolL; COG3594 452662009208 Acyltransferase family; Region: Acyl_transf_3; pfam01757 452662009209 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 452662009210 active site 452662009211 catalytic triad [active] 452662009212 oxyanion hole [active] 452662009213 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 452662009214 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 452662009215 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 452662009216 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 452662009217 23S rRNA binding site [nucleotide binding]; other site 452662009218 L21 binding site [polypeptide binding]; other site 452662009219 L13 binding site [polypeptide binding]; other site 452662009220 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 452662009221 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 452662009222 GIY-YIG motif/motif A; other site 452662009223 putative active site [active] 452662009224 putative metal binding site [ion binding]; other site 452662009225 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 452662009226 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 452662009227 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 452662009228 dimer interface [polypeptide binding]; other site 452662009229 motif 1; other site 452662009230 active site 452662009231 motif 2; other site 452662009232 motif 3; other site 452662009233 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 452662009234 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 452662009235 putative tRNA-binding site [nucleotide binding]; other site 452662009236 B3/4 domain; Region: B3_4; pfam03483 452662009237 tRNA synthetase B5 domain; Region: B5; smart00874 452662009238 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 452662009239 dimer interface [polypeptide binding]; other site 452662009240 motif 1; other site 452662009241 motif 3; other site 452662009242 motif 2; other site 452662009243 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; smart00896 452662009244 Domain of unknown function (DUF4386); Region: DUF4386; pfam14329 452662009245 Aldose 1-epimerase, similar to Lactococcus lactis lacX; Region: Aldose_epim_lacX; cd09024 452662009246 active site 452662009247 catalytic residues [active] 452662009248 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 452662009249 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 452662009250 G1 box; other site 452662009251 putative GEF interaction site [polypeptide binding]; other site 452662009252 GTP/Mg2+ binding site [chemical binding]; other site 452662009253 Switch I region; other site 452662009254 G2 box; other site 452662009255 G3 box; other site 452662009256 Switch II region; other site 452662009257 G4 box; other site 452662009258 G5 box; other site 452662009259 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 452662009260 hypothetical protein; Provisional; Region: PRK07064 452662009261 Protein of unknown function (DUF1134); Region: DUF1134; pfam06577 452662009262 Y-family of DNA polymerases; Region: PolY; cl12025 452662009263 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 452662009264 active site 452662009265 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 452662009266 Ubiquinol-cytochrome C chaperone; Region: Ubiq_cyt_C_chap; cl12045 452662009267 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 452662009268 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 452662009269 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 452662009270 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662009271 NAD(P) binding site [chemical binding]; other site 452662009272 active site 452662009273 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 452662009274 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 452662009275 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 452662009276 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 452662009277 active site 452662009278 metal binding site [ion binding]; metal-binding site 452662009279 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662009280 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 452662009281 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 452662009282 sulfotransferase; Region: PLN02164 452662009283 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662009284 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 452662009285 putative ADP-binding pocket [chemical binding]; other site 452662009286 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; pfam10082 452662009287 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 452662009288 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 452662009289 SLBB domain; Region: SLBB; pfam10531 452662009290 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 452662009291 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 452662009292 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 452662009293 inhibitor-cofactor binding pocket; inhibition site 452662009294 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662009295 catalytic residue [active] 452662009296 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 452662009297 Polysaccharide biosynthesis protein; Region: Polysacc_synt_2; pfam02719 452662009298 NAD(P) binding site [chemical binding]; other site 452662009299 homodimer interface [polypeptide binding]; other site 452662009300 substrate binding site [chemical binding]; other site 452662009301 active site 452662009302 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 452662009303 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662009304 putative ADP-binding pocket [chemical binding]; other site 452662009305 Bacterial sugar transferase; Region: Bac_transf; pfam02397 452662009306 Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]; Region: Fmt; COG0223 452662009307 Formyl transferase catalytic core domain found in a group of proteins with unknown functions; Region: FMT_core_like_4; cd08651 452662009308 putative active site [active] 452662009309 putative substrate binding site [chemical binding]; other site 452662009310 putative cosubstrate binding site; other site 452662009311 catalytic site [active] 452662009312 C-terminal subdomain of the formyltransferase domain on ArnA, which modifies lipid A with 4-amino-4-deoxy-l-arabinose; Region: Arna_FMT_C; cd08702 452662009313 active site 452662009314 hexamer interface [polypeptide binding]; other site 452662009315 Uncharacterized proteins, LmbE homologs [Function unknown]; Region: COG2120 452662009316 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 452662009317 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 452662009318 active site 452662009319 phosphorylation site [posttranslational modification] 452662009320 dimerization interface [polypeptide binding]; other site 452662009321 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 452662009322 DNA binding residues [nucleotide binding] 452662009323 dimerization interface [polypeptide binding]; other site 452662009324 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 452662009325 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 452662009326 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 452662009327 Ca2+ binding site [ion binding]; other site 452662009328 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 452662009329 Ca2+ binding site [ion binding]; other site 452662009330 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 452662009331 Ca2+ binding site [ion binding]; other site 452662009332 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 452662009333 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662009334 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 452662009335 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662009336 Walker A/P-loop; other site 452662009337 ATP binding site [chemical binding]; other site 452662009338 Q-loop/lid; other site 452662009339 ABC transporter signature motif; other site 452662009340 Walker B; other site 452662009341 D-loop; other site 452662009342 H-loop/switch region; other site 452662009343 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 452662009344 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662009345 Pectate lyase; Region: Pec_lyase_C; cl01593 452662009346 Chain length determinant protein; Region: Wzz; pfam02706 452662009347 exopolysaccharide transport protein family; Region: eps_transp_fam; TIGR01005 452662009348 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 452662009349 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 452662009350 DNA binding residues [nucleotide binding] 452662009351 dimerization interface [polypeptide binding]; other site 452662009352 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 452662009353 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 452662009354 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 452662009355 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 452662009356 Malic enzyme, N-terminal domain; Region: malic; pfam00390 452662009357 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 452662009358 putative NAD(P) binding site [chemical binding]; other site 452662009359 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 452662009360 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 452662009361 MutS domain I; Region: MutS_I; pfam01624 452662009362 MutS domain II; Region: MutS_II; pfam05188 452662009363 MutS domain III; Region: MutS_III; pfam05192 452662009364 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 452662009365 Walker A/P-loop; other site 452662009366 ATP binding site [chemical binding]; other site 452662009367 Q-loop/lid; other site 452662009368 ABC transporter signature motif; other site 452662009369 Walker B; other site 452662009370 D-loop; other site 452662009371 H-loop/switch region; other site 452662009372 PII uridylyl-transferase; Provisional; Region: PRK05092 452662009373 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 452662009374 metal binding triad; other site 452662009375 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 452662009376 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 452662009377 Zn2+ binding site [ion binding]; other site 452662009378 Mg2+ binding site [ion binding]; other site 452662009379 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_UUR-like_1; cd04900 452662009380 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_ACR-UUR-like_2; cd04899 452662009381 Winged helix-turn helix; Region: HTH_29; pfam13551 452662009382 DDE superfamily endonuclease; Region: DDE_3; pfam13358 452662009383 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 452662009384 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3786 452662009385 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 452662009386 dimerization interface [polypeptide binding]; other site 452662009387 active site 452662009388 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 452662009389 putative catalytic site [active] 452662009390 putative phosphate binding site [ion binding]; other site 452662009391 active site 452662009392 metal binding site A [ion binding]; metal-binding site 452662009393 DNA binding site [nucleotide binding] 452662009394 putative AP binding site [nucleotide binding]; other site 452662009395 putative metal binding site B [ion binding]; other site 452662009396 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 452662009397 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 452662009398 DsrE/DsrF/DrsH-like family; Region: DrsE_2; cl17453 452662009399 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 452662009400 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 452662009401 ATP binding site [chemical binding]; other site 452662009402 substrate interface [chemical binding]; other site 452662009403 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 452662009404 trimer interface [polypeptide binding]; other site 452662009405 active site 452662009406 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 452662009407 Flavoprotein; Region: Flavoprotein; pfam02441 452662009408 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 452662009409 ergothioneine biosynthesis protein EgtB; Region: egtB_TIGR03440 452662009410 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 452662009411 dimethylhistidine N-methyltransferase; Region: egtD_ergothio; TIGR03438 452662009412 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 452662009413 Protein of unknown function (DUF1176); Region: DUF1176; pfam06674 452662009414 nucleoside transporter; Region: nupC; TIGR00804 452662009415 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 452662009416 Nucleoside recognition; Region: Gate; pfam07670 452662009417 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 452662009418 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 452662009419 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 452662009420 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 452662009421 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 452662009422 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 452662009423 Coenzyme A binding pocket [chemical binding]; other site 452662009424 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 452662009425 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 452662009426 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 452662009427 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 452662009428 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 452662009429 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 452662009430 active site 452662009431 substrate binding site [chemical binding]; other site 452662009432 metal binding site [ion binding]; metal-binding site 452662009433 DnaJ chaperone protein; Provisional; Region: PTZ00100 452662009434 ATPase MipZ; Region: MipZ; pfam09140 452662009435 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 452662009436 P-loop; other site 452662009437 Magnesium ion binding site [ion binding]; other site 452662009438 pantoate--beta-alanine ligase; Region: panC; TIGR00018 452662009439 Pantoate-beta-alanine ligase; Region: PanC; cd00560 452662009440 active site 452662009441 ATP-binding site [chemical binding]; other site 452662009442 pantoate-binding site; other site 452662009443 HXXH motif; other site 452662009444 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 452662009445 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 452662009446 substrate binding site [chemical binding]; other site 452662009447 active site 452662009448 Initiator Replication protein; Region: Rep_3; pfam01051 452662009449 plasmid partitioning protein RepA; Region: partition_RepA; TIGR03453 452662009450 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 452662009451 DNA binding residues [nucleotide binding] 452662009452 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 452662009453 P-loop; other site 452662009454 Magnesium ion binding site [ion binding]; other site 452662009455 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 452662009456 Magnesium ion binding site [ion binding]; other site 452662009457 ParB-like nuclease domain; Region: ParBc; pfam02195 452662009458 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 452662009459 RES domain; Region: RES; smart00953 452662009460 Protein of unknown function (DUF2384); Region: DUF2384; cl17718 452662009461 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 452662009462 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 452662009463 multiple promoter invertase; Provisional; Region: mpi; PRK13413 452662009464 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 452662009465 catalytic residues [active] 452662009466 catalytic nucleophile [active] 452662009467 Presynaptic Site I dimer interface [polypeptide binding]; other site 452662009468 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 452662009469 Synaptic Flat tetramer interface [polypeptide binding]; other site 452662009470 Synaptic Site I dimer interface [polypeptide binding]; other site 452662009471 DNA binding site [nucleotide binding] 452662009472 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 452662009473 DNA-binding interface [nucleotide binding]; DNA binding site 452662009474 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 452662009475 classical (c) SDRs; Region: SDR_c; cd05233 452662009476 NAD(P) binding site [chemical binding]; other site 452662009477 active site 452662009478 Domain of unknown function (DUF4415); Region: DUF4415; pfam14384 452662009479 Protein of unknown function (DUF497); Region: DUF497; pfam04365 452662009480 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662009481 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662009482 Integrase core domain; Region: rve; pfam00665 452662009483 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 452662009484 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 452662009485 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 452662009486 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 452662009487 non-specific DNA binding site [nucleotide binding]; other site 452662009488 salt bridge; other site 452662009489 sequence-specific DNA binding site [nucleotide binding]; other site 452662009490 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 452662009491 N-acetyl-D-glucosamine binding site [chemical binding]; other site 452662009492 catalytic residue [active] 452662009493 may be target duplication site 452662009494 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662009495 