-- dump date 20120504_141152 -- class Genbank::misc_feature -- table misc_feature_note -- id note 565050000001 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 565050000002 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 565050000003 active site 565050000004 dimer interface [polypeptide binding]; other site 565050000005 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 565050000006 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 565050000007 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 565050000008 shikimate binding site; other site 565050000009 NAD(P) binding site [chemical binding]; other site 565050000010 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 565050000011 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 565050000012 CoA-binding site [chemical binding]; other site 565050000013 ATP-binding [chemical binding]; other site 565050000014 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 565050000015 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 565050000016 active site 565050000017 substrate binding site [chemical binding]; other site 565050000018 catalytic site [active] 565050000019 enoyl-CoA hydratase; Provisional; Region: PRK05862 565050000020 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 565050000021 substrate binding site [chemical binding]; other site 565050000022 oxyanion hole (OAH) forming residues; other site 565050000023 trimer interface [polypeptide binding]; other site 565050000024 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 565050000025 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 565050000026 DnaA N-terminal domain; Region: DnaA_N; pfam11638 565050000027 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 565050000028 Walker A motif; other site 565050000029 ATP binding site [chemical binding]; other site 565050000030 Walker B motif; other site 565050000031 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 565050000032 DnaA box-binding interface [nucleotide binding]; other site 565050000033 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 565050000034 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 565050000035 chaperone protein DnaJ; Provisional; Region: PRK10767 565050000036 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 565050000037 HSP70 interaction site [polypeptide binding]; other site 565050000038 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 565050000039 substrate binding site [polypeptide binding]; other site 565050000040 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 565050000041 Zn binding sites [ion binding]; other site 565050000042 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 565050000043 dimer interface [polypeptide binding]; other site 565050000044 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 565050000045 MutS domain I; Region: MutS_I; pfam01624 565050000046 MutS domain II; Region: MutS_II; pfam05188 565050000047 MutS family domain IV; Region: MutS_IV; pfam05190 565050000048 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050000049 Walker A/P-loop; other site 565050000050 ATP binding site [chemical binding]; other site 565050000051 Q-loop/lid; other site 565050000052 ABC transporter signature motif; other site 565050000053 Walker B; other site 565050000054 D-loop; other site 565050000055 H-loop/switch region; other site 565050000056 PII uridylyl-transferase; Provisional; Region: PRK05092 565050000057 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 565050000058 metal binding triad; other site 565050000059 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 565050000060 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 565050000061 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 565050000062 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 565050000063 trimer interface [polypeptide binding]; other site 565050000064 dimer interface [polypeptide binding]; other site 565050000065 putative active site [active] 565050000066 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 565050000067 MPT binding site; other site 565050000068 trimer interface [polypeptide binding]; other site 565050000069 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 565050000070 MoaE homodimer interface [polypeptide binding]; other site 565050000071 MoaD interaction [polypeptide binding]; other site 565050000072 active site residues [active] 565050000073 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 565050000074 MoaE interaction surface [polypeptide binding]; other site 565050000075 MoeB interaction surface [polypeptide binding]; other site 565050000076 thiocarboxylated glycine; other site 565050000077 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 565050000078 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 565050000079 FeS/SAM binding site; other site 565050000080 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 565050000081 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 565050000082 Ligand binding site; other site 565050000083 metal-binding site 565050000084 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 565050000085 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 565050000086 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 565050000087 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 565050000088 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 565050000089 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 565050000090 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 565050000091 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 565050000092 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 565050000093 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050000094 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 565050000095 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 565050000096 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 565050000097 putative substrate translocation pore; other site 565050000098 metabolite-proton symporter; Region: 2A0106; TIGR00883 565050000099 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 565050000100 PAS domain; Region: PAS_9; pfam13426 565050000101 putative active site [active] 565050000102 heme pocket [chemical binding]; other site 565050000103 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 565050000104 putative active site [active] 565050000105 heme pocket [chemical binding]; other site 565050000106 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 565050000107 PAS fold; Region: PAS_4; pfam08448 565050000108 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 565050000109 PAS fold; Region: PAS_3; pfam08447 565050000110 putative active site [active] 565050000111 heme pocket [chemical binding]; other site 565050000112 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 565050000113 dimer interface [polypeptide binding]; other site 565050000114 phosphorylation site [posttranslational modification] 565050000115 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 565050000116 ATP binding site [chemical binding]; other site 565050000117 Mg2+ binding site [ion binding]; other site 565050000118 G-X-G motif; other site 565050000119 Response regulator receiver domain; Region: Response_reg; pfam00072 565050000120 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 565050000121 active site 565050000122 phosphorylation site [posttranslational modification] 565050000123 intermolecular recognition site; other site 565050000124 dimerization interface [polypeptide binding]; other site 565050000125 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 565050000126 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 565050000127 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 565050000128 N-terminal plug; other site 565050000129 ligand-binding site [chemical binding]; other site 565050000130 LysE type translocator; Region: LysE; cl00565 565050000131 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf...; Region: RNase_T2_prok; cd01062 565050000132 B1 nucleotide binding pocket [chemical binding]; other site 565050000133 B2 nucleotide binding pocket [chemical binding]; other site 565050000134 CAS motifs; other site 565050000135 active site 565050000136 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 565050000137 oligomeric interface; other site 565050000138 putative active site [active] 565050000139 homodimer interface [polypeptide binding]; other site 565050000140 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 565050000141 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 565050000142 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 565050000143 RNase E interface [polypeptide binding]; other site 565050000144 trimer interface [polypeptide binding]; other site 565050000145 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 565050000146 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 565050000147 RNase E interface [polypeptide binding]; other site 565050000148 trimer interface [polypeptide binding]; other site 565050000149 active site 565050000150 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 565050000151 putative nucleic acid binding region [nucleotide binding]; other site 565050000152 G-X-X-G motif; other site 565050000153 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 565050000154 RNA binding site [nucleotide binding]; other site 565050000155 domain interface; other site 565050000156 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 565050000157 16S/18S rRNA binding site [nucleotide binding]; other site 565050000158 S13e-L30e interaction site [polypeptide binding]; other site 565050000159 25S rRNA binding site [nucleotide binding]; other site 565050000160 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05389 565050000161 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific...; Region: PseudoU_synth_EcTruB; cd02573 565050000162 RNA binding site [nucleotide binding]; other site 565050000163 active site 565050000164 Ribosome-binding factor A; Region: RBFA; cl00542 565050000165 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 565050000166 Protein of unknown function (DUF2939); Region: DUF2939; pfam11159 565050000167 YcxB-like protein; Region: YcxB; pfam14317 565050000168 translation initiation factor IF-2; Region: IF-2; TIGR00487 565050000169 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 565050000170 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 565050000171 G1 box; other site 565050000172 putative GEF interaction site [polypeptide binding]; other site 565050000173 GTP/Mg2+ binding site [chemical binding]; other site 565050000174 Switch I region; other site 565050000175 G2 box; other site 565050000176 G3 box; other site 565050000177 Switch II region; other site 565050000178 G4 box; other site 565050000179 G5 box; other site 565050000180 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 565050000181 Translation-initiation factor 2; Region: IF-2; pfam11987 565050000182 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 565050000183 hypothetical protein; Provisional; Region: PRK09190 565050000184 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cd00279 565050000185 putative RNA binding cleft [nucleotide binding]; other site 565050000186 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 565050000187 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 565050000188 NusA N-terminal domain; Region: NusA_N; pfam08529 565050000189 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 565050000190 RNA binding site [nucleotide binding]; other site 565050000191 homodimer interface [polypeptide binding]; other site 565050000192 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 565050000193 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 565050000194 G-X-X-G motif; other site 565050000195 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 565050000196 ribosome maturation protein RimP; Reviewed; Region: PRK00092 565050000197 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 565050000198 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 565050000199 Sm1 motif; other site 565050000200 D3 - B interaction site; other site 565050000201 D1 - D2 interaction site; other site 565050000202 Hfq - Hfq interaction site; other site 565050000203 RNA binding pocket [nucleotide binding]; other site 565050000204 Sm2 motif; other site 565050000205 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 565050000206 dimer interface [polypeptide binding]; other site 565050000207 substrate binding site [chemical binding]; other site 565050000208 metal binding sites [ion binding]; metal-binding site 565050000209 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; cl15754 565050000210 S-adenosylmethionine synthetase; Validated; Region: PRK05250 565050000211 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 565050000212 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 565050000213 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 565050000214 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 565050000215 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 565050000216 non-specific DNA binding site [nucleotide binding]; other site 565050000217 salt bridge; other site 565050000218 sequence-specific DNA binding site [nucleotide binding]; other site 565050000219 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 565050000220 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 565050000221 putative active site [active] 565050000222 catalytic triad [active] 565050000223 putative dimer interface [polypeptide binding]; other site 565050000224 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 565050000225 Transporter associated domain; Region: CorC_HlyC; cl08393 565050000226 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 565050000227 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 565050000228 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050000229 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 565050000230 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 565050000231 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 565050000232 FeS/SAM binding site; other site 565050000233 TRAM domain; Region: TRAM; cl01282 565050000234 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 565050000235 metal binding site 2 [ion binding]; metal-binding site 565050000236 putative DNA binding helix; other site 565050000237 metal binding site 1 [ion binding]; metal-binding site 565050000238 dimer interface [polypeptide binding]; other site 565050000239 structural Zn2+ binding site [ion binding]; other site 565050000240 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 565050000241 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050000242 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 565050000243 RpoE-regulated lipoprotein; Provisional; Region: PRK10718 565050000244 Protein of unknown function (DUF1131); Region: DUF1131; pfam06572 565050000245 Nitroreductase-like family 5. 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_5; cd02148 565050000246 putative FMN binding site [chemical binding]; other site 565050000247 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; cl07364 565050000248 NifU-like domain; Region: NifU; cl00484 565050000249 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; cl12078 565050000250 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 565050000251 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 565050000252 active site 565050000253 HIGH motif; other site 565050000254 dimer interface [polypeptide binding]; other site 565050000255 KMSKS motif; other site 565050000256 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 565050000257 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050000258 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050000259 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050000260 dimer interface [polypeptide binding]; other site 565050000261 putative CheW interface [polypeptide binding]; other site 565050000262 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050000263 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; cd03467 565050000264 iron-sulfur cluster [ion binding]; other site 565050000265 [2Fe-2S] cluster binding site [ion binding]; other site 565050000266 YCII-related domain; Region: YCII; cl00999 565050000267 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 565050000268 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050000269 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 565050000270 UGMP family protein; Validated; Region: PRK09604 565050000271 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 565050000272 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; cl03189 565050000273 domain interfaces; other site 565050000274 active site 565050000275 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 565050000276 active site 565050000277 Uroporphyrinogen-III synthase HemD; Region: HEM4; pfam02602 565050000278 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4223 565050000279 Uncharacterized membrane-bound protein [Function unknown]; Region: COG3898 565050000280 HemY protein N-terminus; Region: HemY_N; pfam07219 565050000281 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 565050000282 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 565050000283 substrate binding site [chemical binding]; other site 565050000284 oxyanion hole (OAH) forming residues; other site 565050000285 trimer interface [polypeptide binding]; other site 565050000286 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050000287 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 565050000288 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 565050000289 acetyl-CoA acetyltransferase; Validated; Region: PRK08242 565050000290 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 565050000291 dimer interface [polypeptide binding]; other site 565050000292 active site 565050000293 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 565050000294 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 565050000295 active site 565050000296 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 565050000297 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 565050000298 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 565050000299 active site 565050000300 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 565050000301 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 565050000302 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 565050000303 DNA binding residues [nucleotide binding] 565050000304 putative dimer interface [polypeptide binding]; other site 565050000305 Predicted transcriptional regulator [Transcription]; Region: COG2932 565050000306 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 565050000307 Catalytic site [active] 565050000308 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 565050000309 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 565050000310 active site 565050000311 nucleotide binding site [chemical binding]; other site 565050000312 HIGH motif; other site 565050000313 KMSKS motif; other site 565050000314 phosphoglucomutase; Validated; Region: PRK07564 565050000315 The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine...; Region: phosphohexomutase; cl03757 565050000316 active site 565050000317 substrate binding site [chemical binding]; other site 565050000318 metal binding site [ion binding]; metal-binding site 565050000319 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 565050000320 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 565050000321 purine monophosphate binding site [chemical binding]; other site 565050000322 dimer interface [polypeptide binding]; other site 565050000323 putative catalytic residues [active] 565050000324 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 565050000325 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 565050000326 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 565050000327 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; cl12031 565050000328 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 565050000329 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 565050000330 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 565050000331 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 565050000332 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 565050000333 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 565050000334 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 565050000335 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 565050000336 PAS domain S-box; Region: sensory_box; TIGR00229 565050000337 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 565050000338 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 565050000339 metal binding site [ion binding]; metal-binding site 565050000340 active site 565050000341 I-site; other site 565050000342 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 565050000343 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 565050000344 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 565050000345 NAD binding site [chemical binding]; other site 565050000346 homodimer interface [polypeptide binding]; other site 565050000347 active site 565050000348 substrate binding site [chemical binding]; other site 565050000349 EamA-like transporter family; Region: EamA; cl01037 565050000350 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 565050000351 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050000352 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 565050000353 NAD(P) binding site [chemical binding]; other site 565050000354 active site 565050000355 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 565050000356 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 565050000357 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 565050000358 NAD(P) binding site [chemical binding]; other site 565050000359 L-Asparaginase type 2. L-Asparaginase hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzyme undergoes an autoproteolytic cleavage into alpha and beta subunits to expose a threonine residue which becomes the N-terminal residue of the beta...; Region: Asparaginase_2; cd04701 565050000360 catalytic nucleophile [active] 565050000361 Heparinase II/III-like protein; Region: Hepar_II_III; cl15421 565050000362 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 565050000363 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 565050000364 substrate binding site [chemical binding]; other site 565050000365 hexamer interface [polypeptide binding]; other site 565050000366 metal binding site [ion binding]; metal-binding site 565050000367 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 565050000368 putative RNA binding site [nucleotide binding]; other site 565050000369 16S rRNA methyltransferase B; Provisional; Region: PRK10901 565050000370 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; cl15754 565050000371 S-adenosylmethionine binding site [chemical binding]; other site 565050000372 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 565050000373 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 565050000374 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 565050000375 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 contains two...; Region: OMP_decarboxylase_like; cd04725 565050000376 active site 565050000377 dimer interface [polypeptide binding]; other site 565050000378 MarC family integral membrane protein; Region: MarC; cl00919 565050000379 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050000380 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 565050000381 Trm112p-like protein; Region: Trm112p; cl01066 565050000382 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 565050000383 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 565050000384 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 565050000385 Uncharacterized conserved protein [Function unknown]; Region: COG3760 565050000386 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 565050000387 putative deacylase active site [active] 565050000388 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 565050000389 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050000390 Helix-turn-helix domains; Region: HTH; cl00088 565050000391 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 565050000392 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 565050000393 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 565050000394 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 565050000395 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 565050000396 N-ethylammeline chlorohydrolase; Provisional; Region: PRK06038 565050000397 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 565050000398 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 565050000399 active site 565050000400 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14315 565050000401 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 565050000402 active site 565050000403 substrate binding site [chemical binding]; other site 565050000404 metal binding site [ion binding]; metal-binding site 565050000405 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 565050000406 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 565050000407 glutaminase active site [active] 565050000408 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 565050000409 dimer interface [polypeptide binding]; other site 565050000410 active site 565050000411 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 565050000412 dimer interface [polypeptide binding]; other site 565050000413 active site 565050000414 Tetratricopeptide repeat; Region: TPR_16; pfam13432 565050000415 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 565050000416 TPR motif; other site 565050000417 binding surface 565050000418 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 565050000419 TPR motif; other site 565050000420 binding surface 565050000421 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 565050000422 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 565050000423 binding surface 565050000424 TPR motif; other site 565050000425 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 565050000426 homodimer interaction site [polypeptide binding]; other site 565050000427 cofactor binding site; other site 565050000428 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050000429 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 565050000430 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 565050000431 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 565050000432 NAD binding site [chemical binding]; other site 565050000433 homotetramer interface [polypeptide binding]; other site 565050000434 homodimer interface [polypeptide binding]; other site 565050000435 active site 565050000436 LysE type translocator; Region: LysE; cl00565 565050000437 MAPEG family; Region: MAPEG; cl09190 565050000438 KTSC domain; Region: KTSC; pfam13619 565050000439 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 565050000440 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 565050000441 ANP binding site [chemical binding]; other site 565050000442 Substrate Binding Site II [chemical binding]; other site 565050000443 Substrate Binding Site I [chemical binding]; other site 565050000444 K+ potassium transporter; Region: K_trans; cl15781 565050000445 potassium uptake protein; Region: kup; TIGR00794 565050000446 Helix-turn-helix domains; Region: HTH; cl00088 565050000447 Rrf2 family protein; Region: rrf2_super; TIGR00738 565050000448 classical (c) SDRs; Region: SDR_c; cd05233 565050000449 NAD(P) binding site [chemical binding]; other site 565050000450 active site 565050000451 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 565050000452 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 565050000453 FeS/SAM binding site; other site 565050000454 Predicted membrane protein [Function unknown]; Region: COG3766 565050000455 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 565050000456 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 565050000457 muropeptide transporter; Validated; Region: ampG; PRK11010 565050000458 muropeptide transporter; Validated; Region: ampG; PRK11010 565050000459 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 565050000460 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 565050000461 dimer interface [polypeptide binding]; other site 565050000462 phosphorylation site [posttranslational modification] 565050000463 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 565050000464 Mg2+ binding site [ion binding]; other site 565050000465 G-X-G motif; other site 565050000466 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 565050000467 active site 565050000468 phosphorylation site [posttranslational modification] 565050000469 intermolecular recognition site; other site 565050000470 dimerization interface [polypeptide binding]; other site 565050000471 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 565050000472 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 565050000473 N-terminal plug; other site 565050000474 ligand-binding site [chemical binding]; other site 565050000475 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 565050000476 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 565050000477 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 565050000478 Walker A motif; other site 565050000479 ATP binding site [chemical binding]; other site 565050000480 Walker B motif; other site 565050000481 arginine finger; other site 565050000482 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 565050000483 glutathione synthetase; Provisional; Region: PRK05246 565050000484 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 565050000485 ATP-grasp domain; Region: ATP-grasp_4; cl03087 565050000486 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 565050000487 Restriction endonuclease; Region: Mrr_cat; cl00516 565050000488 Predicted methyltransferases [General function prediction only]; Region: COG0313 565050000489 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 565050000490 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 565050000491 coproporphyrinogen III oxidase; Provisional; Region: PRK09057 565050000492 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 565050000493 FeS/SAM binding site; other site 565050000494 HemN C-terminal domain; Region: HemN_C; pfam06969 565050000495 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 565050000496 active site 565050000497 dimerization interface [polypeptide binding]; other site 565050000498 putative glutathione S-transferase; Provisional; Region: PRK10357 565050000499 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 565050000500 putative C-terminal domain interface [polypeptide binding]; other site 565050000501 putative GSH binding site (G-site) [chemical binding]; other site 565050000502 putative dimer interface [polypeptide binding]; other site 565050000503 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 565050000504 N-terminal domain interface [polypeptide binding]; other site 565050000505 dimer interface [polypeptide binding]; other site 565050000506 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050000507 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 565050000508 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 565050000509 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 565050000510 protein binding site [polypeptide binding]; other site 565050000511 ribonuclease PH; Reviewed; Region: rph; PRK00173 565050000512 Ribonuclease PH; Region: RNase_PH_bact; cd11362 565050000513 hexamer interface [polypeptide binding]; other site 565050000514 active site 565050000515 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 565050000516 Helix-turn-helix domains; Region: HTH; cl00088 565050000517 HrcA protein C terminal domain; Region: HrcA; pfam01628 565050000518 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 565050000519 dimer interface [polypeptide binding]; other site 565050000520 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 565050000521 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 565050000522 DNA polymerase III subunit beta; Validated; Region: PRK05643 565050000523 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 565050000524 putative DNA binding surface [nucleotide binding]; other site 565050000525 dimer interface [polypeptide binding]; other site 565050000526 beta-clamp/clamp loader binding surface; other site 565050000527 beta-clamp/translesion DNA polymerase binding surface; other site 565050000528 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 565050000529 dimerization interface [polypeptide binding]; other site 565050000530 putative DNA binding site [nucleotide binding]; other site 565050000531 putative Zn2+ binding site [ion binding]; other site 565050000532 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050000533 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 565050000534 recombination protein F; Reviewed; Region: recF; PRK00064 565050000535 RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication...; Region: ABC_RecF; cd03242 565050000536 Walker A/P-loop; other site 565050000537 ATP binding site [chemical binding]; other site 565050000538 Q-loop/lid; other site 565050000539 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050000540 ABC transporter signature motif; other site 565050000541 Walker B; other site 565050000542 D-loop; other site 565050000543 H-loop/switch region; other site 565050000544 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 565050000545 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 565050000546 Mg2+ binding site [ion binding]; other site 565050000547 G-X-G motif; other site 565050000548 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 565050000549 anchoring element; other site 565050000550 dimer interface [polypeptide binding]; other site 565050000551 ATP binding site [chemical binding]; other site 565050000552 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 565050000553 active site 565050000554 putative metal-binding site [ion binding]; other site 565050000555 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 565050000556 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050000557 putative CheW interface [polypeptide binding]; other site 565050000558 methyl-accepting chemotaxis protein I; Provisional; Region: PRK15041 565050000559 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; cl12051 565050000560 exopolysaccharide transport protein family; Region: eps_transp_fam; TIGR01005 565050000561 Chain length determinant protein; Region: Wzz; cl15801 565050000562 Chain length determinant protein; Region: Wzz; cl15801 565050000563 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050000564 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 565050000565 O-Antigen ligase; Region: Wzy_C; cl04850 565050000566 Bacterial sugar transferase; Region: Bac_transf; cl00939 565050000567 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 565050000568 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 565050000569 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 565050000570 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 565050000571 active site 565050000572 metal binding site [ion binding]; metal-binding site 565050000573 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 565050000574 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 565050000575 SLBB domain; Region: SLBB; pfam10531 565050000576 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050000577 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; cl00284 565050000578 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; cl00284 565050000579 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 565050000580 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 565050000581 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 565050000582 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 565050000583 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 565050000584 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 565050000585 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 565050000586 Walker A motif; other site 565050000587 ATP binding site [chemical binding]; other site 565050000588 Walker B motif; other site 565050000589 general secretion pathway protein F; Region: GspF; TIGR02120 565050000590 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 565050000591 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 565050000592 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 565050000593 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 565050000594 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 565050000595 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 565050000596 general secretion pathway protein H; Region: typeII_sec_gspH; TIGR01708 565050000597 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 565050000598 general secretion pathway protein I; Region: gspI; TIGR01707 565050000599 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 565050000600 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 565050000601 Type II secretory pathway, component PulJ [Intracellular trafficking and secretion]; Region: PulJ; COG4795 565050000602 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 565050000603 Type II secretory pathway, component PulK [Intracellular trafficking and secretion]; Region: PulK; COG3156 565050000604 Type II secretory pathway, component PulL [Intracellular trafficking and secretion]; Region: PulL; COG3297 565050000605 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 565050000606 GspL periplasmic domain; Region: GspL_C; cl14909 565050000607 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 565050000608 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 565050000609 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 565050000610 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 565050000611 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 565050000612 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050000613 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 565050000614 N-terminal plug; other site 565050000615 ligand-binding site [chemical binding]; other site 565050000616 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 565050000617 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 565050000618 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 565050000619 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050000620 Walker A/P-loop; other site 565050000621 ATP binding site [chemical binding]; other site 565050000622 Q-loop/lid; other site 565050000623 ABC transporter signature motif; other site 565050000624 Walker B; other site 565050000625 D-loop; other site 565050000626 H-loop/switch region; other site 565050000627 Zinc-finger domain; Region: zf-CHCC; cl01821 565050000628 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 565050000629 Predicted acetyltransferase [General function prediction only]; Region: COG3153 565050000630 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 565050000631 Coenzyme A binding pocket [chemical binding]; other site 565050000632 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07008 565050000633 AMP-binding enzyme; Region: AMP-binding; cl15778 565050000634 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 565050000635 tartrate dehydrogenase; Provisional; Region: PRK08194 565050000636 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 