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662009496 Integrase core domain; Region: rve; pfam00665 452662009497 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 452662009498 may be target duplication site 452662009499 recognition site for restriction enzyme PmeI 452662009500 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 452662009501 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 452662009502 active site 452662009503 DNA binding site [nucleotide binding] 452662009504 Int/Topo IB signature motif; other site 452662009505 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 452662009506 catalytic core [active] 452662009507 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 452662009508 RelB antitoxin; Region: RelB; cl01171 452662009509 SprT-like family; Region: SprT-like; pfam10263 452662009510 recognition site for restriction enzyme PmeI 452662009511 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 452662009512 ParA-like protein; Provisional; Region: PHA02518 452662009513 P-loop; other site 452662009514 Magnesium ion binding site [ion binding]; other site 452662009515 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 452662009516 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 452662009517 Coenzyme A binding pocket [chemical binding]; other site 452662009518 Replication initiator protein A; Region: RPA; cl17860 452662009519 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662009520 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662009521 Integrase core domain; Region: rve; pfam00665 452662009522 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 452662009523 Active Sites [active] 452662009524 2-oxoacid ferredoxin oxidoreductase; Provisional; Region: PRK13030 452662009525 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 452662009526 cofactor binding site; other site 452662009527 DNA binding site [nucleotide binding] 452662009528 substrate interaction site [chemical binding]; other site 452662009529 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 452662009530 Protein of unknown function (DUF1778); Region: DUF1778; pfam08681 452662009531 PIN domain of the VapC-like UPF0110 protein Mb0640 and homologs; Region: PIN_UPF0110; cd09871 452662009532 putative active site [active] 452662009533 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 452662009534 Protein of unknown function (DUF1778); Region: DUF1778; pfam08681 452662009535 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 452662009536 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 452662009537 Methyltransferase domain; Region: Methyltransf_26; pfam13659 452662009538 P-loop containing NTP hydrolase pore-1; Region: AAA_34; pfam13872 452662009539 DEAD-like helicases superfamily; Region: DEXDc; smart00487 452662009540 Helicase_C-like; Region: Helicase_C_4; pfam13871 452662009541 ParB-like nuclease domain; Region: ParB; smart00470 452662009542 Toprim domain; Region: Toprim_3; pfam13362 452662009543 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 452662009544 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 452662009545 putative active site [active] 452662009546 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 452662009547 DNA binding residues [nucleotide binding] 452662009548 Autoinducer synthetase; Region: Autoind_synth; cl17404 452662009549 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 452662009550 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 452662009551 IHF dimer interface [polypeptide binding]; other site 452662009552 IHF - DNA interface [nucleotide binding]; other site 452662009553 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 452662009554 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 452662009555 putative NAD(P) binding site [chemical binding]; other site 452662009556 Protein of unknown function (DUF1810); Region: DUF1810; cl02370 452662009557 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 452662009558 PIN domain of the VapC-like Sll0205 protein and homologs; Region: PIN_Sll0205; cd09872 452662009559 putative active site [active] 452662009560 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 452662009561 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 452662009562 DNA binding residues [nucleotide binding] 452662009563 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 452662009564 FecR protein; Region: FecR; pfam04773 452662009565 Secretin and TonB N terminus short domain; Region: STN; smart00965 452662009566 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662009567 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 452662009568 N-terminal plug; other site 452662009569 ligand-binding site [chemical binding]; other site 452662009570 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 452662009571 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 452662009572 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 452662009573 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 452662009574 Ligand Binding Site [chemical binding]; other site 452662009575 Molecular Tunnel; other site 452662009576 Transglutaminase-like superfamily; Region: Transglut_core3; pfam13471 452662009577 Transcriptional regulators [Transcription]; Region: GntR; COG1802 452662009578 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 452662009579 DNA-binding site [nucleotide binding]; DNA binding site 452662009580 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 452662009581 non-specific DNA binding site [nucleotide binding]; other site 452662009582 salt bridge; other site 452662009583 sequence-specific DNA binding site [nucleotide binding]; other site 452662009584 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 452662009585 dimerization domain [polypeptide binding]; other site 452662009586 dimer interface [polypeptide binding]; other site 452662009587 catalytic residues [active] 452662009588 TraE protein; Region: TraE; cl05060 452662009589 TraK protein; Region: TraK; pfam06586 452662009590 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 452662009591 Type IV conjugative transfer system lipoprotein (TraV); Region: TraV; pfam09676 452662009592 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 452662009593 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 452662009594 Sex factor F TraW protein N terminal; Region: TraW_N; cl10149 452662009595 TraU protein; Region: TraU; pfam06834 452662009596 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 452662009597 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; cl09883 452662009598 Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: TraF; COG4959 452662009599 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 452662009600 F plasmid transfer operon protein; Region: TraF; pfam13728 452662009601 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 452662009602 catalytic residues [active] 452662009603 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 452662009604 putative active site [active] 452662009605 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 452662009606 Conjugative relaxosome accessory transposon protein; Region: TraH; pfam06122 452662009607 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 452662009608 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 452662009609 metal-binding site 452662009610 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 452662009611 N-terminal domain interface [polypeptide binding]; other site 452662009612 HPP family; Region: HPP; pfam04982 452662009613 glutathione reductase; Validated; Region: PRK06116 452662009614 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 452662009615 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 452662009616 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 452662009617 S-formylglutathione hydrolase; Region: PLN02442 452662009618 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 452662009619 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 452662009620 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662009621 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 452662009622 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 452662009623 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 452662009624 substrate binding site [chemical binding]; other site 452662009625 catalytic Zn binding site [ion binding]; other site 452662009626 NAD binding site [chemical binding]; other site 452662009627 structural Zn binding site [ion binding]; other site 452662009628 dimer interface [polypeptide binding]; other site 452662009629 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662009630 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662009631 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662009632 dimerization interface [polypeptide binding]; other site 452662009633 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 452662009634 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 452662009635 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 452662009636 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 452662009637 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 452662009638 FMN-binding pocket [chemical binding]; other site 452662009639 flavin binding motif; other site 452662009640 phosphate binding motif [ion binding]; other site 452662009641 beta-alpha-beta structure motif; other site 452662009642 NAD binding pocket [chemical binding]; other site 452662009643 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 452662009644 catalytic loop [active] 452662009645 iron binding site [ion binding]; other site 452662009646 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 452662009647 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 452662009648 C-terminal domain interface [polypeptide binding]; other site 452662009649 GSH binding site (G-site) [chemical binding]; other site 452662009650 dimer interface [polypeptide binding]; other site 452662009651 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 452662009652 N-terminal domain interface [polypeptide binding]; other site 452662009653 YCII-related domain; Region: YCII; cl00999 452662009654 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3224 452662009655 Predicted esterase [General function prediction only]; Region: COG0400 452662009656 putative hydrolase; Provisional; Region: PRK11460 452662009657 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 452662009658 TAP-like protein; Region: Abhydrolase_4; pfam08386 452662009659 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 452662009660 Zn binding site [ion binding]; other site 452662009661 C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_C_like; cd08347 452662009662 Zn binding site [ion binding]; other site 452662009663 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662009664 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662009665 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 452662009666 substrate binding pocket [chemical binding]; other site 452662009667 dimerization interface [polypeptide binding]; other site 452662009668 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662009669 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 452662009670 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 452662009671 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 452662009672 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 452662009673 iron-sulfur cluster [ion binding]; other site 452662009674 [2Fe-2S] cluster binding site [ion binding]; other site 452662009675 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 452662009676 alpha subunit interface [polypeptide binding]; other site 452662009677 active site 452662009678 substrate binding site [chemical binding]; other site 452662009679 Fe binding site [ion binding]; other site 452662009680 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 452662009681 active site 452662009682 Cupin domain; Region: Cupin_2; cl17218 452662009683 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 452662009684 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662009685 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662009686 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 452662009687 dimerization interface [polypeptide binding]; other site 452662009688 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662009689 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662009690 Integrase core domain; Region: rve; pfam00665 452662009691 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl17393 452662009692 Transposase domain (DUF772); Region: DUF772; pfam05598 452662009693 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662009694 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 452662009695 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662009696 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662009697 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 452662009698 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 452662009699 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 452662009700 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662009701 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662009702 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 452662009703 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 452662009704 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 452662009705 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 452662009706 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662009707 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 452662009708 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 452662009709 putative substrate translocation pore; other site 452662009710 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 452662009711 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662009712 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662009713 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 452662009714 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 452662009715 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662009716 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 452662009717 dimerization interface [polypeptide binding]; other site 452662009718 substrate binding pocket [chemical binding]; other site 452662009719 Protein of unknown function (DUF2274); Region: DUF2274; pfam10038 452662009720 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 452662009721 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 452662009722 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 452662009723 VirB7 interaction site; other site 452662009724 conjugal transfer protein TrbF; Provisional; Region: PRK13872 452662009725 conjugal transfer protein TrbL; Provisional; Region: PRK13875 452662009726 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 452662009727 conjugative transfer region protein TrbK; Region: other_trbK; TIGR04360 452662009728 conjugal transfer protein TrbJ; Provisional; Region: PRK13874 452662009729 conjugal transfer ATPase TrbE; Provisional; Region: PRK13873 452662009730 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 452662009731 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 452662009732 Walker A/P-loop; other site 452662009733 ATP binding site [chemical binding]; other site 452662009734 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 452662009735 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 452662009736 TrbC/VIRB2 family; Region: TrbC; cl01583 452662009737 P-type conjugative transfer ATPase TrbB; Region: TrbB_P; TIGR02782 452662009738 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 452662009739 Walker A motif; other site 452662009740 ATP binding site [chemical binding]; other site 452662009741 Walker B motif; other site 452662009742 conjugal transfer coupling protein TraG; Provisional; Region: PRK13876 452662009743 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 452662009744 Walker A motif; other site 452662009745 ATP binding site [chemical binding]; other site 452662009746 Walker B motif; other site 452662009747 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 452662009748 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 452662009749 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 452662009750 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 452662009751 N-acetyl-D-glucosamine binding site [chemical binding]; other site 452662009752 catalytic residue [active] 452662009753 Protein of unknown function (DUF736); Region: DUF736; pfam05284 452662009754 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 452662009755 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 452662009756 Protein of unknown function (DUF2840); Region: DUF2840; pfam11000 452662009757 ParA-like protein; Provisional; Region: PHA02518 452662009758 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 452662009759 P-loop; other site 452662009760 Magnesium ion binding site [ion binding]; other site 452662009761 Replication initiator protein A; Region: RPA; pfam10134 452662009762 Helix-turn-helix domain; Region: HTH_17; pfam12728 452662009763 Uncharacterized conserved protein (DUF2285); Region: DUF2285; pfam10074 452662009764 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 452662009765 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 452662009766 non-specific DNA binding site [nucleotide binding]; other site 452662009767 salt bridge; other site 452662009768 sequence-specific DNA binding site [nucleotide binding]; other site 452662009769 Uncharacterized conserved protein [Function unknown]; Region: COG5489 452662009770 Protein of unknown function (DUF2493); Region: DUF2493; pfam10686 452662009771 Toprim domain; Region: Toprim_3; pfam13362 452662009772 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 452662009773 S-adenosylmethionine binding site [chemical binding]; other site 452662009774 P-loop containing NTP hydrolase pore-1; Region: AAA_34; pfam13872 452662009775 Helicase_C-like; Region: Helicase_C_4; pfam13871 452662009776 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 452662009777 Ligand Binding Site [chemical binding]; other site 452662009778 enoyl-CoA hydratase; Provisional; Region: PRK07468 452662009779 ParB-like nuclease domain; Region: ParBc; pfam02195 452662009780 Protein of unknown function (DUF2958); Region: DUF2958; pfam11171 452662009781 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 452662009782 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 452662009783 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 452662009784 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; pfam02899 452662009785 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 452662009786 active site 452662009787 DNA binding site [nucleotide binding] 452662009788 Int/Topo IB signature motif; other site 452662009789 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 452662009790 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 452662009791 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 452662009792 P-loop containing NTP hydrolase pore-1; Region: AAA_34; pfam13872 452662009793 Helicase_C-like; Region: Helicase_C_4; pfam13871 452662009794 Toprim domain; Region: Toprim_3; pfam13362 452662009795 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 452662009796 dimer interface [polypeptide binding]; other site 452662009797 ssDNA binding site [nucleotide binding]; other site 452662009798 tetramer (dimer of dimers) interface [polypeptide binding]; other site 452662009799 Helix-turn-helix domain; Region: HTH_36; pfam13730 452662009800 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 452662009801 DNA binding residues [nucleotide binding] 452662009802 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 452662009803 MobA/MobL family; Region: MobA_MobL; pfam03389 452662009804 TopoisomeraseII; Region: TOP2c; smart00433 452662009805 PemK-like protein; Region: PemK; pfam02452 452662009806 Protein of unknown function (DUF3018); Region: DUF3018; pfam11455 452662009807 Replication initiator protein A; Region: RPA; pfam10134 452662009808 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 452662009809 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 452662009810 IHF - DNA interface [nucleotide binding]; other site 452662009811 IHF dimer interface [polypeptide binding]; other site 452662009812 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 452662009813 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 452662009814 Surface antigen; Region: Bac_surface_Ag; pfam01103 452662009815 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; cl17304 452662009816 Autotransporter beta-domain; Region: Autotransporter; smart00869 452662009817 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 452662009818 ParB-like nuclease domain; Region: ParB; smart00470 452662009819 quinohemoprotein amine dehydrogenase, alpha subunit; Region: QH_alpha; TIGR03908 452662009820 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 452662009821 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 452662009822 Moco binding site; other site 452662009823 metal coordination site [ion binding]; other site 452662009824 Sugar-binding cellulase-like; Region: Cellulase-like; pfam12876 452662009825 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 452662009826 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 452662009827 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 452662009828 NADP binding site [chemical binding]; other site 452662009829 active site 452662009830 putative substrate binding site [chemical binding]; other site 452662009831 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: GT1_like_1; cd04950 452662009832 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662009833 putative homodimer interface [polypeptide binding]; other site 452662009834 UDP-galactopyranose mutase [Cell envelope biogenesis, outer membrane]; Region: Glf; COG0562 452662009835 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 452662009836 UDP-galactopyranose mutase; Region: GLF; pfam03275 452662009837 Putative Tad-like Flp pilus-assembly; Region: Tad_C; pfam09977 452662009838 Predicted membrane protein [Function unknown]; Region: COG4655 452662009839 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 452662009840 binding surface 452662009841 TPR motif; other site 452662009842 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 452662009843 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 452662009844 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 452662009845 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 452662009846 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 452662009847 ATP binding site [chemical binding]; other site 452662009848 Walker A motif; other site 452662009849 hexamer interface [polypeptide binding]; other site 452662009850 Walker B motif; other site 452662009851 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 452662009852 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 452662009853 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 452662009854 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 452662009855 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 452662009856 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 452662009857 dimer interface [polypeptide binding]; other site 452662009858 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 452662009859 active site 452662009860 Fe binding site [ion binding]; other site 452662009861 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH); Region: pro_PheOH; cd03348 452662009862 cofactor binding site; other site 452662009863 metal binding site [ion binding]; metal-binding site 452662009864 Uncharacterized protein conserved in bacteria (DUF2236); Region: DUF2236; pfam09995 452662009865 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 452662009866 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 452662009867 putative substrate translocation pore; other site 452662009868 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 452662009869 putative acyl-acceptor binding pocket; other site 452662009870 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 452662009871 acyl-activating enzyme (AAE) consensus motif; other site 452662009872 putative AMP binding site [chemical binding]; other site 452662009873 Predicted membrane protein [Function unknown]; Region: COG5373 452662009874 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 452662009875 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662009876 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662009877 WHG domain; Region: WHG; pfam13305 452662009878 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 452662009879 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 452662009880 Protein of unknown function (DUF1326); Region: DUF1326; cl02375 452662009881 Predicted metal-binding integral membrane protein (DUF2182); Region: DUF2182; pfam09948 452662009882 response regulator FixJ; Provisional; Region: fixJ; PRK09390 452662009883 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 452662009884 active site 452662009885 phosphorylation site [posttranslational modification] 452662009886 intermolecular recognition site; other site 452662009887 dimerization interface [polypeptide binding]; other site 452662009888 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 452662009889 DNA binding residues [nucleotide binding] 452662009890 dimerization interface [polypeptide binding]; other site 452662009891 PAS domain S-box; Region: sensory_box; TIGR00229 452662009892 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662009893 putative active site [active] 452662009894 heme pocket [chemical binding]; other site 452662009895 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 452662009896 dimer interface [polypeptide binding]; other site 452662009897 phosphorylation site [posttranslational modification] 452662009898 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 452662009899 ATP binding site [chemical binding]; other site 452662009900 Mg2+ binding site [ion binding]; other site 452662009901 G-X-G motif; other site 452662009902 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 452662009903 Ligand Binding Site [chemical binding]; other site 452662009904 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 452662009905 Ligand Binding Site [chemical binding]; other site 452662009906 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662009907 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 452662009908 N-terminal plug; other site 452662009909 ligand-binding site [chemical binding]; other site 452662009910 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 452662009911 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 452662009912 Predicted phosphoesterases, related to the Icc protein [General function prediction only]; Region: COG2129 452662009913 active site 452662009914 metal binding site [ion binding]; metal-binding site 452662009915 putative phosphoesterase; Region: acc_ester; TIGR03729 452662009916 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 452662009917 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 452662009918 tetrameric interface [polypeptide binding]; other site 452662009919 NAD binding site [chemical binding]; other site 452662009920 catalytic residues [active] 452662009921 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662009922 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662009923 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662009924 dimerization interface [polypeptide binding]; other site 452662009925 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 452662009926 S-adenosylmethionine binding site [chemical binding]; other site 452662009927 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 452662009928 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 452662009929 active site 452662009930 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 452662009931 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 452662009932 CysD dimerization site [polypeptide binding]; other site 452662009933 G1 box; other site 452662009934 putative GEF interaction site [polypeptide binding]; other site 452662009935 GTP/Mg2+ binding site [chemical binding]; other site 452662009936 Switch I region; other site 452662009937 G2 box; other site 452662009938 G3 box; other site 452662009939 Switch II region; other site 452662009940 G4 box; other site 452662009941 G5 box; other site 452662009942 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 452662009943 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 452662009944 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form...; Region: APSK; cd02027 452662009945 ligand-binding site [chemical binding]; other site 452662009946 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 452662009947 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 452662009948 Active Sites [active] 452662009949 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 452662009950 dimerization interface [polypeptide binding]; other site 452662009951 DNA binding residues [nucleotide binding] 452662009952 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 452662009953 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 452662009954 FeS/SAM binding site; other site 452662009955 HemN C-terminal domain; Region: HemN_C; pfam06969 452662009956 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 452662009957 recognition site for restriction enzyme PmeI 452662009958 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 452662009959 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 452662009960 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 452662009961 ligand binding site [chemical binding]; other site 452662009962 flexible hinge region; other site 452662009963 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 452662009964 non-specific DNA interactions [nucleotide binding]; other site 452662009965 DNA binding site [nucleotide binding] 452662009966 sequence specific DNA binding site [nucleotide binding]; other site 452662009967 putative cAMP binding site [chemical binding]; other site 452662009968 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 452662009969 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 452662009970 Low-spin heme binding site [chemical binding]; other site 452662009971 Putative water exit pathway; other site 452662009972 Binuclear center (active site) [active] 452662009973 Putative proton exit pathway; other site 452662009974 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 452662009975 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; pfam02433 452662009976 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 452662009977 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 452662009978 Cytochrome c; Region: Cytochrom_C; pfam00034 452662009979 Cytochrome c; Region: Cytochrom_C; pfam00034 452662009980 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 452662009981 4Fe-4S binding domain; Region: Fer4_5; pfam12801 452662009982 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 452662009983 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 452662009984 Predicted integral membrane protein linked to a cation pump [Inorganic ion transport and metabolism]; Region: COG5456 452662009985 FixH; Region: FixH; pfam05751 452662009986 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 452662009987 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 452662009988 metal-binding site [ion binding] 452662009989 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 452662009990 Soluble P-type ATPase [General function prediction only]; Region: COG4087 452662009991 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 452662009992 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11905 452662009993 Proline dehydrogenase [Amino acid transport and metabolism]; Region: PutA; COG0506 452662009994 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 452662009995 Glutamate binding site [chemical binding]; other site 452662009996 NAD binding site [chemical binding]; other site 452662009997 catalytic residues [active] 452662009998 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 452662009999 active site 452662010000 catalytic triad [active] 452662010001 oxyanion hole [active] 452662010002 switch loop; other site 452662010003 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 452662010004 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 452662010005 Walker A/P-loop; other site 452662010006 ATP binding site [chemical binding]; other site 452662010007 Q-loop/lid; other site 452662010008 ABC transporter signature motif; other site 452662010009 Walker B; other site 452662010010 D-loop; other site 452662010011 H-loop/switch region; other site 452662010012 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 452662010013 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 452662010014 dimer interface [polypeptide binding]; other site 452662010015 phosphorylation site [posttranslational modification] 452662010016 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 452662010017 ATP binding site [chemical binding]; other site 452662010018 Mg2+ binding site [ion binding]; other site 452662010019 G-X-G motif; other site 452662010020 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 452662010021 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 452662010022 active site 452662010023 phosphorylation site [posttranslational modification] 452662010024 intermolecular recognition site; other site 452662010025 dimerization interface [polypeptide binding]; other site 452662010026 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 452662010027 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662010028 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 452662010029 N-terminal plug; other site 452662010030 ligand-binding site [chemical binding]; other site 452662010031 PAS domain; Region: PAS_9; pfam13426 452662010032 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662010033 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 452662010034 dimer interface [polypeptide binding]; other site 452662010035 phosphorylation site [posttranslational modification] 452662010036 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 452662010037 ATP binding site [chemical binding]; other site 452662010038 Mg2+ binding site [ion binding]; other site 452662010039 G-X-G motif; other site 452662010040 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 452662010041 Response regulator receiver domain; Region: Response_reg; pfam00072 452662010042 active site 452662010043 phosphorylation site [posttranslational modification] 452662010044 intermolecular recognition site; other site 452662010045 dimerization interface [polypeptide binding]; other site 452662010046 circadian clock protein KaiC; Reviewed; Region: PRK09302 452662010047 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 