565050000637 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 565050000638 substrate binding site [chemical binding]; other site 565050000639 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 565050000640 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 565050000641 substrate binding site [chemical binding]; other site 565050000642 ligand binding site [chemical binding]; other site 565050000643 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 565050000644 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 565050000645 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050000646 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 565050000647 metal ion-dependent adhesion site (MIDAS); other site 565050000648 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 565050000649 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; cl14733 565050000650 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 565050000651 putative outer membrane lipoprotein; Provisional; Region: PRK10510 565050000652 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 565050000653 ligand binding site [chemical binding]; other site 565050000654 Fatty acid desaturase; Region: FA_desaturase; pfam00487 565050000655 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 565050000656 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 565050000657 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 565050000658 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 565050000659 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 565050000660 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050000661 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 565050000662 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 565050000663 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 565050000664 DJ-1 family protein; Region: not_thiJ; TIGR01383 565050000665 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 565050000666 conserved cys residue [active] 565050000667 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 565050000668 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 565050000669 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050000670 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; cl00284 565050000671 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; cl00284 565050000672 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; cl01113 565050000673 agmatine deiminase; Region: agmatine_aguA; TIGR03380 565050000674 N-carbamolyputrescine amidase; Region: PLN02747 565050000675 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 565050000676 putative active site; other site 565050000677 catalytic triad [active] 565050000678 putative dimer interface [polypeptide binding]; other site 565050000679 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 565050000680 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 565050000681 N-terminal plug; other site 565050000682 ligand-binding site [chemical binding]; other site 565050000683 SapC; Region: SapC; pfam07277 565050000684 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 565050000685 active site 1 [active] 565050000686 active site 2 [active] 565050000687 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 565050000688 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 565050000689 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 565050000690 DsbD alpha interface [polypeptide binding]; other site 565050000691 catalytic residues [active] 565050000692 Protein of unknown function (DUF1353); Region: DUF1353; pfam07087 565050000693 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 565050000694 putative catalytic residue [active] 565050000695 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 565050000696 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 565050000697 active site 565050000698 dimer interface [polypeptide binding]; other site 565050000699 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 565050000700 dimer interface [polypeptide binding]; other site 565050000701 active site 565050000702 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; cl12031 565050000703 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050000704 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; cl00284 565050000705 Uncharacterized protein conserved in bacteria (DUF2084); Region: DUF2084; cl01566 565050000706 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 565050000707 S-adenosylmethionine binding site [chemical binding]; other site 565050000708 Protein of unknown function (DUF1211); Region: DUF1211; cl01421 565050000709 CAAX protease self-immunity; Region: Abi; cl00558 565050000710 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 565050000711 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 565050000712 RNA binding surface [nucleotide binding]; other site 565050000713 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 565050000714 probable active site [active] 565050000715 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 565050000716 nucleoside/Zn binding site; other site 565050000717 dimer interface [polypeptide binding]; other site 565050000718 catalytic motif [active] 565050000719 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 565050000720 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 565050000721 NAD(P) binding site [chemical binding]; other site 565050000722 homodimer interface [polypeptide binding]; other site 565050000723 substrate binding site [chemical binding]; other site 565050000724 active site 565050000725 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 565050000726 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 565050000727 inhibitor-cofactor binding pocket; inhibition site 565050000728 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050000729 catalytic residue [active] 565050000730 DNA-binding response regulator CreB; Provisional; Region: PRK11083 565050000731 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 565050000732 active site 565050000733 phosphorylation site [posttranslational modification] 565050000734 intermolecular recognition site; other site 565050000735 dimerization interface [polypeptide binding]; other site 565050000736 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 565050000737 DNA binding site [nucleotide binding] 565050000738 Sensor N-terminal transmembrane domain; Region: Sensor_TM1; pfam13755 565050000739 Stimulus-sensing domain; Region: Stimulus_sens_1; pfam13756 565050000740 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 565050000741 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050000742 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 565050000743 dimer interface [polypeptide binding]; other site 565050000744 phosphorylation site [posttranslational modification] 565050000745 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 565050000746 ATP binding site [chemical binding]; other site 565050000747 Mg2+ binding site [ion binding]; other site 565050000748 G-X-G motif; other site 565050000749 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 565050000750 Hpr binding site; other site 565050000751 active site 565050000752 homohexamer subunit interaction site [polypeptide binding]; other site 565050000753 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 565050000754 active pocket/dimerization site; other site 565050000755 active site 565050000756 phosphorylation site [posttranslational modification] 565050000757 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 565050000758 dimerization domain swap beta strand [polypeptide binding]; other site 565050000759 regulatory protein interface [polypeptide binding]; other site 565050000760 active site 565050000761 regulatory phosphorylation site [posttranslational modification]; other site 565050000762 epoxide hydrolase N-terminal domain-like phosphatase; Region: HAD-1A3-hyp; TIGR02247 565050000763 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 565050000764 motif II; other site 565050000765 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 565050000766 aromatic arch; other site 565050000767 DCoH dimer interaction site [polypeptide binding]; other site 565050000768 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 565050000769 DCoH tetramer interaction site [polypeptide binding]; other site 565050000770 substrate binding site [chemical binding]; other site 565050000771 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050000772 short chain dehydrogenase; Validated; Region: PRK07069 565050000773 NAD(P) binding site [chemical binding]; other site 565050000774 active site 565050000775 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 565050000776 active site 565050000777 phosphorylation site [posttranslational modification] 565050000778 intermolecular recognition site; other site 565050000779 Helix-turn-helix domains; Region: HTH; cl00088 565050000780 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 565050000781 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 565050000782 ATP binding site [chemical binding]; other site 565050000783 Mg2+ binding site [ion binding]; other site 565050000784 G-X-G motif; other site 565050000785 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 565050000786 Cu(I) binding site [ion binding]; other site 565050000787 polyhydroxyalkanoate depolymerase, intracellular; Region: PHB_depoly_PhaZ; TIGR01849 565050000788 PHB de-polymerase C-terminus; Region: PHB_depo_C; cl14907 565050000789 Protein of unknown function DUF45; Region: DUF45; cl00636 565050000790 Transglycosylase; Region: Transgly; cl07896 565050000791 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 565050000792 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050000793 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 565050000794 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050000795 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 565050000796 Predicted permeases [General function prediction only]; Region: RarD; COG2962 565050000797 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 565050000798 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050000799 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 565050000800 pyridoxal binding site [chemical binding]; other site 565050000801 dimer interface [polypeptide binding]; other site 565050000802 ATP binding site [chemical binding]; other site 565050000803 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 565050000804 S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado and...; Region: AdoHcyase; cd00401 565050000805 oligomerization interface [polypeptide binding]; other site 565050000806 active site 565050000807 NAD+ binding site [chemical binding]; other site 565050000808 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 565050000809 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 565050000810 dimer interface [polypeptide binding]; other site 565050000811 N-terminal domain interface [polypeptide binding]; other site 565050000812 substrate binding pocket (H-site) [chemical binding]; other site 565050000813 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 565050000814 dimer interface [polypeptide binding]; other site 565050000815 putative radical transfer pathway; other site 565050000816 diiron center [ion binding]; other site 565050000817 tyrosyl radical; other site 565050000818 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 565050000819 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050000820 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 565050000821 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 565050000822 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 565050000823 AMP nucleosidase; Provisional; Region: PRK08292 565050000824 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 565050000825 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 565050000826 acetyl-CoA acetyltransferase; Provisional; Region: PRK06025 565050000827 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 565050000828 dimer interface [polypeptide binding]; other site 565050000829 active site 565050000830 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]; Region: NPY1; COG2816 565050000831 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 565050000832 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 565050000833 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 565050000834 putative NADH binding site [chemical binding]; other site 565050000835 putative active site [active] 565050000836 nudix motif; other site 565050000837 putative metal binding site [ion binding]; other site 565050000838 DNA polymerase III subunits gamma and tau; Validated; Region: PRK09111 565050000839 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 565050000840 Walker A motif; other site 565050000841 ATP binding site [chemical binding]; other site 565050000842 Walker B motif; other site 565050000843 arginine finger; other site 565050000844 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 565050000845 DNA polymerase III gamma and tau subunits C terminal; Region: DUF3646; pfam12362 565050000846 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 565050000847 recombination protein RecR; Reviewed; Region: recR; PRK00076 565050000848 RecR protein; Region: RecR; pfam02132 565050000849 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 565050000850 putative active site [active] 565050000851 putative metal-binding site [ion binding]; other site 565050000852 tetramer interface [polypeptide binding]; other site 565050000853 RmuC family; Region: RmuC; pfam02646 565050000854 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 565050000855 active site 565050000856 catalytic residues [active] 565050000857 metal binding site [ion binding]; metal-binding site 565050000858 Transposase domain (DUF772); Region: DUF772; cl15789 565050000859 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 565050000860 Transposase domain (DUF772); Region: DUF772; cl15789 565050000861 Cupin domain; Region: Cupin_2; cl09118 565050000862 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 565050000863 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 565050000864 metal binding site [ion binding]; metal-binding site 565050000865 dimer interface [polypeptide binding]; other site 565050000866 Glutaminase; Region: Glutaminase; cl00907 565050000867 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 565050000868 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 565050000869 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 565050000870 dimerization interface 3.5A [polypeptide binding]; other site 565050000871 active site 565050000872 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 565050000873 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 565050000874 putative active site [active] 565050000875 substrate binding site [chemical binding]; other site 565050000876 putative cosubstrate binding site; other site 565050000877 catalytic site [active] 565050000878 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 565050000879 substrate binding site [chemical binding]; other site 565050000880 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 565050000881 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 565050000882 trimer interface [polypeptide binding]; other site 565050000883 active site 565050000884 substrate binding site [chemical binding]; other site 565050000885 CoA binding site [chemical binding]; other site 565050000886 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050000887 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 565050000888 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 565050000889 feedback inhibition sensing region; other site 565050000890 homohexameric interface [polypeptide binding]; other site 565050000891 nucleotide binding site [chemical binding]; other site 565050000892 N-acetyl-L-glutamate binding site [chemical binding]; other site 565050000893 Response regulator receiver domain; Region: Response_reg; pfam00072 565050000894 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 565050000895 active site 565050000896 phosphorylation site [posttranslational modification] 565050000897 intermolecular recognition site; other site 565050000898 dimerization interface [polypeptide binding]; other site 565050000899 hypothetical protein; Provisional; Region: PRK13559 565050000900 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 565050000901 putative active site [active] 565050000902 heme pocket [chemical binding]; other site 565050000903 Histidine kinase; Region: HisKA_2; cl06527 565050000904 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 565050000905 ATP binding site [chemical binding]; other site 565050000906 Mg2+ binding site [ion binding]; other site 565050000907 G-X-G motif; other site 565050000908 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 565050000909 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 565050000910 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 565050000911 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 565050000912 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 565050000913 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 565050000914 dimer interface [polypeptide binding]; other site 565050000915 phosphorylation site [posttranslational modification] 565050000916 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 565050000917 ATP binding site [chemical binding]; other site 565050000918 Mg2+ binding site [ion binding]; other site 565050000919 G-X-G motif; other site 565050000920 Phosphate ATP-binding cassette transporter; Region: DUF3708; pfam12501 565050000921 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 565050000922 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 565050000923 dimer interface [polypeptide binding]; other site 565050000924 conserved gate region; other site 565050000925 putative PBP binding loops; other site 565050000926 ABC-ATPase subunit interface; other site 565050000927 Domain of unknown function (DUF3333); Region: DUF3333; pfam11812 565050000928 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 565050000929 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 565050000930 dimer interface [polypeptide binding]; other site 565050000931 conserved gate region; other site 565050000932 putative PBP binding loops; other site 565050000933 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 565050000934 ABC-ATPase subunit interface; other site 565050000935 phosphate transporter ATP-binding protein; Provisional; Region: PRK14235 565050000936 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 565050000937 Walker A/P-loop; other site 565050000938 ATP binding site [chemical binding]; other site 565050000939 Q-loop/lid; other site 565050000940 ABC transporter signature motif; other site 565050000941 Walker B; other site 565050000942 D-loop; other site 565050000943 H-loop/switch region; other site 565050000944 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 565050000945 PhoU domain; Region: PhoU; pfam01895 565050000946 PhoU domain; Region: PhoU; pfam01895 565050000947 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 565050000948 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 565050000949 active site 565050000950 phosphorylation site [posttranslational modification] 565050000951 intermolecular recognition site; other site 565050000952 dimerization interface [polypeptide binding]; other site 565050000953 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 565050000954 DNA binding site [nucleotide binding] 565050000955 LytTr DNA-binding domain; Region: LytTR; cl04498 565050000956 Predicted membrane protein (DUF2306); Region: DUF2306; cl02232 565050000957 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 565050000958 