452662010048 Walker A motif; other site 452662010049 ATP binding site [chemical binding]; other site 452662010050 Walker B motif; other site 452662010051 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 452662010052 KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea; Region: KaiC; cd01124 452662010053 Walker A motif; other site 452662010054 Walker A motif; other site 452662010055 ATP binding site [chemical binding]; other site 452662010056 Walker B motif; other site 452662010057 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 452662010058 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 452662010059 ligand binding site [chemical binding]; other site 452662010060 flexible hinge region; other site 452662010061 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 452662010062 Uncharacterized stress protein (general stress protein 26) [General function prediction only]; Region: COG3871 452662010063 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 452662010064 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 452662010065 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 452662010066 DNA-binding site [nucleotide binding]; DNA binding site 452662010067 Transcriptional regulators [Transcription]; Region: FadR; COG2186 452662010068 FCD domain; Region: FCD; pfam07729 452662010069 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 452662010070 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 452662010071 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 452662010072 active site 452662010073 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 452662010074 D-galactonate transporter; Region: 2A0114; TIGR00893 452662010075 putative substrate translocation pore; other site 452662010076 Cytochrome c2 [Energy production and conversion]; Region: COG3474 452662010077 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 452662010078 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 452662010079 active site 452662010080 NAD binding site [chemical binding]; other site 452662010081 metal binding site [ion binding]; metal-binding site 452662010082 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 452662010083 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 452662010084 tetramerization interface [polypeptide binding]; other site 452662010085 NAD(P) binding site [chemical binding]; other site 452662010086 catalytic residues [active] 452662010087 Membrane-bound PQQ-dependent glucose dehydrogenase; Region: PQQ_mGDH; cd10280 452662010088 Trp docking motif [polypeptide binding]; other site 452662010089 putative active site [active] 452662010090 Cytochrome c; Region: Cytochrom_C; pfam00034 452662010091 enoyl-CoA hydratase; Provisional; Region: PRK06144 452662010092 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662010093 substrate binding site [chemical binding]; other site 452662010094 oxyanion hole (OAH) forming residues; other site 452662010095 trimer interface [polypeptide binding]; other site 452662010096 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 452662010097 CoA-transferase family III; Region: CoA_transf_3; pfam02515 452662010098 Membrane-bound PQQ-dependent glucose dehydrogenase; Region: PQQ_mGDH; cd10280 452662010099 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 452662010100 Trp docking motif [polypeptide binding]; other site 452662010101 putative active site [active] 452662010102 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 452662010103 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 452662010104 Cupin domain; Region: Cupin_2; pfam07883 452662010105 Cupin domain; Region: Cupin_2; cl17218 452662010106 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 452662010107 D-galactonate transporter; Region: 2A0114; TIGR00893 452662010108 putative substrate translocation pore; other site 452662010109 Cupin domain; Region: Cupin_2; cl17218 452662010110 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 452662010111 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 452662010112 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 452662010113 threonine and homoserine efflux system; Provisional; Region: PRK10532 452662010114 EamA-like transporter family; Region: EamA; pfam00892 452662010115 recognition site for restriction enzyme I-CeuI 452662010116 Protein of unknown function (DUF3142); Region: DUF3142; pfam11340 452662010117 FAD binding domain; Region: FAD_binding_3; pfam01494 452662010118 hypothetical protein; Provisional; Region: PRK07236 452662010119 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 452662010120 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662010121 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662010122 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 452662010123 substrate binding pocket [chemical binding]; other site 452662010124 dimerization interface [polypeptide binding]; other site 452662010125 benzoate transport; Region: 2A0115; TIGR00895 452662010126 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 452662010127 putative substrate translocation pore; other site 452662010128 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662010129 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 452662010130 N-terminal plug; other site 452662010131 ligand-binding site [chemical binding]; other site 452662010132 methyl indole-3-acetate methyltransferase; Region: PLN02211; cl17657 452662010133 methyl indole-3-acetate methyltransferase; Region: PLN02211; cl17657 452662010134 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 452662010135 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 452662010136 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 452662010137 putative active site [active] 452662010138 putative substrate binding site [chemical binding]; other site 452662010139 putative cosubstrate binding site; other site 452662010140 catalytic site [active] 452662010141 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662010142 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 452662010143 N-terminal plug; other site 452662010144 ligand-binding site [chemical binding]; other site 452662010145 Dihydroneopterin aldolase; Region: FolB; smart00905 452662010146 active site 452662010147 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662010148 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662010149 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 452662010150 substrate binding pocket [chemical binding]; other site 452662010151 dimerization interface [polypeptide binding]; other site 452662010152 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 452662010153 FAD binding site [chemical binding]; other site 452662010154 Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]; Region: GcvT; COG0404 452662010155 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 452662010156 Domain of unknown function (DUF4173); Region: DUF4173; pfam13777 452662010157 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 452662010158 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 452662010159 active site 452662010160 phosphorylation site [posttranslational modification] 452662010161 intermolecular recognition site; other site 452662010162 dimerization interface [polypeptide binding]; other site 452662010163 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 452662010164 DNA binding site [nucleotide binding] 452662010165 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 452662010166 HAMP domain; Region: HAMP; pfam00672 452662010167 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 452662010168 dimer interface [polypeptide binding]; other site 452662010169 phosphorylation site [posttranslational modification] 452662010170 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 452662010171 ATP binding site [chemical binding]; other site 452662010172 Mg2+ binding site [ion binding]; other site 452662010173 G-X-G motif; other site 452662010174 Predicted membrane protein (DUF2306); Region: DUF2306; cl02232 452662010175 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11552 452662010176 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662010177 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 452662010178 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 452662010179 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 452662010180 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662010181 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 452662010182 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 452662010183 ABC transporter periplasmic binding protein, urea carboxylase region; Region: ABC_peri_uca; TIGR03427 452662010184 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 452662010185 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 452662010186 putative PBP binding loops; other site 452662010187 ABC-ATPase subunit interface; other site 452662010188 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 452662010189 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 452662010190 Walker A/P-loop; other site 452662010191 ATP binding site [chemical binding]; other site 452662010192 Q-loop/lid; other site 452662010193 ABC transporter signature motif; other site 452662010194 Walker B; other site 452662010195 D-loop; other site 452662010196 H-loop/switch region; other site 452662010197 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 452662010198 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 452662010199 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 452662010200 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 452662010201 urea carboxylase-associated protein 2; Region: urea_degr_2; TIGR03425 452662010202 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 452662010203 Domain of unknown function (DUF1989); Region: DUF1989; pfam09347 452662010204 urea carboxylase; Region: urea_carbox; TIGR02712 452662010205 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 452662010206 ATP-grasp domain; Region: ATP-grasp_4; cl17255 452662010207 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 452662010208 Allophanate hydrolase subunit 2; Region: AHS2; smart00797 452662010209 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 452662010210 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 452662010211 carboxyltransferase (CT) interaction site; other site 452662010212 biotinylation site [posttranslational modification]; other site 452662010213 allophanate hydrolase; Provisional; Region: PRK08186 452662010214 Amidase; Region: Amidase; cl11426 452662010215 Uncharacterized conserved protein [Function unknown]; Region: COG3391 452662010216 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 452662010217 binding surface 452662010218 TPR motif; other site 452662010219 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 452662010220 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 452662010221 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 452662010222 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662010223 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662010224 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 452662010225 dimerization interface [polypeptide binding]; other site 452662010226 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 452662010227 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 452662010228 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 452662010229 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these...; Region: PRX_like2; cd02970 452662010230 putative catalytic residues [active] 452662010231 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 452662010232 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 452662010233 active site 452662010234 non-prolyl cis peptide bond; other site 452662010235 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 452662010236 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 452662010237 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 452662010238 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 452662010239 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662010240 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662010241 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662010242 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662010243 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662010244 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 452662010245 dimerization interface [polypeptide binding]; other site 452662010246 Transcriptional regulators [Transcription]; Region: MarR; COG1846 452662010247 MarR family; Region: MarR_2; pfam12802 452662010248 homogentisate 1,2-dioxygenase; Provisional; Region: PRK05341 452662010249 fumarylacetoacetase; Region: fum_ac_acetase; TIGR01266 452662010250 Domain of unknown function (DUF1969); Region: DUF1969; pfam09298 452662010251 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 452662010252 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 452662010253 maleylacetoacetate isomerase; Region: maiA; TIGR01262 452662010254 C-terminal domain interface [polypeptide binding]; other site 452662010255 GSH binding site (G-site) [chemical binding]; other site 452662010256 putative dimer interface [polypeptide binding]; other site 452662010257 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 452662010258 dimer interface [polypeptide binding]; other site 452662010259 N-terminal domain interface [polypeptide binding]; other site 452662010260 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 452662010261 formate dehydrogenase subunit gamma; Validated; Region: PRK05988 452662010262 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 452662010263 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of...; Region: TRX_Fd_FDH_beta; cd03063 452662010264 putative dimer interface [polypeptide binding]; other site 452662010265 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 452662010266 SLBB domain; Region: SLBB; pfam10531 452662010267 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 452662010268 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 452662010269 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 452662010270 catalytic loop [active] 452662010271 iron binding site [ion binding]; other site 452662010272 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 452662010273 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 452662010274 [4Fe-4S] binding site [ion binding]; other site 452662010275 molybdopterin cofactor binding site; other site 452662010276 This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate...; Region: MopB_CT_Fdh-Nap-like; cd00508 452662010277 molybdopterin cofactor binding site; other site 452662010278 NADH-dependant formate dehydrogenase delta subunit FdsD; Region: FdsD; pfam11390 452662010279 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 452662010280 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 452662010281 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 452662010282 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 452662010283 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 452662010284 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 452662010285 ligand binding site [chemical binding]; other site 452662010286 homodimer interface [polypeptide binding]; other site 452662010287 NAD(P) binding site [chemical binding]; other site 452662010288 trimer interface B [polypeptide binding]; other site 452662010289 trimer interface A [polypeptide binding]; other site 452662010290 Transcriptional regulators [Transcription]; Region: FadR; COG2186 452662010291 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl17414 452662010292 DNA-binding site [nucleotide binding]; DNA binding site 452662010293 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662010294 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662010295 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl17217 452662010296 PilZ domain; Region: PilZ; pfam07238 452662010297 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 452662010298 sequence-specific DNA binding site [nucleotide binding]; other site 452662010299 salt bridge; other site 452662010300 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 452662010301 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662010302 active site 452662010303 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 452662010304 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662010305 substrate binding site [chemical binding]; other site 452662010306 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 452662010307 oxyanion hole (OAH) forming residues; other site 452662010308 trimer interface [polypeptide binding]; other site 452662010309 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 452662010310 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662010311 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662010312 Uncharacterized protein conserved in bacteria (DUF2171); Region: DUF2171; pfam09939 452662010313 Protein of unknown function (DUF2945); Region: DUF2945; pfam11160 452662010314 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 452662010315 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 452662010316 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 452662010317 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 452662010318 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 452662010319 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 452662010320 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 452662010321 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 452662010322 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 452662010323 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 452662010324 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 452662010325 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 452662010326 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 452662010327 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 452662010328 Amidohydrolase; Region: Amidohydro_4; pfam13147 452662010329 active site 452662010330 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_3; cd06151 452662010331 homotrimer interaction site [polypeptide binding]; other site 452662010332 putative active site [active] 452662010333 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 452662010334 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 452662010335 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 452662010336 hypothetical protein; Validated; Region: PRK08238 452662010337 phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase; Provisional; Region: PRK12324 452662010338 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 452662010339 Predicted membrane protein [Function unknown]; Region: COG4763 452662010340 Acyltransferase family; Region: Acyl_transf_3; pfam01757 452662010341 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 452662010342 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662010343 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 452662010344 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662010345 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 452662010346 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 452662010347 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 452662010348 active site 452662010349 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; pfam04230 452662010350 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 452662010351 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 452662010352 active site 452662010353 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662010354 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 452662010355 Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]; Region: WecG; COG1922 452662010356 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 452662010357 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 452662010358 Chain length determinant protein; Region: Wzz; cl15801 452662010359 chain length determinant protein EpsF; Region: EpsF; TIGR03017 452662010360 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 452662010361 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 452662010362 Walker A motif; other site 452662010363 ATP binding site [chemical binding]; other site 452662010364 Walker B motif; other site 452662010365 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 452662010366 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 452662010367 SLBB domain; Region: SLBB; pfam10531 452662010368 exopolysaccharide biosynthesis operon protein EpsL; Region: EpsL; TIGR03014 452662010369 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; pfam00150 452662010370 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 452662010371 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662010372 NAD(P) binding site [chemical binding]; other site 452662010373 active site 452662010374 Methyltransferase domain; Region: Methyltransf_11; pfam08241 452662010375 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 452662010376 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 452662010377 Ligand binding site; other site 452662010378 Putative Catalytic site; other site 452662010379 DXD motif; other site 452662010380 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 452662010381 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 452662010382 active site 452662010383 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 452662010384 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 452662010385 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 452662010386 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 452662010387 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 452662010388 Predicted enzyme involved in methoxymalonyl-ACP biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FkbH; COG3882 452662010389 HAD-superfamily phosphatase, subfamily IIIC; Region: HAD-SF-IIIC; TIGR01681 452662010390 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 452662010391 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 452662010392 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 452662010393 trimer interface [polypeptide binding]; other site 452662010394 active site 452662010395 substrate binding site [chemical binding]; other site 452662010396 CoA binding site [chemical binding]; other site 452662010397 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 452662010398 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 452662010399 trimer interface [polypeptide binding]; other site 452662010400 active site 452662010401 substrate binding site [chemical binding]; other site 452662010402 CoA binding site [chemical binding]; other site 452662010403 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 452662010404 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 452662010405 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662010406 putative active site [active] 452662010407 heme pocket [chemical binding]; other site 452662010408 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662010409 putative active site [active] 452662010410 heme pocket [chemical binding]; other site 452662010411 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 452662010412 dimer interface [polypeptide binding]; other site 452662010413 phosphorylation site [posttranslational modification] 452662010414 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 452662010415 ATP binding site [chemical binding]; other site 452662010416 Mg2+ binding site [ion binding]; other site 452662010417 G-X-G motif; other site 452662010418 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 452662010419 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 452662010420 active site 452662010421 phosphorylation site [posttranslational modification] 452662010422 intermolecular recognition site; other site 452662010423 dimerization interface [polypeptide binding]; other site 452662010424 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 452662010425 DNA binding residues [nucleotide binding] 452662010426 dimerization interface [polypeptide binding]; other site 452662010427 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 452662010428 Bacterial sugar transferase; Region: Bac_transf; pfam02397 452662010429 YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze...; Region: YbaK_like; cl00022 452662010430 Alpha-L-arabinofuranosidase [Carbohydrate transport and metabolism]; Region: AbfA; COG3534 452662010431 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; pfam06964 452662010432 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 452662010433 PA14 domain; Region: PA14; cl08459 452662010434 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 452662010435 Glycosyl hydrolase family 43, includes arabinoxylan arabinofuranohydrolase, beta-xylosidase, endo-1,4-beta-xylanase, alpha-L-arabinofuranosidase; Region: GH43_AXH_like; cd08990 452662010436 substrate binding site [chemical binding]; other site 452662010437 active site 452662010438 Tryptophan halogenase; Region: Trp_halogenase; pfam04820 452662010439 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 452662010440 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 452662010441 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 452662010442 SapC; Region: SapC; pfam07277 452662010443 Cupin-like domain; Region: Cupin_8; pfam13621 452662010444 Domain of unknown function (DUF303); Region: DUF303; pfam03629 452662010445 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 452662010446 Domain of unknown function (DUF303); Region: DUF303; pfam03629 452662010447 alpha-galactosidase; Region: PLN02808; cl17638 452662010448 NPCBM/NEW2 domain; Region: NPCBM; pfam08305 452662010449 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_2; cd09001 452662010450 active site 452662010451 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 452662010452 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_1; cd09000 452662010453 inhibitor binding site; inhibition site 452662010454 active site 452662010455 Carboxylesterase type B [Lipid metabolism]; Region: PnbA; COG2272 452662010456 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 452662010457 substrate binding pocket [chemical binding]; other site 452662010458 catalytic triad [active] 452662010459 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 452662010460 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_1; cd09000 452662010461 inhibitor binding site; inhibition site 452662010462 active site 452662010463 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 452662010464 D-galactonate transporter; Region: 2A0114; TIGR00893 452662010465 putative substrate translocation pore; other site 452662010466 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 452662010467 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 452662010468 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 452662010469 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 452662010470 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 452662010471 Cupin; Region: Cupin_6; pfam12852 452662010472 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 452662010473 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 452662010474 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 452662010475 short chain dehydrogenase; Provisional; Region: PRK08267 452662010476 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 452662010477 NADP binding site [chemical binding]; other site 452662010478 active site 452662010479 steroid binding site; other site 452662010480 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 452662010481 EamA-like transporter family; Region: EamA; pfam00892 452662010482 EamA-like transporter family; Region: EamA; pfam00892 452662010483 Transcriptional regulators [Transcription]; Region: PurR; COG1609 452662010484 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 452662010485 DNA binding site [nucleotide binding] 452662010486 domain linker motif; other site 452662010487 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 452662010488 putative ligand binding site [chemical binding]; other site 452662010489 putative dimerization interface [polypeptide binding]; other site 452662010490 L-fucose transporter; Provisional; Region: PRK10133; cl17665 452662010491 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662010492 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 452662010493 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 452662010494 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 452662010495 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 452662010496 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 452662010497 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 452662010498 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 452662010499 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 452662010500 Serine hydrolase; Region: Ser_hydrolase; pfam06821 452662010501 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 452662010502 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 452662010503 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 452662010504 recognition site for restriction enzyme I-CeuI 452662010505 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 452662010506 potassium uptake protein; Region: kup; TIGR00794 452662010507 Chalcone and stilbene synthases; plant-specific polyketide synthases (PKS) and related enzymes, also called type III PKSs. PKS generate an array of different products, dependent on the nature of the starter molecule. They share a common chemical strategy; Region: CHS_like; cd00831 452662010508 Predicted naringenin-chalcone synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BcsA; COG3424 452662010509 malonyl-CoA binding site [chemical binding]; other site 452662010510 dimer interface [polypeptide binding]; other site 452662010511 active site 452662010512 product binding site; other site 452662010513 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 452662010514 S-adenosylmethionine binding site [chemical binding]; other site 452662010515 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 452662010516 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 452662010517 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 452662010518 putative substrate translocation pore; other site 452662010519 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 452662010520 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 452662010521 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662010522 Transcriptional regulators [Transcription]; Region: MarR; COG1846 452662010523 MarR family; Region: MarR; pfam01047 452662010524 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 452662010525 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 452662010526 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662010527 The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; Region: PBP2_IlvR; cd08453 452662010528 putative dimerization interface [polypeptide binding]; other site 452662010529 putative substrate binding pocket [chemical binding]; other site 452662010530 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 452662010531 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 452662010532 classical (c) SDR, subgroup 3; Region: SDR_c3; cd05360 452662010533 putative NAD(P) binding site [chemical binding]; other site 452662010534 active site 452662010535 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 452662010536 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 452662010537 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 452662010538 Helix-turn-helix domain; Region: HTH_38; pfam13936 452662010539 Integrase core domain; Region: rve; pfam00665 452662010540 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 452662010541 Integrase core domain; Region: rve; pfam00665 452662010542 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 452662010543 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 452662010544 ligand binding site [chemical binding]; other site 452662010545 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 452662010546 classical (c) SDRs; Region: SDR_c; cd05233 452662010547 NAD(P) binding site [chemical binding]; other site 452662010548 active site 452662010549 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 452662010550 classical (c) SDRs; Region: SDR_c; cd05233 452662010551 NAD(P) binding site [chemical binding]; other site 452662010552 active site 452662010553 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily 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: ACAD10_11_like; cd05154 452662010554 putative active site [active] 452662010555 putative substrate binding site [chemical binding]; other site 452662010556 ATP binding site [chemical binding]; other site 452662010557 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 452662010558 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662010559 active site 452662010560 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662010561 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662010562 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662010563 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662010564 S-formylglutathione hydrolase; Region: PLN02442 452662010565 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 452662010566 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 452662010567 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 452662010568 substrate binding site [chemical binding]; other site 452662010569 catalytic Zn binding site [ion binding]; other site 452662010570 NAD binding site [chemical binding]; other site 452662010571 structural Zn binding site [ion binding]; other site 452662010572 dimer interface [polypeptide binding]; other site 452662010573 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662010574 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662010575 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662010576 dimerization interface [polypeptide binding]; other site 452662010577 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 452662010578 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 452662010579 active site 452662010580 metal binding site [ion binding]; metal-binding site 452662010581 hexamer interface [polypeptide binding]; other site 452662010582 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cl00062 452662010583 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cl03439 452662010584 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 452662010585 putative bacillithiol system oxidoreductase, YpdA family; Region: Bthiol_YpdA; TIGR04018 452662010586 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 452662010587 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 452662010588 ligand binding site [chemical binding]; other site 452662010589 flexible hinge region; other site 452662010590 