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 565050000959 ATP-grasp domain; Region: ATP-grasp_4; cl03087 565050000960 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 565050000961 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050000962 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 565050000963 active site 565050000964 Predicted aminoglycoside phosphotransferase [General function prediction only]; Region: COG3173 565050000965 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 565050000966 putative active site [active] 565050000967 putative substrate binding site [chemical binding]; other site 565050000968 ATP binding site [chemical binding]; other site 565050000969 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 565050000970 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 565050000971 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_A; cd01299 565050000972 active site 565050000973 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 565050000974 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 565050000975 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 565050000976 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 565050000977 Cation efflux family; Region: Cation_efflux; cl00316 565050000978 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 565050000979 putative acyl-acceptor binding pocket; other site 565050000980 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 565050000981 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 565050000982 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 565050000983 Walker A/P-loop; other site 565050000984 ATP binding site [chemical binding]; other site 565050000985 Q-loop/lid; other site 565050000986 ABC transporter signature motif; other site 565050000987 Walker B; other site 565050000988 D-loop; other site 565050000989 H-loop/switch region; other site 565050000990 Protein tyrosine/serine phosphatase [Signal transduction mechanisms]; Region: COG2365 565050000991 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 565050000992 Domain of unknown function (DUF4170); Region: DUF4170; pfam13773 565050000993 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 cysteine...; Region: CysQ; cd01638 565050000994 active site 565050000995 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 565050000996 MAPEG family; Region: MAPEG; cl09190 565050000997 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_4; cd06241 565050000998 putative active site [active] 565050000999 Zn binding site [ion binding]; other site 565050001000 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 565050001001 gamma-glutamyl kinase; Provisional; Region: PRK05429 565050001002 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 565050001003 nucleotide binding site [chemical binding]; other site 565050001004 homotetrameric interface [polypeptide binding]; other site 565050001005 putative phosphate binding site [ion binding]; other site 565050001006 putative allosteric binding site; other site 565050001007 PUA domain; Region: PUA; cl00607 565050001008 GTPase CgtA; Reviewed; Region: obgE; PRK12299 565050001009 GTP1/OBG; Region: GTP1_OBG; pfam01018 565050001010 Obg GTPase; Region: Obg; cd01898 565050001011 G1 box; other site 565050001012 GTP/Mg2+ binding site [chemical binding]; other site 565050001013 Switch I region; other site 565050001014 G2 box; other site 565050001015 G3 box; other site 565050001016 Switch II region; other site 565050001017 G4 box; other site 565050001018 G5 box; other site 565050001019 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 565050001020 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050001021 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 565050001022 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 565050001023 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 565050001024 The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage...; Region: CobW_like; cd03112 565050001025 P-loop, Walker A motif; other site 565050001026 Base recognition motif; other site 565050001027 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 565050001028 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 565050001029 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 565050001030 structural tetrad; other site 565050001031 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source...; Region: Nitroreductase; cd02136 565050001032 putative FMN binding site [chemical binding]; other site 565050001033 Transglycosylase; Region: Transgly; cl07896 565050001034 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 565050001035 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050001036 Helix-turn-helix domains; Region: HTH; cl00088 565050001037 TOBE domain; Region: TOBE_2; cl01440 565050001038 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 565050001039 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 565050001040 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 565050001041 dimer interface [polypeptide binding]; other site 565050001042 conserved gate region; other site 565050001043 putative PBP binding loops; other site 565050001044 ABC-ATPase subunit interface; other site 565050001045 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 565050001046 LytTr DNA-binding domain; Region: LytTR; cl04498 565050001047 Predicted membrane protein (DUF2306); Region: DUF2306; cl02232 565050001048 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; cl01930 565050001049 Lignostilbene-alpha,beta-dioxygenase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3670 565050001050 Retinal pigment epithelial membrane protein; Region: RPE65; cl10080 565050001051 transcriptional repressor BetI; Region: betaine_BetI; TIGR03384 565050001052 Helix-turn-helix domains; Region: HTH; cl00088 565050001053 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050001054 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 565050001055 N-terminal plug; other site 565050001056 ligand-binding site [chemical binding]; other site 565050001057 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 565050001058 Major Facilitator Superfamily; Region: MFS_1; pfam07690 565050001059 putative substrate translocation pore; other site 565050001060 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 565050001061 ATP-grasp domain; Region: ATP-grasp_4; cl03087 565050001062 CoA-ligase; Region: Ligase_CoA; cl02894 565050001063 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 565050001064 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001065 CoA-ligase; Region: Ligase_CoA; cl02894 565050001066 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 565050001067 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 565050001068 TPP-binding site [chemical binding]; other site 565050001069 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 565050001070 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 565050001071 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 565050001072 E3 interaction surface; other site 565050001073 lipoyl attachment site [posttranslational modification]; other site 565050001074 e3 binding domain; Region: E3_binding; pfam02817 565050001075 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 565050001076 Protein of unknown function (DUF3088); Region: DUF3088; pfam11287 565050001077 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; cl12031 565050001078 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06115 565050001079 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001080 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 565050001081 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 565050001082 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050001083 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050001084 dimer interface [polypeptide binding]; other site 565050001085 putative CheW interface [polypeptide binding]; other site 565050001086 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 565050001087 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 565050001088 DNA binding site [nucleotide binding] 565050001089 Int/Topo IB signature motif; other site 565050001090 active site 565050001091 GAF domain; Region: GAF; cl15785 565050001092 primosome assembly protein PriA; Validated; Region: PRK05580 565050001093 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 565050001094 ATP binding site [chemical binding]; other site 565050001095 putative Mg++ binding site [ion binding]; other site 565050001096 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 565050001097 nucleotide binding region [chemical binding]; other site 565050001098 ATP-binding site [chemical binding]; other site 565050001099 Integral membrane protein TerC family; Region: TerC; cl10468 565050001100 OpgC protein; Region: OpgC_C; cl00792 565050001101 NlpC/P60 family; Region: NLPC_P60; cl11438 565050001102 Surface antigen [General function prediction only]; Region: COG3942 565050001103 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050001104 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 565050001105 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050001106 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050001107 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050001108 MltA-interacting protein MipA; Region: MipA; cl01504 565050001109 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; cl12031 565050001110 enoyl-CoA hydratase; Provisional; Region: PRK06142 565050001111 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 565050001112 substrate binding site [chemical binding]; other site 565050001113 oxyanion hole (OAH) forming residues; other site 565050001114 trimer interface [polypeptide binding]; other site 565050001115 Bacterial SH3 domain; Region: SH3_3; cl02551 565050001116 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050001117 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 565050001118 active site 565050001119 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 565050001120 active site 565050001121 Helix-turn-helix domains; Region: HTH; cl00088 565050001122 metal binding site 2 [ion binding]; metal-binding site 565050001123 putative DNA binding helix; other site 565050001124 metal binding site 1 [ion binding]; metal-binding site 565050001125 dimer interface [polypeptide binding]; other site 565050001126 structural Zn2+ binding site [ion binding]; other site 565050001127 PAP2, bacterial acid phosphatase or class A non-specific acid phosphatases. These enzymes catalyze phosphomonoester hydrolysis, with optimal activity in low pH conditions. They are secreted into the periplasmic space, and their physiological role remains...; Region: PAP2_acid_phosphatase; cd03397 565050001128 active site 565050001129 Deoxyhypusine synthase; Region: DS; cl00826 565050001130 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 565050001131 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 565050001132 dimer interface [polypeptide binding]; other site 565050001133 active site 565050001134 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 565050001135 catalytic residues [active] 565050001136 substrate binding site [chemical binding]; other site 565050001137 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 565050001138 ABC-type phosphate/phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all...; Region: ABC_PhnC_transporter; cd03256 565050001139 Walker A/P-loop; other site 565050001140 ATP binding site [chemical binding]; other site 565050001141 Q-loop/lid; other site 565050001142 ABC transporter signature motif; other site 565050001143 Walker B; other site 565050001144 D-loop; other site 565050001145 H-loop/switch region; other site 565050001146 phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein; Region: 3A0109s03R; TIGR01098 565050001147 NMT1-like family; Region: NMT1_2; cl15260 565050001148 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 565050001149 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 565050001150 dimer interface [polypeptide binding]; other site 565050001151 conserved gate region; other site 565050001152 putative PBP binding loops; other site 565050001153 ABC-ATPase subunit interface; other site 565050001154 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 565050001155 Domain of unknown function DUF21; Region: DUF21; pfam01595 565050001156 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 565050001157 Transporter associated domain; Region: CorC_HlyC; cl08393 565050001158 F0F1 ATP synthase subunit B; Provisional; Region: PRK14475 565050001159 Plant ATP synthase F0; Region: YMF19; cl07975 565050001160 Plant ATP synthase F0; Region: YMF19; cl07975 565050001161 ATP synthase subunit C; Region: ATP-synt_C; cl00466 565050001162 ATP synthase A chain; Region: ATP-synt_A; cl00413 565050001163 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 565050001164 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 565050001165 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 565050001166 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 565050001167 Walker A/P-loop; other site 565050001168 ATP binding site [chemical binding]; other site 565050001169 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 565050001170 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 565050001171 ABC transporter signature motif; other site 565050001172 Walker B; other site 565050001173 D-loop; other site 565050001174 H-loop/switch region; other site 565050001175 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 565050001176 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 565050001177 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 565050001178 Protein of unknown function (DUF721); Region: DUF721; cl02324 565050001179 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 565050001180 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 565050001181 minor groove reading motif; other site 565050001182 helix-hairpin-helix signature motif; other site 565050001183 substrate binding pocket [chemical binding]; other site 565050001184 active site 565050001185 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 565050001186 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 565050001187 DNA binding and oxoG recognition site [nucleotide binding] 565050001188 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 565050001189 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001190 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 565050001191 RNA/DNA hybrid binding site [nucleotide binding]; other site 565050001192 active site 565050001193 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 565050001194 active site 565050001195 catalytic residues [active] 565050001196 H+ Antiporter protein; Region: 2A0121; TIGR00900 565050001197 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 565050001198 putative substrate translocation pore; other site 565050001199 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 565050001200 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050001201 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 565050001202 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 565050001203 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 565050001204 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 565050001205 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 565050001206 putative active site [active] 565050001207 dihydroorotase; Validated; Region: PRK09060 565050001208 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 565050001209 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 565050001210 active site 565050001211 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]; Region: COG4941 565050001212 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050001213 YCII-related domain; Region: YCII; cl00999 565050001214 feruloyl-CoA synthase; Reviewed; Region: PRK08180 565050001215 AMP-binding enzyme; Region: AMP-binding; cl15778 565050001216 YhhN-like protein; Region: YhhN; cl01505 565050001217 hypothetical protein; Validated; Region: PRK07586 565050001218 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 565050001219 PYR/PP interface [polypeptide binding]; other site 565050001220 dimer interface [polypeptide binding]; other site 565050001221 TPP binding site [chemical binding]; other site 565050001222 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 565050001223 TPP-binding site [chemical binding]; other site 565050001224 dimer interface [polypeptide binding]; other site 565050001225 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 565050001226 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 565050001227 Helix-turn-helix domains; Region: HTH; cl00088 565050001228 enoyl-CoA hydratase; Provisional; Region: PRK06688 565050001229 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 565050001230 substrate binding site [chemical binding]; other site 565050001231 oxyanion hole (OAH) forming residues; other site 565050001232 trimer interface [polypeptide binding]; other site 565050001233 Protein of unknown function (DUF3995); Region: DUF3995; pfam13160 565050001234 oxidoreductase; Provisional; Region: PRK06196 565050001235 retinol dehydrogenase (retinol-DH), Light dependent Protochlorophyllide (Pchlide) OxidoReductase (LPOR) and related proteins, classical (c) SDRs; Region: retinol-DH_like_SDR_c_like; cd05327 565050001236 putative NAD(P) binding site [chemical binding]; other site 565050001237 active site 565050001238 short chain dehydrogenase; Provisional; Region: PRK08278 565050001239 human hydroxysteroid dehydrogenase-like protein 2 (HSDL2), classical (c) SDRs; Region: HSDL2_SDR_c; cd09762 565050001240 NAD(P) binding site [chemical binding]; other site 565050001241 homodimer interface [polypeptide binding]; other site 565050001242 active site 565050001243 TfoX N-terminal domain; Region: TfoX_N; cl01167 565050001244 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050001245 H+ Antiporter protein; Region: 2A0121; TIGR00900 565050001246 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 565050001247 putative substrate translocation pore; other site 565050001248 Predicted acetyltransferase [General function prediction only]; Region: COG3153 565050001249 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 565050001250 Coenzyme A binding pocket [chemical binding]; other site 565050001251 Protein of unknown function (DUF1285); Region: DUF1285; cl01571 565050001252 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 565050001253 putative active site [active] 565050001254 putative CoA binding site [chemical binding]; other site 565050001255 nudix motif; other site 565050001256 metal binding site [ion binding]; metal-binding site 565050001257 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 565050001258 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 565050001259 active site 565050001260 NTP binding site [chemical binding]; other site 565050001261 metal binding triad [ion binding]; metal-binding site 565050001262 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 565050001263 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 565050001264 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 565050001265 catalytic triad [active] 565050001266 Tetratricopeptide repeat; Region: TPR_12; pfam13424 565050001267 Predicted membrane protein [Function unknown]; Region: COG3671 565050001268 Predicted membrane protein [Function unknown]; Region: COG3671 565050001269 Fasciclin domain; Region: Fasciclin; cl02663 565050001270 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 565050001271 active site 565050001272 pteridine reductase; Provisional; Region: PRK09135 565050001273 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001274 NAD(P) binding site [chemical binding]; other