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 452662010591 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 452662010592 ligand binding site [chemical binding]; other site 452662010593 flexible hinge region; other site 452662010594 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 452662010595 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 452662010596 4Fe-4S binding domain; Region: Fer4; pfam00037 452662010597 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 452662010598 TPR repeat; Region: TPR_11; pfam13414 452662010599 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 452662010600 binding surface 452662010601 TPR motif; other site 452662010602 LVIVD repeat; Region: LVIVD; pfam08309 452662010603 Domain of unknown function (DUF336); Region: DUF336; cl01249 452662010604 Domain of unknown function (DUF336); Region: DUF336; cl01249 452662010605 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 452662010606 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 452662010607 Surface antigen; Region: Bac_surface_Ag; pfam01103 452662010608 CHASE2 domain; Region: CHASE2; pfam05226 452662010609 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 452662010610 cyclase homology domain; Region: CHD; cd07302 452662010611 nucleotidyl binding site; other site 452662010612 metal binding site [ion binding]; metal-binding site 452662010613 dimer interface [polypeptide binding]; other site 452662010614 CHAT domain; Region: CHAT; pfam12770 452662010615 High-affinity nickel-transport protein; Region: NicO; cl00964 452662010616 cobalamin biosynthesis protein CobW; Region: CobW; TIGR02475 452662010617 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 452662010618 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 452662010619 cobaltochelatase subunit CobN; Reviewed; Region: cobN; PRK05989 452662010620 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 452662010621 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 452662010622 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 452662010623 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 452662010624 homodimer interface [polypeptide binding]; other site 452662010625 Walker A motif; other site 452662010626 ATP binding site [chemical binding]; other site 452662010627 hydroxycobalamin binding site [chemical binding]; other site 452662010628 Walker B motif; other site 452662010629 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 452662010630 FMN binding site [chemical binding]; other site 452662010631 dimer interface [polypeptide binding]; other site 452662010632 precorrin-3B synthase; Region: CobG; TIGR02435 452662010633 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 452662010634 precorrin-8X methylmutase; Reviewed; Region: cobH; PRK08285 452662010635 Precorrin-8X methylmutase; Region: CbiC; pfam02570 452662010636 Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Region: Precorrin_2_C20_MT; cd11645 452662010637 active site 452662010638 SAM binding site [chemical binding]; other site 452662010639 homodimer interface [polypeptide binding]; other site 452662010640 Precorrin-3B C(17)-methyltransferase (CobJ/CbiH); Region: Precorrin_3B_C17_MT; cd11646 452662010641 homodimer interface [polypeptide binding]; other site 452662010642 active site 452662010643 SAM binding site [chemical binding]; other site 452662010644 cobalt-precorrin-6x reductase; Reviewed; Region: PRK08057 452662010645 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 452662010646 active site 452662010647 putative homodimer interface [polypeptide binding]; other site 452662010648 SAM binding site [chemical binding]; other site 452662010649 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 452662010650 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 452662010651 S-adenosylmethionine binding site [chemical binding]; other site 452662010652 Cobalamin synthesis G C-terminus; Region: CbiG_C; pfam01890 452662010653 Precorrin-4 C11-methyltransferase (CbiF/CobM); Region: Precorrin-4_C11-MT; cd11641 452662010654 active site 452662010655 SAM binding site [chemical binding]; other site 452662010656 homodimer interface [polypeptide binding]; other site 452662010657 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 452662010658 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 452662010659 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 452662010660 catalytic triad [active] 452662010661 Precorrin-6A synthase, the cobalamin biosynthesis enzyme CobF; Region: Precorrin-6A-synthase; cd11643 452662010662 active site 452662010663 SAM binding site [chemical binding]; other site 452662010664 homodimer interface [polypeptide binding]; other site 452662010665 SpoVR family protein; Provisional; Region: PRK11767 452662010666 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 452662010667 hypothetical protein; Provisional; Region: PRK05325 452662010668 PrkA family serine protein kinase; Provisional; Region: PRK15455 452662010669 AAA ATPase domain; Region: AAA_16; pfam13191 452662010670 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 452662010671 recognition site for restriction enzyme SwaI 452662010672 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 452662010673 dimerization interface [polypeptide binding]; other site 452662010674 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 452662010675 ATP binding site [chemical binding]; other site 452662010676 Mg2+ binding site [ion binding]; other site 452662010677 G-X-G motif; other site 452662010678 two-component response regulator VirG; Provisional; Region: PRK13856 452662010679 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 452662010680 active site 452662010681 phosphorylation site [posttranslational modification] 452662010682 intermolecular recognition site; other site 452662010683 dimerization interface [polypeptide binding]; other site 452662010684 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 452662010685 DNA binding site [nucleotide binding] 452662010686 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 452662010687 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 452662010688 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662010689 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 452662010690 Protein export membrane protein; Region: SecD_SecF; cl14618 452662010691 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 452662010692 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 452662010693 homotrimer interface [polypeptide binding]; other site 452662010694 Walker A motif; other site 452662010695 GTP binding site [chemical binding]; other site 452662010696 Walker B motif; other site 452662010697 CobD/Cbib protein; Region: CobD_Cbib; pfam03186 452662010698 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 452662010699 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 452662010700 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662010701 homodimer interface [polypeptide binding]; other site 452662010702 catalytic residue [active] 452662010703 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 452662010704 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 452662010705 catalytic core [active] 452662010706 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 452662010707 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 452662010708 putative dimer interface [polypeptide binding]; other site 452662010709 active site pocket [active] 452662010710 putative cataytic base [active] 452662010711 Protein of unknown function (DUF1636); Region: DUF1636; pfam07845 452662010712 MgtC family; Region: MgtC; pfam02308 452662010713 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 452662010714 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 452662010715 dimer interface [polypeptide binding]; other site 452662010716 active site 452662010717 Protein of unknown function (DUF3422); Region: DUF3422; pfam11902 452662010718 SGNH_hydrolase subfamily, similar to the putative arylesterase/acylhydrolase from the rumen anaerobe Prevotella bryantii XynE. The P. bryantii XynE gene is located in a xylanase gene cluster. SGNH hydrolases are a diverse family of lipases and esterases; Region: XynE_like; cd01830 452662010719 active site 452662010720 catalytic triad [active] 452662010721 oxyanion hole [active] 452662010722 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 452662010723 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 452662010724 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 452662010725 ligand-binding site [chemical binding]; other site 452662010726 Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism]; Region: MtlD; COG0246 452662010727 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 452662010728 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 452662010729 glucuronate isomerase; Reviewed; Region: PRK02925 452662010730 Glucuronate isomerase [Carbohydrate transport and metabolism]; Region: UxaC; COG1904 452662010731 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 452662010732 D-galactonate transporter; Region: 2A0114; TIGR00893 452662010733 putative substrate translocation pore; other site 452662010734 bifunctional D-altronate/D-mannonate dehydratase; Provisional; Region: PRK15072 452662010735 The starvation sensing protein RpsA from E.coli and its homologs are lactonizing enzymes whose putative targets are homoserine lactone (HSL)-derivative. They are part of the mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of...; Region: rpsA; cd03322 452662010736 putative active site pocket [active] 452662010737 putative metal binding site [ion binding]; other site 452662010738 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 452662010739 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 452662010740 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 452662010741 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 452662010742 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 452662010743 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 452662010744 Alpha-glucuronidase [Carbohydrate transport and metabolism]; Region: AguA; COG3661 452662010745 Glycosyl hydrolase family 67 N-terminus; Region: Glyco_hydro_67N; pfam03648 452662010746 Glycosyl hydrolase family 67 C-terminus; Region: Glyco_hydro_67C; pfam07477 452662010747 Transcriptional regulators [Transcription]; Region: PurR; COG1609 452662010748 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 452662010749 DNA binding site [nucleotide binding] 452662010750 domain linker motif; other site 452662010751 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 452662010752 putative dimerization interface [polypeptide binding]; other site 452662010753 putative ligand binding site [chemical binding]; other site 452662010754 MarR family; Region: MarR_2; pfam12802 452662010755 MarR family; Region: MarR_2; cl17246 452662010756 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 452662010757 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 452662010758 This CD includes the dihydrorhizobitoxine fatty acid desaturase (RtxC) characterized in Bradyrhizobium japonicum USDA110, and other related proteins. Dihydrorhizobitoxine desaturase is reported to be involved in the final step of rhizobitoxine...; Region: Rhizobitoxine-FADS-like; cd03510 452662010759 Fatty acid desaturase; Region: FA_desaturase; pfam00487 452662010760 putative di-iron ligands [ion binding]; other site 452662010761 The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the...; Region: Membrane-FADS-like; cl00615 452662010762 DNA-binding transcriptional regulator CsiR; Provisional; Region: PRK11534 452662010763 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 452662010764 DNA-binding site [nucleotide binding]; DNA binding site 452662010765 FCD domain; Region: FCD; pfam07729 452662010766 2-dehydropantoate 2-reductase; Provisional; Region: PRK12921 452662010767 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 452662010768 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 452662010769 long-chain-fatty-acid--CoA ligase; Provisional; Region: PRK12406 452662010770 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 452662010771 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 452662010772 acyl-activating enzyme (AAE) consensus motif; other site 452662010773 putative AMP binding site [chemical binding]; other site 452662010774 putative active site [active] 452662010775 putative CoA binding site [chemical binding]; other site 452662010776 hydroxypyruvate isomerase; Region: OH-pyruv-isom; TIGR03234 452662010777 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 452662010778 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 452662010779 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 452662010780 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 452662010781 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662010782 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 452662010783 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 452662010784 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 452662010785 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 452662010786 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662010787 WHG domain; Region: WHG; pfam13305 452662010788 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 452662010789 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 452662010790 conserved cys residue [active] 452662010791 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 452662010792 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 452662010793 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662010794 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662010795 dimerization interface [polypeptide binding]; other site 452662010796 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 452662010797 EthD domain; Region: EthD; pfam07110 452662010798 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662010799 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662010800 NAD(P) binding site [chemical binding]; other site 452662010801 active site 452662010802 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662010803 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 452662010804 N-terminal plug; other site 452662010805 ligand-binding site [chemical binding]; other site 452662010806 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 452662010807 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 452662010808 [2Fe-2S] cluster binding site [ion binding]; other site 452662010809 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 452662010810 alpha subunit interface [polypeptide binding]; other site 452662010811 active site 452662010812 substrate binding site [chemical binding]; other site 452662010813 Fe binding site [ion binding]; other site 452662010814 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 452662010815 classical (c) SDRs; Region: SDR_c; cd05233 452662010816 NAD(P) binding site [chemical binding]; other site 452662010817 active site 452662010818 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662010819 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662010820 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662010821 The single-domain 2,3-dihydroxybiphenyl 1,2-dioxygenases (BphC, EC 1.13.11.39) from Rhodococcus globerulus P6, BphC2-RGP6 and BphC3-RGP6, and similar proteins; Region: BphC2-C3-RGP6_C_like; cd08348 452662010822 putative active site [active] 452662010823 putative metal binding site [ion binding]; other site 452662010824 hypothetical protein; Provisional; Region: PRK06126 452662010825 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 452662010826 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 452662010827 SnoaL-like domain; Region: SnoaL_4; pfam13577 452662010828 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662010829 classical (c) SDRs; Region: SDR_c; cd05233 452662010830 NAD(P) binding site [chemical binding]; other site 452662010831 active site 452662010832 Aromatic ring hydroxylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2368 452662010833 4-hydroxyphenylacetate 3-hydroxylase C terminal; Region: HpaB; pfam03241 452662010834 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 452662010835 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 452662010836 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 452662010837 dimerization interface [polypeptide binding]; other site 452662010838 active site 452662010839 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662010840 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 452662010841 substrate binding site [chemical binding]; other site 452662010842 oxyanion hole (OAH) forming residues; other site 452662010843 trimer interface [polypeptide binding]; other site 452662010844 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 452662010845 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662010846 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662010847 enoyl-CoA hydratase; Provisional; Region: PRK06190 452662010848 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662010849 substrate binding site [chemical binding]; other site 452662010850 oxyanion hole (OAH) forming residues; other site 452662010851 trimer interface [polypeptide binding]; other site 452662010852 acetyl-CoA acetyltransferase; Provisional; Region: PRK06504 452662010853 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 452662010854 dimer interface [polypeptide binding]; other site 452662010855 active site 452662010856 enoyl-CoA hydratase; Region: PLN02864 452662010857 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 452662010858 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 452662010859 active site 2 [active] 452662010860 active site 1 [active] 452662010861 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 452662010862 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662010863 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 452662010864 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08276 452662010865 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 452662010866 putative AMP binding site [chemical binding]; other site 452662010867 putative active site [active] 452662010868 acyl-activating enzyme (AAE) consensus motif; other site 452662010869 putative CoA binding site [chemical binding]; other site 452662010870 enoyl-CoA hydratase; Provisional; Region: PRK08140 452662010871 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662010872 substrate binding site [chemical binding]; other site 452662010873 oxyanion hole (OAH) forming residues; other site 452662010874 trimer interface [polypeptide binding]; other site 452662010875 enoyl-CoA hydratase; Provisional; Region: PRK07509 452662010876 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662010877 substrate binding site [chemical binding]; other site 452662010878 oxyanion hole (OAH) forming residues; other site 452662010879 trimer interface [polypeptide binding]; other site 452662010880 SnoaL-like domain; Region: SnoaL_4; pfam13577 452662010881 SnoaL-like domain; Region: SnoaL_3; pfam13474 452662010882 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 452662010883 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 452662010884 active site 452662010885 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662010886 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662010887 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 452662010888 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662010889 substrate binding site [chemical binding]; other site 452662010890 oxyanion hole (OAH) forming residues; other site 452662010891 trimer interface [polypeptide binding]; other site 452662010892 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 452662010893 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662010894 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 452662010895 acetyl-CoA acetyltransferase; Validated; Region: PRK08242 452662010896 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 452662010897 dimer interface [polypeptide binding]; other site 452662010898 active site 452662010899 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 452662010900 CoA-transferase family III; Region: CoA_transf_3; pfam02515 452662010901 SnoaL-like domain; Region: SnoaL_2; pfam12680 452662010902 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 452662010903 PQQ_like domain of the quinohemoprotein alcohol dehydrogenase (type II); Region: PQQ_ADH_II; cd10279 452662010904 Trp docking motif [polypeptide binding]; other site 452662010905 active site 452662010906 cytochrome domain interface [polypeptide binding]; other site 452662010907 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 452662010908 putative FAD-binding dehydrogenase; Reviewed; Region: PRK06134 452662010909 Predicted oxidoreductase [General function prediction only]; Region: COG3573 452662010910 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 452662010911 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 452662010912 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662010913 NAD(P) binding site [chemical binding]; other site 452662010914 active site 452662010915 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 452662010916 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08276 452662010917 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 452662010918 putative AMP binding site [chemical binding]; other site 452662010919 putative active site [active] 452662010920 acyl-activating enzyme (AAE) consensus motif; other site 452662010921 putative CoA binding site [chemical binding]; other site 452662010922 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 452662010923 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 452662010924 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 452662010925 active site 452662010926 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 452662010927 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 452662010928 [2Fe-2S] cluster binding site [ion binding]; other site 452662010929 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 452662010930 alpha subunit interface [polypeptide binding]; other site 452662010931 active site 452662010932 substrate binding site [chemical binding]; other site 452662010933 Fe binding site [ion binding]; other site 452662010934 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 452662010935 putative active site [active] 452662010936 putative catalytic site [active] 452662010937 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 452662010938 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 452662010939 NAD(P) binding site [chemical binding]; other site 452662010940 Phosphotransferase enzyme family; Region: APH; pfam01636 452662010941 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily 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: ACAD10_11_like; cd05154 452662010942 putative active site [active] 452662010943 putative substrate binding site [chemical binding]; other site 452662010944 ATP binding site [chemical binding]; other site 452662010945 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 452662010946 classical (c) SDRs; Region: SDR_c; cd05233 452662010947 NAD(P) binding site [chemical binding]; other site 452662010948 active site 452662010949 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 452662010950 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 452662010951 N-terminal plug; other site 452662010952 ligand-binding site [chemical binding]; other site 452662010953 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 452662010954 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 452662010955 substrate binding site [chemical binding]; other site 452662010956 oxyanion hole (OAH) forming residues; other site 452662010957 trimer interface [polypeptide binding]; other site 452662010958 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 452662010959 Cytochrome P450; Region: p450; cl12078 452662010960 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662010961 classical (c) SDRs; Region: SDR_c; cd05233 452662010962 NAD(P) binding site [chemical binding]; other site 452662010963 active site 452662010964 SnoaL-like domain; Region: SnoaL_4; pfam13577 452662010965 hypothetical protein; Provisional; Region: PRK06126 452662010966 hypothetical protein; Provisional; Region: PRK07236 452662010967 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 452662010968 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662010969 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662010970 recognition site for restriction enzyme PacI 452662010971 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 452662010972 The single-domain 2,3-dihydroxybiphenyl 1,2-dioxygenases (BphC, EC 1.13.11.39) from Rhodococcus globerulus P6, BphC2-RGP6 and BphC3-RGP6, and similar proteins; Region: BphC2-C3-RGP6_C_like; cd08348 452662010973 putative active site [active] 452662010974 putative metal binding site [ion binding]; other site 452662010975 Domain of unknown function (DUF2437); Region: DUF2437; pfam10370 452662010976 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 452662010977 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 452662010978 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 452662010979 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 452662010980 putative DNA binding site [nucleotide binding]; other site 452662010981 putative Zn2+ binding site [ion binding]; other site 452662010982 AsnC family; Region: AsnC_trans_reg; pfam01037 452662010983 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 452662010984 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 452662010985 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 452662010986 pyridoxal 5'-phosphate binding site [chemical binding]; other site 452662010987 homodimer interface [polypeptide binding]; other site 452662010988 catalytic residue [active] 452662010989 aldolase II superfamily protein; Provisional; Region: PRK07044 452662010990 intersubunit interface [polypeptide binding]; other site 452662010991 active site 452662010992 Zn2+ binding site [ion binding]; other site 452662010993 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 452662010994 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 452662010995 membrane-bound complex binding site; other site 452662010996 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 452662010997 active site residue [active] 452662010998 Member of the Rhodanese Homology Domain superfamily, repeat 2. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic...; Region: 4RHOD_Repeat_2; cd01533 452662010999 active site residue [active] 452662011000 Member of the Rhodanese Homology Domain superfamily, repeat 3. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative...; Region: 4RHOD_Repeat_3; cd01534 452662011001 active site residue [active] 452662011002 Predicted metal-dependent enzyme of the double-stranded beta helix superfamily [General function prediction only]; Region: COG5553 452662011003 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 452662011004 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 452662011005 Walker A/P-loop; other site 452662011006 ATP binding site [chemical binding]; other site 452662011007 Q-loop/lid; other site 452662011008 ABC transporter signature motif; other site 452662011009 Walker B; other site 452662011010 D-loop; other site 452662011011 H-loop/switch region; other site 452662011012 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 452662011013 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 452662011014 dimer interface [polypeptide binding]; other site 452662011015 conserved gate region; other site 452662011016 ABC-ATPase subunit interface; other site 452662011017 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662011018 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662011019 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 452662011020 dimerization interface [polypeptide binding]; other site 452662011021 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 452662011022 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain; Region: 2-Hacid_dh; pfam00389 452662011023 NAD binding site [chemical binding]; other site 452662011024 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 452662011025 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 452662011026 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 452662011027 active site 452662011028 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 452662011029 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 452662011030 substrate binding pocket [chemical binding]; other site 452662011031 membrane-bound complex binding site; other site 452662011032 reductive dehalogenase; Region: RDH; TIGR02486 452662011033 4Fe-4S binding domain; Region: Fer4; pfam00037 452662011034 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 452662011035 active site 452662011036 metal binding site [ion binding]; metal-binding site 452662011037 Bacillus subtilis YvnB and related proteins, metallophosphatase domain; Region: MPP_YvnB; cd07399 452662011038 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 452662011039 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662011040 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 452662011041 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 452662011042 catalytic residues [active] 452662011043 catalytic nucleophile [active] 452662011044 Presynaptic Site I dimer interface [polypeptide binding]; other site 452662011045 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 452662011046 Synaptic Flat tetramer interface [polypeptide binding]; other site 452662011047 Synaptic Site I dimer interface [polypeptide binding]; other site 452662011048 DNA binding site [nucleotide binding] 452662011049 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 452662011050 DNA-binding interface [nucleotide binding]; DNA binding site 452662011051 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 452662011052 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 452662011053 ParB-like nuclease domain; Region: ParB; smart00470 452662011054 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 452662011055 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 452662011056 Fic/DOC family; Region: Fic; cl00960 452662011057 Protein of unknown function (DUF3768); Region: DUF3768; pfam12599 452662011058 Methyltransferase domain; Region: Methyltransf_27; pfam13708 452662011059 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 452662011060 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 452662011061 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 452662011062 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662011063 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 452662011064 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 452662011065 non-specific DNA binding site [nucleotide binding]; other site 452662011066 salt bridge; other site 452662011067 sequence-specific DNA binding site [nucleotide binding]; other site 452662011068 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 452662011069 DNA binding residues [nucleotide binding] 452662011070 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 452662011071 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 452662011072 catalytic residues [active] 452662011073 catalytic nucleophile [active] 452662011074 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl17393 452662011075 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 452662011076 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 452662011077 dimer interface [polypeptide binding]; other site 452662011078 ssDNA binding site [nucleotide binding]; other site 452662011079 tetramer (dimer of dimers) interface [polypeptide binding]; other site 452662011080 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 452662011081 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 452662011082 P-loop; other site 452662011083 Magnesium ion binding site [ion binding]; other site 452662011084 ParB-like nuclease domain; Region: ParBc; pfam02195 452662011085 may be target duplication site 452662011086 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662011087 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662011088 Integrase core domain; Region: rve; pfam00665 452662011089 type IV secretion system T-DNA border endonuclease VirD2; Provisional; Region: PRK13863 452662011090 may be target duplication site 452662011091 may be target duplication site 452662011092 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 452662011093 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 452662011094 Integrase core domain; Region: rve; pfam00665 452662011095 may be target duplication site 452662011096 glutathionine S-transferase; Provisional; Region: PRK10542 452662011097 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 452662011098 C-terminal domain interface [polypeptide binding]; other site 452662011099 GSH binding site (G-site) [chemical binding]; other site 452662011100 dimer interface [polypeptide binding]; other site 452662011101 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 452662011102 substrate binding pocket (H-site) [chemical binding]; other site 452662011103 dimer interface [polypeptide binding]; other site 452662011104 N-terminal domain interface [polypeptide binding]; other site 452662011105 putative hydrolase; Provisional; Region: PRK11460 452662011106 Predicted esterase [General function prediction only]; Region: COG0400 452662011107 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 452662011108 Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes; Region: MAR; cd08177 452662011109 active site 452662011110 dimer interface [polypeptide binding]; other site 452662011111 metal binding site [ion binding]; metal-binding site 452662011112 Transcriptional regulator [Transcription]; Region: LysR; COG0583 452662011113 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 452662011114 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 452662011115 substrate binding pocket [chemical binding]; other site 452662011116 dimerization interface [polypeptide binding]; other site 452662011117 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 452662011118 Zn binding site [ion binding]; other site 452662011119 C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_C_like; cd08347 452662011120 Zn binding site [ion binding]; other site 452662011121 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 452662011122 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 452662011123 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 452662011124 Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: ECM4; COG0435 452662011125 Glutathione S-transferase, N-terminal domain; Region: GST_N_2; pfam13409 452662011126 C-terminal, alpha helical