site 565050001275 active site 565050001276 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_21; cd04680 565050001277 nudix motif; other site 565050001278 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 565050001279 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 565050001280 NAD binding site [chemical binding]; other site 565050001281 catalytic residues [active] 565050001282 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 565050001283 putative active site [active] 565050001284 Protein of unknown function (DUF3606); Region: DUF3606; pfam12244 565050001285 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 565050001286 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 565050001287 putative DNA binding site [nucleotide binding]; other site 565050001288 putative Zn2+ binding site [ion binding]; other site 565050001289 Helix-turn-helix domains; Region: HTH; cl00088 565050001290 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 565050001291 amino acid transporter; Region: 2A0306; TIGR00909 565050001292 Spore germination protein; Region: Spore_permease; cl15802 565050001293 Spore germination protein; Region: Spore_permease; cl15802 565050001294 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 565050001295 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 565050001296 active site 565050001297 Globin domain present in Globin-Coupled-Sensors (GCS). These domains detect changes in intracellular concentrations of oxygen, carbon monoxyde, or nitrous oxide, which result in aerotaxis and/or gene regulation. One subgroup, the HemATs, are aerotactic...; Region: sensor_globin; cd01068 565050001298 heme-binding site [chemical binding]; other site 565050001299 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050001300 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050001301 dimer interface [polypeptide binding]; other site 565050001302 putative CheW interface [polypeptide binding]; other site 565050001303 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050001304 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050001305 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 565050001306 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050001307 dimer interface [polypeptide binding]; other site 565050001308 putative CheW interface [polypeptide binding]; other site 565050001309 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 565050001310 Response regulator receiver domain; Region: Response_reg; pfam00072 565050001311 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 565050001312 active site 565050001313 phosphorylation site [posttranslational modification] 565050001314 intermolecular recognition site; other site 565050001315 dimerization interface [polypeptide binding]; other site 565050001316 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 565050001317 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 565050001318 putative binding surface; other site 565050001319 active site 565050001320 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 565050001321 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 565050001322 ATP binding site [chemical binding]; other site 565050001323 Mg2+ binding site [ion binding]; other site 565050001324 G-X-G motif; other site 565050001325 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 565050001326 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 565050001327 putative CheA interaction surface; other site 565050001328 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 565050001329 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 565050001330 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001331 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 565050001332 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 565050001333 active site 565050001334 phosphorylation site [posttranslational modification] 565050001335 intermolecular recognition site; other site 565050001336 dimerization interface [polypeptide binding]; other site 565050001337 CheB methylesterase; Region: CheB_methylest; pfam01339 565050001338 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 565050001339 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 565050001340 active site 565050001341 phosphorylation site [posttranslational modification] 565050001342 intermolecular recognition site; other site 565050001343 dimerization interface [polypeptide binding]; other site 565050001344 CheD chemotactic sensory transduction; Region: CheD; cl00810 565050001345 Response regulator receiver domain; Region: Response_reg; pfam00072 565050001346 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 565050001347 active site 565050001348 phosphorylation site [posttranslational modification] 565050001349 intermolecular recognition site; other site 565050001350 dimerization interface [polypeptide binding]; other site 565050001351 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050001352 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; cl00284 565050001353 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 565050001354 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 565050001355 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 565050001356 active site 565050001357 dimer interface [polypeptide binding]; other site 565050001358 Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]; Region: AgaS; COG2222 565050001359 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 565050001360 dimer interface [polypeptide binding]; other site 565050001361 active site 565050001362 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 565050001363 dimer interface [polypeptide binding]; other site 565050001364 active site 565050001365 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 565050001366 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050001367 DNA-binding site [nucleotide binding]; DNA binding site 565050001368 UTRA domain; Region: UTRA; cl01230 565050001369 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050001370 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; cl00284 565050001371 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 565050001372 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i)...; Region: GH20_chitobiase-like; cd06563 565050001373 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 565050001374 active site 565050001375 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 565050001376 PTS_IIA, PTS system, glucose/sucrose 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_glc; cl00162 565050001377 HPr interaction site; other site 565050001378 glycerol kinase (GK) interaction site [polypeptide binding]; other site 565050001379 active site 565050001380 phosphorylation site [posttranslational modification] 565050001381 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 565050001382 dimerization domain swap beta strand [polypeptide binding]; other site 565050001383 regulatory protein interface [polypeptide binding]; other site 565050001384 active site 565050001385 regulatory phosphorylation site [posttranslational modification]; other site 565050001386 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 565050001387 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 565050001388 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 565050001389 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; cl09155 565050001390 PTS system, N-acetylglucosamine-specific IIBC component; Region: PTS-II-BC-nag; TIGR01998 565050001391 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 565050001392 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 565050001393 active site turn [active] 565050001394 phosphorylation site [posttranslational modification] 565050001395 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cl00164 565050001396 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 565050001397 prophage element 565050001398 Bacterial sugar transferase; Region: Bac_transf; cl00939 565050001399 UDP-galactopyranose mutase [Cell envelope biogenesis, outer membrane]; Region: Glf; COG0562 565050001400 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001401 UDP-galactopyranose mutase; Region: GLF; pfam03275 565050001402 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 565050001403 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 565050001404 MatE; Region: MatE; cl10513 565050001405 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001406 This family is most closely related to the GT1 family of glycosyltransferases. ExpE7 in Sinorhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucans (exopolysaccharide II); Region: GT1_ExpE7_like; cd03823 565050001407 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 565050001408 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 565050001409 NADP binding site [chemical binding]; other site 565050001410 active site 565050001411 putative substrate binding site [chemical binding]; other site 565050001412 GDP-mannose 4,6-dehydratase; Region: gmd; TIGR01472 565050001413 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 565050001414 NADP-binding site; other site 565050001415 homotetramer interface [polypeptide binding]; other site 565050001416 substrate binding site [chemical binding]; other site 565050001417 homodimer interface [polypeptide binding]; other site 565050001418 active site 565050001419 TrwC relaxase; Region: TrwC; pfam08751 565050001420 conjugative relaxase domain, TrwC/TraI family; Region: relax_trwC; TIGR02686 565050001421 conjugative transfer relaxase protein TraI; Region: TraI_TIGR; TIGR02760 565050001422 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050001423 Family description; Region: UvrD_C_2; cl15862 565050001424 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050001425 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 565050001426 Walker A motif; other site 565050001427 ATP binding site [chemical binding]; other site 565050001428 Walker B motif; other site 565050001429 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 565050001430 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 565050001431 non-specific DNA binding site [nucleotide binding]; other site 565050001432 salt bridge; other site 565050001433 sequence-specific DNA binding site [nucleotide binding]; other site 565050001434 integrase; Provisional; Region: PRK09692 565050001435 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 565050001436 active site 565050001437 Int/Topo IB signature motif; other site 565050001438 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050001439 HipA N-terminal domain; Region: Couple_hipA; cl11853 565050001440 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 565050001441 HipA-like N-terminal domain; Region: HipA_N; pfam07805 565050001442 HipA-like C-terminal domain; Region: HipA_C; pfam07804 565050001443 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 565050001444 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 565050001445 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 565050001446 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 565050001447 RNA binding surface [nucleotide binding]; other site 565050001448 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 565050001449 active site 565050001450 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050001451 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; cl00284 565050001452 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; cl00284 565050001453 Phosphodiesterase/alkaline phosphatase D [Inorganic ion transport and metabolism]; Region: PhoD; COG3540 565050001454 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 565050001455 putative active site [active] 565050001456 putative metal binding site [ion binding]; other site 565050001457 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 565050001458 LysE type translocator; Region: LysE; cl00565 565050001459 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 565050001460 Protein of unknown function (DUF817); Region: DUF817; cl01520 565050001461 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 565050001462 GTP cyclohydrolase I; Provisional; Region: PLN03044 565050001463 active site 565050001464 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 565050001465 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 565050001466 active site 565050001467 HIGH motif; other site 565050001468 nucleotide binding site [chemical binding]; other site 565050001469 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 565050001470 KMSKS motif; other site 565050001471 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 565050001472 tRNA binding surface [nucleotide binding]; other site 565050001473 anticodon binding site; other site 565050001474 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_4; cd07822 565050001475 putative hydrophobic ligand binding site [chemical binding]; other site 565050001476 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 565050001477 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 565050001478 trimerization site [polypeptide binding]; other site 565050001479 active site 565050001480 Haemolytic domain; Region: Haemolytic; cl00506 565050001481 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 565050001482 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 565050001483 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 565050001484 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 565050001485 active site 565050001486 dimer interface [polypeptide binding]; other site 565050001487 motif 1; other site 565050001488 motif 2; other site 565050001489 motif 3; other site 565050001490 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 565050001491 anticodon binding site; other site 565050001492 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 565050001493 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 565050001494 Probable Catalytic site; other site 565050001495 metal-binding site 565050001496 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 565050001497 active site 565050001498 catalytic residues [active] 565050001499 metal binding site [ion binding]; metal-binding site 565050001500 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 565050001501 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 565050001502 Ligand binding site; other site 565050001503 Putative Catalytic site; other site 565050001504 DXD motif; other site 565050001505 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 565050001506 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 565050001507 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 565050001508 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 565050001509 [2Fe-2S] cluster binding site [ion binding]; other site 565050001510 cytochrome b; Provisional; Region: CYTB; MTH00191 565050001511 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 565050001512 Qi binding site; other site 565050001513 intrachain domain interface; other site 565050001514 interchain domain interface [polypeptide binding]; other site 565050001515 heme bH binding site [chemical binding]; other site 565050001516 heme bL binding site [chemical binding]; other site 565050001517 Qo binding site; other site 565050001518 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 565050001519 interchain domain interface [polypeptide binding]; other site 565050001520 intrachain domain interface; other site 565050001521 Qi binding site; other site 565050001522 Qo binding site; other site 565050001523 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 565050001524 Cellular and retroviral pepsin-like aspartate proteases; Region: pepsin_retropepsin_like; cl11403 565050001525 inhibitor binding site; inhibition site 565050001526 catalytic motif [active] 565050001527 Catalytic residue [active] 565050001528 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 565050001529 catalytic core [active] 565050001530 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 565050001531 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 565050001532 GTP-binding protein YchF; Reviewed; Region: PRK09601 565050001533 YchF GTPase; Region: YchF; cd01900 565050001534 G1 box; other site 565050001535 GTP/Mg2+ binding site [chemical binding]; other site 565050001536 Switch I region; other site 565050001537 G2 box; other site 565050001538 Switch II region; other site 565050001539 G3 box; other site 565050001540 G4 box; other site 565050001541 G5 box; other site 565050001542 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 565050001543 Pirin-related protein [General function prediction only]; Region: COG1741 565050001544 Cupin domain; Region: Cupin_2; cl09118 565050001545 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 565050001546 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 565050001547 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 565050001548 THF binding site; other site 565050001549 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 565050001550 substrate binding site [chemical binding]; other site 565050001551 THF binding site; other site 565050001552 zinc-binding site [ion binding]; other site 565050001553 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]; Region: COG4700 565050001554 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 565050001555 putative active site [active] 565050001556 catalytic residue [active] 565050001557 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 565050001558 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 565050001559 5S rRNA interface [nucleotide binding]; other site 565050001560 CTC domain interface [polypeptide binding]; other site 565050001561 L16 interface [polypeptide binding]; other site 565050001562 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 565050001563 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 565050001564 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 565050001565 active site 565050001566 Protein of unknown function (DUF3680); Region: DUF3680; cl02189 565050001567 Protein of unknown function (DUF497); Region: DUF497; cl01108 565050001568 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 565050001569 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 565050001570 Uncharacterized conserved protein [Function unknown]; Region: COG1565 565050001571 Putative S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_28; pfam02636 565050001572 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 565050001573 Membrane fusogenic activity; Region: BMFP; cl01115 565050001574 Putative bacterial sensory transduction regulator; Region: YbjN; cl15834 565050001575 pyrroline-5-carboxylate reductase; Region: proC; TIGR00112 565050001576 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001577 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 565050001578 23S rRNA interface [nucleotide binding]; other site 565050001579 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 565050001580 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 565050001581 L11 interface [polypeptide binding]; other site 565050001582 putative EF-Tu interaction site [polypeptide binding]; other site 565050001583 putative EF-G interaction site [polypeptide binding]; other site 565050001584 RDD family; Region: RDD; cl00746 565050001585 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 565050001586 O-Antigen ligase; Region: Wzy_C; cl04850 565050001587 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 565050001588 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; cl04593 565050001589 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 565050001590 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 565050001591 RPB12 interaction site [polypeptide binding]; other site 565050001592 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; cl04593 