domain of Class Omega-like Glutathione S-transferases; Region: GST_C_Omega_like; cd03190 452662011127 putative dimer interface [polypeptide binding]; other site 452662011128 N-terminal domain interface [polypeptide binding]; other site 452662011129 putative substrate binding pocket (H-site) [chemical binding]; other site 452662011130 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 452662011131 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 452662011132 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 452662011133 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; cd02933 452662011134 FMN binding site [chemical binding]; other site 452662011135 active site 452662011136 substrate binding site [chemical binding]; other site 452662011137 catalytic residue [active] 452662011138 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662011139 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662011140 Protein of unknown function (DUF1271); Region: DUF1271; cl01443 452662011141 4Fe-4S single cluster domain; Region: Fer4_15; pfam13459 452662011142 Benzyl alcohol dehydrogenase; Region: benzyl_alcohol_DH; cd08278 452662011143 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 452662011144 catalytic Zn binding site [ion binding]; other site 452662011145 NAD binding site [chemical binding]; other site 452662011146 structural Zn binding site [ion binding]; other site 452662011147 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 452662011148 Cytochrome P450; Region: p450; cl12078 452662011149 (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel...; Region: R_hydratase_like; cd03441 452662011150 active site 452662011151 catalytic site [active] 452662011152 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 452662011153 active site 2 [active] 452662011154 active site 1 [active] 452662011155 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 452662011156 CoA-transferase family III; Region: CoA_transf_3; pfam02515 452662011157 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 452662011158 CoA-transferase family III; Region: CoA_transf_3; pfam02515 452662011159 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 452662011160 Streptomyces aureofaciens putative aldehyde dehydrogenase AldA (AAD23400)-like; Region: ALDH_AldA-AAD23400; cd07106 452662011161 NAD(P) binding site [chemical binding]; other site 452662011162 catalytic residues [active] 452662011163 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662011164 NAD(P) binding site [chemical binding]; other site 452662011165 active site 452662011166 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 452662011167 DUF35 OB-fold domain; Region: DUF35; pfam01796 452662011168 thiolase; Provisional; Region: PRK06158 452662011169 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 452662011170 active site 452662011171 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662011172 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 452662011173 N-terminal plug; other site 452662011174 ligand-binding site [chemical binding]; other site 452662011175 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 452662011176 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 452662011177 tetramerization interface [polypeptide binding]; other site 452662011178 NAD(P) binding site [chemical binding]; other site 452662011179 catalytic residues [active] 452662011180 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 452662011181 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 452662011182 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662011183 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662011184 NAD(P) binding site [chemical binding]; other site 452662011185 active site 452662011186 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 452662011187 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 452662011188 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 452662011189 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 452662011190 NAD(P) binding site [chemical binding]; other site 452662011191 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 452662011192 classical (c) SDRs; Region: SDR_c; cd05233 452662011193 NAD(P) binding site [chemical binding]; other site 452662011194 active site 452662011195 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662011196 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 452662011197 N-terminal plug; other site 452662011198 ligand-binding site [chemical binding]; other site 452662011199 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 452662011200 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 452662011201 FMN binding site [chemical binding]; other site 452662011202 substrate binding site [chemical binding]; other site 452662011203 putative catalytic residue [active] 452662011204 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662011205 WHG domain; Region: WHG; pfam13305 452662011206 Predicted transcriptional regulators [Transcription]; Region: COG1733 452662011207 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 452662011208 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 452662011209 Prostaglandin dehydrogenases; Region: PGDH; cd05288 452662011210 NAD(P) binding site [chemical binding]; other site 452662011211 substrate binding site [chemical binding]; other site 452662011212 dimer interface [polypeptide binding]; other site 452662011213 acetyl-CoA acetyltransferase; Provisional; Region: PRK06205 452662011214 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 452662011215 dimer interface [polypeptide binding]; other site 452662011216 active site 452662011217 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 452662011218 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 452662011219 Bacterial transcriptional regulator; Region: IclR; pfam01614 452662011220 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 452662011221 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 452662011222 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 452662011223 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 452662011224 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 452662011225 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 452662011226 Protein export membrane protein; Region: SecD_SecF; cl14618 452662011227 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 452662011228 HlyD family secretion protein; Region: HlyD_3; pfam13437 452662011229 MltA-interacting protein MipA; Region: MipA; cl01504 452662011230 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 452662011231 LytTr DNA-binding domain; Region: LytTR; pfam04397 452662011232 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662011233 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662011234 WHG domain; Region: WHG; pfam13305 452662011235 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 452662011236 Cupin superfamily protein; Region: Cupin_4; pfam08007 452662011237 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 452662011238 pseudouridine synthase; Region: TIGR00093 452662011239 active site 452662011240 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 452662011241 Protein of unknown function (DUF328); Region: DUF328; pfam03883 452662011242 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 452662011243 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 452662011244 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 452662011245 cellulose synthase operon protein YhjQ; Region: cellulose_yhjQ; TIGR03371 452662011246 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 452662011247 cellulose synthase catalytic subunit (UDP-forming); Region: CelA; TIGR03030 452662011248 CESA_CelA_like are involved in the elongation of the glucan chain of cellulose; Region: CESA_CelA_like; cd06421 452662011249 DXD motif; other site 452662011250 PilZ domain; Region: PilZ; pfam07238 452662011251 cellulose synthase regulator protein; Provisional; Region: PRK11114 452662011252 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 452662011253 TPR motif; other site 452662011254 binding surface 452662011255 Cellulose synthase operon protein C C-terminus (BCSC_C); Region: BCSC_C; pfam05420 452662011256 Glycosyl hydrolases family 8; Region: Glyco_hydro_8; cl01351 452662011257 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 452662011258 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 452662011259 active site 452662011260 Zn binding site [ion binding]; other site 452662011261 gluconate 5-dehydrogenase; Provisional; Region: PRK06124 452662011262 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 452662011263 NAD(P) binding site [chemical binding]; other site 452662011264 active site 452662011265 Major Facilitator Superfamily; Region: MFS_1; pfam07690 452662011266 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 452662011267 short chain dehydrogenase; Provisional; Region: PRK06701 452662011268 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 452662011269 NAD binding site [chemical binding]; other site 452662011270 metal binding site [ion binding]; metal-binding site 452662011271 active site 452662011272 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 452662011273 PAS fold; Region: PAS_3; pfam08447 452662011274 putative active site [active] 452662011275 heme pocket [chemical binding]; other site 452662011276 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 452662011277 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 452662011278 metal binding site [ion binding]; metal-binding site 452662011279 active site 452662011280 I-site; other site 452662011281 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 452662011282 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662011283 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 452662011284 N-terminal plug; other site 452662011285 ligand-binding site [chemical binding]; other site 452662011286 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 452662011287 DNA binding residues [nucleotide binding] 452662011288 Autoinducer synthetase; Region: Autoind_synth; cl17404 452662011289 Phosphopantetheine attachment site; Region: PP-binding; cl09936 452662011290 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 452662011291 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 452662011292 S-adenosylmethionine binding site [chemical binding]; other site 452662011293 acyl-CoA synthetase; Validated; Region: PRK05850 452662011294 Fatty acyl-AMP ligase (FAAL); Region: FAAL; cd05931 452662011295 acyl-activating enzyme (AAE) consensus motif; other site 452662011296 active site 452662011297 Protein of unknown function (DUF3121); Region: DUF3121; cl11879 452662011298 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 452662011299 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 452662011300 dimer interface [polypeptide binding]; other site 452662011301 phosphorylation site [posttranslational modification] 452662011302 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 452662011303 ATP binding site [chemical binding]; other site 452662011304 Mg2+ binding site [ion binding]; other site 452662011305 G-X-G motif; other site 452662011306 Response regulator receiver domain; Region: Response_reg; pfam00072 452662011307 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 452662011308 active site 452662011309 phosphorylation site [posttranslational modification] 452662011310 intermolecular recognition site; other site 452662011311 dimerization interface [polypeptide binding]; other site 452662011312 acetyl-CoA synthetase; Provisional; Region: PRK00174 452662011313 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 452662011314 active site 452662011315 CoA binding site [chemical binding]; other site 452662011316 acyl-activating enzyme (AAE) consensus motif; other site 452662011317 AMP binding site [chemical binding]; other site 452662011318 acetate binding site [chemical binding]; other site 452662011319 Plastocyanin [Energy production and conversion]; Region: PetE; COG3794 452662011320 Cupredoxin-like domain; Region: Cupredoxin_1; cl17234 452662011321 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 452662011322 active site residue [active] 452662011323 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 452662011324 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 452662011325 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 452662011326 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 452662011327 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 452662011328 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 452662011329 Short C-terminal domain; Region: SHOCT; pfam09851 452662011330 Gram-negative porin; Region: Porin_4; pfam13609 452662011331 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 452662011332 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 452662011333 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 452662011334 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 452662011335 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 452662011336 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 452662011337 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 452662011338 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 452662011339 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 452662011340 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 452662011341 dimer interface [polypeptide binding]; other site 452662011342 Trp docking motif [polypeptide binding]; other site 452662011343 active site 452662011344 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 452662011345 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 452662011346 active site 452662011347 phosphorylation site [posttranslational modification] 452662011348 intermolecular recognition site; other site 452662011349 dimerization interface [polypeptide binding]; other site 452662011350 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 452662011351 DNA binding residues [nucleotide binding] 452662011352 dimerization interface [polypeptide binding]; other site 452662011353 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 452662011354 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 452662011355 Coenzyme A binding pocket [chemical binding]; other site 452662011356 YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze...; Region: YbaK_like; cd04332 452662011357 putative deacylase active site [active] 452662011358 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 452662011359 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 452662011360 dimer interface [polypeptide binding]; other site 452662011361 active site 452662011362 heme binding site [chemical binding]; other site 452662011363 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 452662011364 PAS fold; Region: PAS_7; pfam12860 452662011365 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 452662011366 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 452662011367 dimer interface [polypeptide binding]; other site 452662011368 phosphorylation site [posttranslational modification] 452662011369 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 452662011370 ATP binding site [chemical binding]; other site 452662011371 Mg2+ binding site [ion binding]; other site 452662011372 G-X-G motif; other site 452662011373 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 452662011374 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 452662011375 active site 452662011376 phosphorylation site [posttranslational modification] 452662011377 intermolecular recognition site; other site 452662011378 dimerization interface [polypeptide binding]; other site 452662011379 Uncharacterized conserved protein [Function unknown]; Region: COG3287 452662011380 FIST N domain; Region: FIST; pfam08495 452662011381 FIST C domain; Region: FIST_C; pfam10442 452662011382 Protein of unknown function (DUF779); Region: DUF779; pfam05610 452662011383 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 452662011384 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 452662011385 NAD(P) binding site [chemical binding]; other site 452662011386 catalytic residues [active] 452662011387 putative acyltransferase; Provisional; Region: PRK05790 452662011388 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 452662011389 dimer interface [polypeptide binding]; other site 452662011390 active site 452662011391 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 452662011392 CoenzymeA binding site [chemical binding]; other site 452662011393 subunit interaction site [polypeptide binding]; other site 452662011394 PHB binding site; other site 452662011395 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 452662011396 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 452662011397 glycosyl hydrolase family 16; Region: Glyco_hydrolase_16; cl00218 452662011398 active site 452662011399 catalytic residues [active] 452662011400 plasmid partitioning protein RepA; Region: partition_RepA; TIGR03453 452662011401 MerR family regulatory protein; Region: MerR; pfam00376 452662011402 DNA binding residues [nucleotide binding] 452662011403 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 452662011404 P-loop; other site 452662011405 Magnesium ion binding site [ion binding]; other site 452662011406 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 452662011407 Magnesium ion binding site [ion binding]; other site 452662011408 ParB-like nuclease domain; Region: ParBc; pfam02195