565050001593 RPB11 interaction site [polypeptide binding]; other site 565050001594 RPB12 interaction site [polypeptide binding]; other site 565050001595 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 565050001596 RPB1 interaction site [polypeptide binding]; other site 565050001597 RPB11 interaction site [polypeptide binding]; other site 565050001598 RPB10 interaction site [polypeptide binding]; other site 565050001599 RPB3 interaction site [polypeptide binding]; other site 565050001600 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 565050001601 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 565050001602 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 565050001603 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 565050001604 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 565050001605 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 565050001606 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 565050001607 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 565050001608 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 565050001609 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 565050001610 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 565050001611 DNA binding site [nucleotide binding] 565050001612 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 565050001613 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050001614 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050001615 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050001616 dimer interface [polypeptide binding]; other site 565050001617 putative CheW interface [polypeptide binding]; other site 565050001618 nuc_hydro: Nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. This group contains eukaryotic, bacterial and archeal...; Region: nuc_hydro; cl00226 565050001619 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 565050001620 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5394 565050001621 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 565050001622 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 565050001623 putative acyltransferase; Provisional; Region: PRK05790 565050001624 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 565050001625 dimer interface [polypeptide binding]; other site 565050001626 active site 565050001627 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 565050001628 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 565050001629 NAD(P) binding site [chemical binding]; other site 565050001630 homotetramer interface [polypeptide binding]; other site 565050001631 homodimer interface [polypeptide binding]; other site 565050001632 active site 565050001633 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 565050001634 Helix-turn-helix domains; Region: HTH; cl00088 565050001635 insertion element IS2 transposase InsD; Provisional; Region: PRK14702 565050001636 HTH-like domain; Region: HTH_21; pfam13276 565050001637 Integrase core domain; Region: rve; cl01316 565050001638 Integrase core domain; Region: rve_3; cl15866 565050001639 Transcriptional regulators [Transcription]; Region: PurR; COG1609 565050001640 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050001641 Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators; Region: PBP1_CelR; cd06295 565050001642 putative dimerization interface [polypeptide binding]; other site 565050001643 putative ligand binding site [chemical binding]; other site 565050001644 Cupin superfamily (DUF985); Region: Cupin_5; cl01418 565050001645 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 565050001646 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001647 Nitrogen regulatory protein P-II; Region: P-II; cl00412 565050001648 Nitrogen regulatory protein P-II; Region: P-II; smart00938 565050001649 Catalytic domain, repeat 1, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Region: PLDc_vPLD1_2_like_bac_1; cd09140 565050001650 putative active site [active] 565050001651 catalytic site [active] 565050001652 Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Region: PLDc_vPLD1_2_like_bac_2; cd09143 565050001653 putative active site [active] 565050001654 catalytic site [active] 565050001655 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 565050001656 putative catalytic site [active] 565050001657 putative metal binding site [ion binding]; other site 565050001658 putative phosphate binding site [ion binding]; other site 565050001659 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 565050001660 S-adenosylmethionine binding site [chemical binding]; other site 565050001661 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 565050001662 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; cl12031 565050001663 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 565050001664 catalytic core [active] 565050001665 Protein of unknown function (DUF952); Region: DUF952; cl01393 565050001666 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 565050001667 quinone interaction residues [chemical binding]; other site 565050001668 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 565050001669 active site 565050001670 catalytic residues [active] 565050001671 FMN binding site [chemical binding]; other site 565050001672 substrate binding site [chemical binding]; other site 565050001673 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 565050001674 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 565050001675 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050001676 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 565050001677 dimer interface [polypeptide binding]; other site 565050001678 phosphorylation site [posttranslational modification] 565050001679 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 565050001680 ATP binding site [chemical binding]; other site 565050001681 Mg2+ binding site [ion binding]; other site 565050001682 G-X-G motif; other site 565050001683 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 565050001684 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 565050001685 bifunctional D-altronate/D-mannonate dehydratase; Provisional; Region: PRK15072 565050001686 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; cl09108 565050001687 metal binding site [ion binding]; metal-binding site 565050001688 substrate binding pocket [chemical binding]; other site 565050001689 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 565050001690 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; cl15460 565050001691 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 565050001692 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 565050001693 active site 565050001694 dimer interface [polypeptide binding]; other site 565050001695 Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]; Region: AgaS; COG2222 565050001696 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 565050001697 dimer interface [polypeptide binding]; other site 565050001698 active site 565050001699 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 565050001700 dimer interface [polypeptide binding]; other site 565050001701 active site 565050001702 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 565050001703 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050001704 DNA-binding site [nucleotide binding]; DNA binding site 565050001705 UTRA domain; Region: UTRA; cl01230 565050001706 PTS_IIA, PTS system, glucose/sucrose 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_glc; cl00162 565050001707 HPr interaction site; other site 565050001708 glycerol kinase (GK) interaction site [polypeptide binding]; other site 565050001709 active site 565050001710 phosphorylation site [posttranslational modification] 565050001711 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 565050001712 dimerization domain swap beta strand [polypeptide binding]; other site 565050001713 regulatory protein interface [polypeptide binding]; other site 565050001714 active site 565050001715 regulatory phosphorylation site [posttranslational modification]; other site 565050001716 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 565050001717 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 565050001718 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 565050001719 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; cl09155 565050001720 PTS system, N-acetylglucosamine-specific IIBC component; Region: PTS-II-BC-nag; TIGR01998 565050001721 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 565050001722 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 565050001723 active site turn [active] 565050001724 phosphorylation site [posttranslational modification] 565050001725 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cl00164 565050001726 active site turn [active] 565050001727 phosphorylation site [posttranslational modification] 565050001728 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050001729 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; cl00284 565050001730 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 565050001731 Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain; Region: NAGLU_N; pfam12971 565050001732 Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain; Region: NAGLU; pfam05089 565050001733 Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain; Region: NAGLU_C; pfam12972 565050001734 Protein of unknown function (DUF1624); Region: DUF1624; cl01394 565050001735 glucose-1-phosphatase/inositol phosphatase; Provisional; Region: PRK10173 565050001736 Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction; Region: HP_HAP_like; cd07061 565050001737 catalytic core [active] 565050001738 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 565050001739 Glycosyl hydrolase family 67 N-terminus; Region: Glyco_hydro_67N; pfam03648 565050001740 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 565050001741 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cd00091 565050001742 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 565050001743 active site 565050001744 substrate binding site [chemical binding]; other site 565050001745 Mg2+ binding site [ion binding]; other site 565050001746 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050001747 Protein of unknown function (DUF1353); Region: DUF1353; pfam07087 565050001748 Lysozyme family protein [General function prediction only]; Region: COG5526 565050001749 LytTr DNA-binding domain; Region: LytTR; cl04498 565050001750 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 565050001751 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050001752 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; cl12031 565050001753 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 565050001754 amidophosphoribosyltransferase; Provisional; Region: PRK07847 565050001755 Ferritin-like; Region: Ferritin-like; pfam12902 565050001756 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 565050001757 FecR protein; Region: FecR; pfam04773 565050001758 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 565050001759 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 565050001760 DNA binding residues [nucleotide binding] 565050001761 Secretin and TonB N terminus short domain; Region: STN; cl06624 565050001762 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; cl00284 565050001763 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050001764 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; cl00284 565050001765 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050001766 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; cl00284 565050001767 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; cl00284 565050001768 MoxR-like ATPases [General function prediction only]; Region: COG0714 565050001769 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 565050001770 Walker A motif; other site 565050001771 ATP binding site [chemical binding]; other site 565050001772 Walker B motif; other site 565050001773 arginine finger; other site 565050001774 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 565050001775 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 565050001776 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 565050001777 metal ion-dependent adhesion site (MIDAS); other site 565050001778 Integral membrane protein DUF95; Region: DUF95; cl00572 565050001779 RDD family; Region: RDD; cl00746 565050001780 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050001781 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; cl00284 565050001782 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; cl00284 565050001783 Endopygalactorunase [Cell envelope biogenesis, outer membrane]; Region: PGU1; COG5434 565050001784 Probable polygalacturonase At3g15720; Region: PLN03003; cl14103 565050001785 Transcriptional regulators [Transcription]; Region: PurR; COG1609 565050001786 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 565050001787 DNA binding site [nucleotide binding] 565050001788 domain linker motif; other site 565050001789 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 565050001790 dimerization interface [polypeptide binding]; other site 565050001791 ligand binding site [chemical binding]; other site 565050001792 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]; Region: COG3537 565050001793 Glycosyl hydrolase family 92; Region: Glyco_hydro_92; cl15460 565050001794 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 565050001795 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050001796 L-Asparaginase type 2. L-Asparaginase hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzyme undergoes an autoproteolytic cleavage into alpha and beta subunits to expose a threonine residue which becomes the N-terminal residue of the beta...; Region: Asparaginase_2; cd04701 565050001797 catalytic nucleophile [active] 565050001798 Type 1 glutamine amidotransferase (GATase1)-like domain found in cyanophycinase; Region: GAT1_cyanophycinase; cd03145 565050001799 proposed catalytic triad [active] 565050001800 active site nucleophile [active] 565050001801 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 565050001802 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; cl00284 565050001803 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; cl00284 565050001804 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 565050001805 Helix-turn-helix domains; Region: HTH; cl00088 565050001806 Arginine N-succinyltransferase beta subunit; Region: AstA; cl11440 565050001807 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 565050001808 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 565050001809 NAD(P) binding site [chemical binding]; other site 565050001810 catalytic residues [active] 565050001811 Succinylarginine dihydrolase; Region: AstB; cl01511 565050001812 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 565050001813 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 565050001814 inhibitor-cofactor binding pocket; inhibition site 565050001815 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050001816 catalytic residue [active] 565050001817 PAS domain S-box; Region: sensory_box; TIGR00229 565050001818 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 565050001819 putative active site [active] 565050001820 heme pocket [chemical binding]; other site 565050001821 PAS domain S-box; Region: sensory_box; TIGR00229 565050001822 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 565050001823 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 565050001824 dimer interface [polypeptide binding]; other site 565050001825 phosphorylation site [posttranslational modification] 565050001826 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 565050001827 ATP binding site [chemical binding]; other site 565050001828 Mg2+ binding site [ion binding]; other site 565050001829 G-X-G motif; other site 565050001830 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; cl09944 565050001831 phosphorylation site [posttranslational modification] 565050001832 intermolecular recognition site; other site 565050001833 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 565050001834 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050001835 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050001836 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 565050001837 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050001838 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050001839 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050001840 Response regulator receiver domain; Region: Response_reg; pfam00072 565050001841 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 565050001842 active site 565050001843 phosphorylation site [posttranslational modification] 565050001844 intermolecular recognition site; other site 565050001845 dimerization interface [polypeptide binding]; other site 565050001846 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050001847 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050001848 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050001849 dimer interface [polypeptide binding]; other site 565050001850 putative CheW interface [polypeptide binding]; other site 565050001851 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 565050001852 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 565050001853 active site 565050001854 phosphorylation site [posttranslational modification] 565050001855 intermolecular recognition site; other site 565050001856 dimerization interface [polypeptide binding]; other site 565050001857 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 565050001858 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050001859 dimer interface [polypeptide binding]; other site 565050001860 putative CheW interface [polypeptide binding]; other site 565050001861 chemotaxis protein CheA; Provisional; Region: PRK10547 565050001862 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 565050001863 putative binding surface; other site 565050001864 active site 565050001865 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 565050001866 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 565050001867 ATP binding site [chemical binding]; other site 565050001868 Mg2+ binding site [ion binding]; other site 565050001869 G-X-G motif; other site 565050001870 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 565050001871 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 565050001872 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 565050001873 Response regulator receiver domain; Region: Response_reg; pfam00072 565050001874 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 565050001875 active site 565050001876 phosphorylation site [posttranslational modification] 565050001877 intermolecular recognition site; other site 565050001878 dimerization interface [polypeptide binding]; other site 565050001879 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 565050001880 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 565050001881 active site 565050001882 phosphorylation site [posttranslational modification] 565050001883 intermolecular recognition site; other site 565050001884 dimerization interface [polypeptide binding]; other site 565050001885 CheB methylesterase; Region: CheB_methylest; pfam01339 565050001886 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 565050001887 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 565050001888 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001889 CHASE2 domain; Region: CHASE2; cl01732 565050001890 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4995 565050001891 CHAT domain; Region: CHAT; pfam12770 565050001892 haemagglutination activity domain; Region: Haemagg_act; cl05436 565050001893 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 565050001894 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 565050001895 Surface antigen; Region: Bac_surface_Ag; cl03097 565050001896 NMT1-like family; Region: NMT1_2; cl15260 565050001897 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 565050001898 dimer interface [polypeptide binding]; other site 565050001899 conserved gate region; other site 565050001900 putative PBP binding loops; other site 565050001901 ABC-ATPase subunit interface; other site 565050001902 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 565050001903 nitrate transport ATP-binding subunits C and D; Region: ntrCD; TIGR01184 565050001904 Walker A/P-loop; other site 565050001905 ATP binding site [chemical binding]; other site 565050001906 Q-loop/lid; other site 565050001907 ABC transporter signature motif; other site 565050001908 Walker B; other site 565050001909 D-loop; other site 565050001910 H-loop/switch region; other site 565050001911 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 565050001912 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; cl09944 565050001913 active site 565050001914 phosphorylation site [posttranslational modification] 565050001915 intermolecular recognition site; other site 565050001916 dimerization interface [polypeptide binding]; other site 565050001917 ANTAR domain; Region: ANTAR; cl04297 565050001918 NMT1-like family; Region: NMT1_2; cl15260 565050001919 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 565050001920 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 565050001921 putative substrate translocation pore; other site 565050001922 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 565050001923 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 565050001924 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 565050001925 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 565050001926 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 565050001927 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 565050001928 [2Fe-2S] cluster binding site [ion binding]; other site 565050001929 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 565050001930 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 565050001931 [4Fe-4S] binding site [ion binding]; other site 565050001932 molybdopterin cofactor binding site; other site 565050001933 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 565050001934 molybdopterin cofactor binding site; other site 565050001935 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 565050001936 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 565050001937 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 565050001938 HsdM N-terminal domain; Region: HsdM_N; pfam12161 565050001939 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001940 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 565050001941 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 565050001942 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 565050001943 Uncharacterized conserved protein [Function unknown]; Region: COG4127 565050001944 Restriction endonuclease; Region: Mrr_cat; cl00516 565050001945 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 565050001946 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 565050001947 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050001948 ATP binding site [chemical binding]; other site 565050001949 putative Mg++ binding site [ion binding]; other site 565050001950 Helix-turn-helix domains; Region: HTH; cl00088 565050001951 putative transposase OrfB; Reviewed; Region: PHA02517 565050001952 Helix-turn-helix domains; Region: HTH; cl00088 565050001953 Integrase core domain; Region: rve; cl01316 565050001954 Integrase core domain; Region: rve_3; cl15866 565050001955 Helix-turn-helix domains; Region: HTH; cl00088 565050001956 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 565050001957 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 565050001958 GAF domain; Region: GAF_2; pfam13185 565050001959 GAF domain; Region: GAF; cl15785 565050001960 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 565050001961 Histidine kinase; Region: HisKA_2; cl06527 565050001962 Response regulator receiver domain; Region: Response_reg; pfam00072 565050001963 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 565050001964 active site 565050001965 phosphorylation site [posttranslational modification] 565050001966 intermolecular recognition site; other site 565050001967 dimerization interface [polypeptide binding]; other site 565050001968 Protein of unknown function (DUF563); Region: DUF563; cl15705 565050001969 Protein of unknown function (DUF563); Region: DUF563; cl15705 565050001970 Rhamnan synthesis protein F; Region: RgpF; cl01529 565050001971 Rhamnan synthesis protein F; Region: RgpF; cl01529 565050001972 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 565050001973 ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and...; Region: ABC_KpsT_Wzt; cd03220 565050001974 Walker A/P-loop; other site 565050001975 ATP binding site [chemical binding]; other site 565050001976 Q-loop/lid; other site 565050001977 ABC transporter signature motif; other site 565050001978 Walker B; other site 565050001979 D-loop; other site 565050001980 H-loop/switch region; other site 565050001981 ABC-2 type transporter; Region: ABC2_membrane; cl11417 565050001982 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 565050001983 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 565050001984 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 565050001985 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001986 HI0933-like protein; Region: HI0933_like; pfam03486 565050001987 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050001988 PIN domain of the VapC-like UPF0110 protein Mb0640 and homologs; Region: PIN_UPF0110; cd09871 565050001989 putative active site [active] 565050001990 Rv0623-like transcription factor; Region: PSK_trans_fac; cl01834 565050001991 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 565050001992 mRNA/rRNA interface [nucleotide binding]; other site 565050001993 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 565050001994 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 565050001995 23S rRNA interface [nucleotide binding]; other site 565050001996 L7/L12 interface [polypeptide binding]; other site 565050001997 putative thiostrepton binding site; other site 565050001998 L25 interface [polypeptide binding]; other site 565050001999 Transposase; Region: DEDD_Tnp_IS110; pfam01548 565050002000 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 565050002001 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 565050002002 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 565050002003 putative catalytic residue [active] 565050002004 classical (c) SDR, subgroup 10; Region: SDR_c10; cd05373 565050002005 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 565050002006 putative NAD(P) binding site [chemical binding]; other site 565050002007 active site 565050002008 Helix-turn-helix domains; Region: HTH; cl00088 565050002009 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 565050002010 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 565050002011 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 565050002012 Cupin domain; Region: Cupin_2; cl09118 565050002013 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 565050002014 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050002015 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 565050002016 DNA binding residues [nucleotide binding] 565050002017 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 565050002018 Active site serine [active] 565050002019 PAS domain S-box; Region: sensory_box; TIGR00229 565050002020 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 565050002021 putative active site [active] 565050002022 heme pocket [chemical binding]; other site 565050002023 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 565050002024 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 565050002025 putative active site [active] 565050002026 heme pocket [chemical binding]; other site 565050002027 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 565050002028 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 565050002029 putative active site [active] 565050002030 heme pocket [chemical binding]; other site 565050002031 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 565050002032 dimer interface [polypeptide binding]; other site 565050002033 phosphorylation site [posttranslational modification] 565050002034 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 565050002035 ATP binding site [chemical binding]; other site 565050002036 Mg2+ binding site [ion binding]; other site 565050002037 G-X-G motif; other site 565050002038 Response regulator receiver domain; Region: Response_reg; pfam00072 565050002039 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 565050002040 active site 565050002041 phosphorylation site [posttranslational modification] 565050002042 intermolecular recognition site; other site 565050002043 dimerization interface [polypeptide binding]; other site 565050002044 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 565050002045 Ferredoxin [Energy production and conversion]; Region: COG1146 565050002046 4Fe-4S binding domain; Region: Fer4; cl02805 565050002047 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 565050002048 putative diguanylate cyclase; Provisional; Region: PRK09776 565050002049 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 565050002050 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 565050002051 metal binding site [ion binding]; metal-binding site 565050002052 active site 565050002053 I-site; other site 565050002054 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 565050002055 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 565050002056 RNA binding surface [nucleotide binding]; other site 565050002057 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050002058 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 565050002059 nucleotide binding region [chemical binding]; other site 565050002060 Superfamily II RNA helicase [DNA replication, recombination, and repair]; Region: COG4581 565050002061 ATP-binding site [chemical binding]; other site 565050002062 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 565050002063 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 565050002064 active site 565050002065 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 565050002066 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 565050002067 DNA binding site [nucleotide binding] 565050002068 active site 565050002069 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 565050002070 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 565050002071 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; cl00284 565050002072 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050002073 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 protein; Region: CSP_CDS; cd04458 565050002074 DNA-binding site [nucleotide binding]; DNA binding site 565050002075 RNA-binding motif; other site 565050002076 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4246 565050002077 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 565050002078 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 565050002079 cobaltochelatase, CobT subunit; Region: CobT; TIGR01651 565050002080 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 565050002081 metal ion-dependent adhesion site (MIDAS); other site 565050002082 Protein of unknown function (DUF3089); Region: DUF3089; pfam11288 565050002083 CAAX protease self-immunity; Region: Abi; cl00558 565050002084 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 565050002085 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 565050002086 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 565050002087 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins; Region: Peptidase_C39C; cd02419 565050002088 putative active site [active] 565050002089 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 565050002090 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050002091 Walker A/P-loop; other site 565050002092 ATP binding site [chemical binding]; other site 565050002093 Q-loop/lid; other site 565050002094 ABC transporter signature motif; other site 565050002095 Walker B; other site 565050002096 D-loop; other site 565050002097 H-loop/switch region; other site 565050002098 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 565050002099 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 565050002100 ring oligomerisation interface [polypeptide binding]; other site 565050002101 ATP/Mg binding site [chemical binding]; other site 565050002102 stacking interactions; other site 565050002103 hinge regions; other site 565050002104 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 565050002105 oligomerisation interface [polypeptide binding]; other site 565050002106 mobile loop; other site 565050002107 roof hairpin; other site 565050002108 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 565050002109 metal binding site [ion binding]; metal-binding site 565050002110 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 565050002111 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 565050002112 DNA binding site [nucleotide binding] 565050002113 active site 565050002114 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 565050002115 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 565050002116 active site 565050002117 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 565050002118 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050002119 Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA; Region: HTH_TipAL-Mta; cd01106 565050002120 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 565050002121 DNA binding residues [nucleotide binding] 565050002122 dimer interface [polypeptide binding]; other site 565050002123 TipAS antibiotic-recognition domain; Region: TipAS; pfam07739 565050002124 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 565050002125 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 565050002126 ATP binding site [chemical binding]; other site 565050002127 Mg2+ binding site [ion binding]; other site 565050002128 G-X-G motif; other site 565050002129 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 565050002130 ATP binding site [chemical binding]; other site 565050002131 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 565050002132 TraB family; Region: TraB; cl12050 565050002133 TraB family; Region: TraB; cl12050 565050002134 TraB family; Region: TraB; cl12050 565050002135 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 565050002136 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 565050002137 isoleucyl-tRNA synthetase; Provisional; Region: ileS; PRK13804 565050002138 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 565050002139 active site 565050002140 HIGH motif; other site 565050002141 nucleotide binding site [chemical binding]; other site 565050002142 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 565050002143 active site 565050002144 KMSKS motif; other site 565050002145 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 565050002146 tRNA binding surface [nucleotide binding]; other site 565050002147 anticodon binding site; other site 565050002148 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 565050002149 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 565050002150 protein binding site [polypeptide binding]; other site 565050002151 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 565050002152 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 565050002153 active site 565050002154 Riboflavin kinase; Region: Flavokinase; cl03312 565050002155 (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. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 565050002156 dimer interaction site [polypeptide binding]; other site 565050002157 substrate-binding tunnel; other site 565050002158 active site 565050002159 catalytic site [active] 565050002160 substrate binding site [chemical binding]; other site 565050002161 Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]; Region: NagD; COG0647 565050002162 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050002163 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050002164 Phospholipid methyltransferase; Region: PEMT; cl00763 565050002165 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 565050002166 GIY-YIG motif/motif A; other site 565050002167 putative active site [active] 565050002168 putative metal binding site [ion binding]; other site 565050002169 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 565050002170 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 565050002171 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 565050002172 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 565050002173 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 565050002174 DNA binding site [nucleotide binding] 565050002175 active site 565050002176 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 565050002177 FeoA domain; Region: FeoA; cl00838 565050002178 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 565050002179 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 565050002180 G1 box; other site 565050002181 GTP/Mg2+ binding site [chemical binding]; other site 565050002182 Switch I region; other site 565050002183 G2 box; other site 565050002184 G3 box; other site 565050002185 Switch II region; other site 565050002186 G4 box; other site 565050002187 G5 box; other site 565050002188 Nucleoside recognition; Region: Gate; cl00486 565050002189 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 565050002190 Nucleoside recognition; Region: Gate; cl00486 565050002191 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 565050002192 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 565050002193 Predicted membrane protein [Function unknown]; Region: COG2311 565050002194 Protein of unknown function (DUF418); Region: DUF418; cl12135 565050002195 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK07530 565050002196 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050002197 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 565050002198 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 565050002199 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 565050002200 FeS/SAM binding site; other site 565050002201 Lysine-2,3-aminomutase; Region: LAM_C; pfam12544 565050002202 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 565050002203 tellurium resistance terB-like protein; Region: terB_like; cl11965 565050002204 Truncated, possibly inactive, lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]; Region: COG2269 565050002205 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 attaches...; Region: class_II_aaRS-like_core; cl00268 565050002206 motif 1; other site 565050002207 dimer interface [polypeptide binding]; other site 565050002208 active site 565050002209 motif 2; other site 565050002210 motif 3; other site 565050002211 elongation factor P; Validated; Region: PRK00529 565050002212 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 565050002213 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 565050002214 RNA binding site [nucleotide binding]; other site 565050002215 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 565050002216 RNA binding site [nucleotide binding]; other site 565050002217 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050002218 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 565050002219 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; cl00284 565050002220 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 565050002221 dimer interface [polypeptide binding]; other site 565050002222 phosphorylation site [posttranslational modification] 565050002223 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 565050002224 ATP binding site [chemical binding]; other site 565050002225 Mg2+ binding site [ion binding]; other site 565050002226 G-X-G motif; other site 565050002227 Response regulator receiver domain; Region: Response_reg; pfam00072 565050002228 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 565050002229 active site 565050002230 phosphorylation site [posttranslational modification] 565050002231 intermolecular recognition site; other site 565050002232 dimerization interface [polypeptide binding]; other site 565050002233 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 565050002234 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 565050002235 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 565050002236 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 565050002237 Ligand binding site [chemical binding]; other site 565050002238 Electron transfer flavoprotein domain; Region: ETF; pfam01012 565050002239 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 565050002240 DNA-binding transcriptional regulator EnvR; Provisional; Region: PRK09975 565050002241 Helix-turn-helix domains; Region: HTH; cl00088 565050002242 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050002243 Helix-turn-helix domains; Region: HTH; cl00088 565050002244 hypothetical protein; Provisional; Region: PRK08262 565050002245 M20 Peptidase, carboxypeptidase yscS; Region: M20_yscS; cd05674 565050002246 metal binding site [ion binding]; metal-binding site 565050002247 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 565050002248 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 565050002249 [2Fe-2S] cluster binding site [ion binding]; other site 565050002250 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 565050002251 hydrophobic ligand binding site; other site 565050002252 hypothetical protein; Provisional; Region: PRK08912 565050002253 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 565050002254 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050002255 homodimer interface [polypeptide binding]; other site 565050002256 catalytic residue [active] 565050002257 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 565050002258 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 565050002259 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; cl00284 565050002260 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 565050002261 PAS domain; Region: PAS_9; pfam13426 565050002262 putative active site [active] 565050002263 heme pocket [chemical binding]; other site 565050002264 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 565050002265 metal binding site [ion binding]; metal-binding site 565050002266 active site 565050002267 I-site; other site 565050002268 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 565050002269 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 565050002270 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 565050002271 G1 box; other site 565050002272 putative GEF interaction site [polypeptide binding]; other site 565050002273 GTP/Mg2+ binding site [chemical binding]; other site 565050002274 Switch I region; other site 565050002275 G2 box; other site 565050002276 G3 box; other site 565050002277 Switch II region; other site 565050002278 G4 box; other site 565050002279 G5 box; other site 565050002280 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 565050002281 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 565050002282 Gram-negative bacterial tonB protein; Region: TonB; cl10048 565050002283 N-formylglutamate amidohydrolase; Region: FGase; cl01522 565050002284 Response regulator receiver domain; Region: Response_reg; pfam00072 565050002285 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 565050002286 active site 565050002287 phosphorylation site [posttranslational modification] 565050002288 intermolecular recognition site; other site 565050002289 dimerization interface [polypeptide binding]; other site 565050002290 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 565050002291 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 565050002292 Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not...; Region: ZnMc_serralysin_like; cd04277 565050002293 active site 565050002294 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 565050002295 long tail fiber, proximal subunit; Provisional; Region: 34; PHA02584 565050002296 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 565050002297 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 565050002298 ligand binding site [chemical binding]; other site 565050002299 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; cl15754 565050002300 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 565050002301 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 565050002302 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 565050002303 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 565050002304 Major Facilitator Superfamily; Region: MFS_1; pfam07690 565050002305 putative substrate translocation pore; other site 565050002306 transcriptional regulator FixK; Provisional; Region: fixK; PRK09391 565050002307 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 565050002308 ligand binding site [chemical binding]; other site 565050002309 flexible hinge region; other site 565050002310 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 565050002311 putative switch regulator; other site 565050002312 non-specific DNA interactions [nucleotide binding]; other site 565050002313 DNA binding site [nucleotide binding] 565050002314 sequence specific DNA binding site [nucleotide binding]; other site 565050002315 putative cAMP binding site [chemical binding]; other site 565050002316 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 565050002317 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 565050002318 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 565050002319 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 565050002320 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 565050002321 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 565050002322 response regulator FixJ; Provisional; Region: fixJ; PRK09390 565050002323 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 565050002324 active site 565050002325 phosphorylation site [posttranslational modification] 565050002326 intermolecular recognition site; other site 565050002327 dimerization interface [polypeptide binding]; other site 565050002328 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 565050002329 DNA binding residues [nucleotide binding] 565050002330 dimerization interface [polypeptide binding]; other site 565050002331 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 565050002332 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 565050002333 putative active site [active] 565050002334 heme pocket [chemical binding]; other site 565050002335 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 565050002336 dimer interface [polypeptide binding]; other site 565050002337 phosphorylation site [posttranslational modification] 565050002338 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 565050002339 ATP binding site [chemical binding]; other site 565050002340 Mg2+ binding site [ion binding]; other site 565050002341 G-X-G motif; other site 565050002342 ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydC; COG4987 565050002343 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050002344 Walker A/P-loop; other site 565050002345 ATP binding site [chemical binding]; other site 565050002346 Q-loop/lid; other site 565050002347 ABC transporter signature motif; other site 565050002348 Walker B; other site 565050002349 D-loop; other site 565050002350 H-loop/switch region; other site 565050002351 thiol reductant ABC exporter, CydD subunit; Region: CydD; TIGR02857 565050002352 The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a...; Region: ABCC_MRP_Like; cd03228 565050002353 Walker A/P-loop; other site 565050002354 ATP binding site [chemical binding]; other site 565050002355 Q-loop/lid; other site 565050002356 ABC transporter signature motif; other site 565050002357 Walker B; other site 565050002358 D-loop; other site 565050002359 H-loop/switch region; other site 565050002360 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 565050002361 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 565050002362 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 565050002363 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 565050002364 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 565050002365 putative CheA interaction surface; other site 565050002366 ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation; Region: ASCH; cl01020 565050002367 Predicted GTPase [General function prediction only]; Region: COG0218 565050002368 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 565050002369 G1 box; other site 565050002370 GTP/Mg2+ binding site [chemical binding]; other site 565050002371 Switch I region; other site 565050002372 G2 box; other site 565050002373 G3 box; other site 565050002374 Switch II region; other site 565050002375 G4 box; other site 565050002376 G5 box; other site 565050002377 membrane protein insertase; Provisional; Region: PRK01318 565050002378 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 565050002379 Ribonuclease P; Region: Ribonuclease_P; cl00457 565050002380 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 565050002381 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 565050002382 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 565050002383 NAD(P) binding site [chemical binding]; other site 565050002384 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; cl12031 565050002385 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 565050002386 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050002387 Helix-turn-helix domains; Region: HTH; cl00088 565050002388 Uncharacterized conserved protein (DUF2164); Region: DUF2164; cl02278 565050002389 Flavin-binding monooxygenase-like; Region: FMO-like; pfam00743 565050002390 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050002391 Lignostilbene-alpha,beta-dioxygenase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3670 565050002392 Retinal pigment epithelial membrane protein; Region: RPE65; cl10080 565050002393 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 565050002394 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 565050002395 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 565050002396 putative C-terminal domain interface [polypeptide binding]; other site 565050002397 putative GSH binding site (G-site) [chemical binding]; other site 565050002398 putative dimer interface [polypeptide binding]; other site 565050002399 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 565050002400 N-terminal domain interface [polypeptide binding]; other site 565050002401 acetyl-CoA acetyltransferase; Provisional; Region: PRK06504 565050002402 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 565050002403 dimer interface [polypeptide binding]; other site 565050002404 active site 565050002405 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 565050002406 dimerization interface [polypeptide binding]; other site 565050002407 DNA binding residues [nucleotide binding] 565050002408 Transcriptional regulators [Transcription]; Region: FadR; COG2186 565050002409 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050002410 DNA-binding site [nucleotide binding]; DNA binding site 565050002411 FCD domain; Region: FCD; cl11656 565050002412 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 565050002413 active site 565050002414 intersubunit interface [polypeptide binding]; other site 565050002415 catalytic residue [active] 565050002416 2-keto-3-deoxy-galactonokinase [Carbohydrate transport and metabolism]; Region: DgoK; COG3734 565050002417 2-keto-3-deoxy-galactonokinase; Region: DGOK; pfam05035 565050002418 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050002419 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; cl00284 565050002420 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; cl00284 565050002421 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050002422 Beta-galactosidase [Carbohydrate transport and metabolism]; Region: LacA; COG1874 565050002423 Beta-galactosidase; Region: Glyco_hydro_42; cl03154 565050002424 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 565050002425 Galactose mutarotase-like; Region: Gal_mutarotas_2; pfam13802 565050002426 PA14 domain; Region: PA14; cl08459 565050002427 XylS is a glycosyl hydrolase family 31 (GH31) alpha-xylosidase found in prokaryotes, eukaryotes, and archaea, that catalyzes the release of alpha-xylose from the non-reducing terminal side of the alpha-xyloside substrate. XylS has been characterized in...; Region: GH31_xylosidase_XylS; cd06591 565050002428 putative active site [active] 565050002429 putative catalytic site [active] 565050002430 Transcriptional regulator [Transcription]; Region: LysR; COG0583 565050002431 Helix-turn-helix domains; Region: HTH; cl00088 565050002432 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 565050002433 dimerization interface [polypeptide binding]; other site 565050002434 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 565050002435 flagellin; Provisional; Region: PRK12802 565050002436 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 565050002437 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 565050002438 flagellin; Provisional; Region: PRK12802 565050002439 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 565050002440 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 565050002441 flagellin; Provisional; Region: PRK12802 565050002442 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 565050002443 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 565050002444 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 565050002445 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 565050002446 Glycoside hydrolase 97; Region: Glyco_hydro_97; pfam10566 565050002447 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 565050002448 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 565050002449 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 565050002450 Domain of unknown function (DUF303); Region: DUF303; pfam03629 565050002451 Domain of unknown function (DUF303); Region: DUF303; pfam03629 565050002452 Carboxylesterase type B [Lipid metabolism]; Region: PnbA; COG2272 565050002453 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; cl12031 565050002454 substrate binding pocket [chemical binding]; other site 565050002455 catalytic triad [active] 565050002456 Endo-beta-mannanase [Carbohydrate transport and metabolism]; Region: COG3934 565050002457 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 565050002458 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 565050002459 Proline dehydrogenase; Region: Pro_dh; cl03282 565050002460 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 565050002461 Glutamate binding site [chemical binding]; other site 565050002462 NAD binding site [chemical binding]; other site 565050002463 catalytic residues [active] 565050002464 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 565050002465 Helix-turn-helix domains; Region: HTH; cl00088 565050002466 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 565050002467 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 565050002468 Protein export membrane protein; Region: SecD_SecF; cl14618 565050002469 Protein export membrane protein; Region: SecD_SecF; cl14618 565050002470 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 565050002471 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050002472 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050002473 Helix-turn-helix domains; Region: HTH; cl00088 565050002474 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 565050002475 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 565050002476 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 565050002477 Beta-Casp domain; Region: Beta-Casp; cl12567 565050002478 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 565050002479 Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are...; Region: Rhamnogalacturan_acetylesterase_like; cd01821 565050002480 active site 565050002481 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 565050002482 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_3; cd09002 565050002483 active site 565050002484 D-xylose transporter XylE; Provisional; Region: xylE; PRK10077 565050002485 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 565050002486 putative substrate translocation pore; other site 565050002487 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 565050002488 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050002489 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 565050002490 N-terminal plug; other site 565050002491 ligand-binding site [chemical binding]; other site 565050002492 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050002493 Dehydratase family; Region: ILVD_EDD; cl00340 565050002494 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 565050002495 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 565050002496 classical (c) SDRs; Region: SDR_c; cd05233 565050002497 NAD(P) binding site [chemical binding]; other site 565050002498 active site 565050002499 Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like; Region: ALDH_KGSADH-YcbD; cd07097 565050002500 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 565050002501 NAD(P) binding site [chemical binding]; other site 565050002502 catalytic residues [active] 565050002503 Fumarylacetoacetate (FAA) hydrolase family protein [General function prediction only]; Region: COG3970 565050002504 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 565050002505 Type II restriction enzyme, methylase subunits [Defense mechanisms]; Region: COG1002 565050002506 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050002507 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 565050002508 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 565050002509 putative active site [active] 565050002510 catalytic triad [active] 565050002511 dimer interface [polypeptide binding]; other site 565050002512 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 565050002513 GSH binding site [chemical binding]; other site 565050002514 catalytic residues [active] 565050002515 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 565050002516 active site 565050002517 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 565050002518 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050002519 Flp/Fap pilin component; Region: Flp_Fap; cl01585 565050002520 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 565050002521 active site 565050002522 8-oxo-dGMP binding site [chemical binding]; other site 565050002523 nudix motif; other site 565050002524 metal binding site [ion binding]; metal-binding site 565050002525 DEAD-like helicases superfamily; Region: DEXDc; smart00487 565050002526 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 565050002527 ATP binding site [chemical binding]; other site 565050002528 Mg++ binding site [ion binding]; other site 565050002529 motif III; other site 565050002530 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 565050002531 nucleotide binding region [chemical binding]; other site 565050002532 ATP-binding site [chemical binding]; other site 565050002533 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 565050002534 PAS fold; Region: PAS_3; pfam08447 565050002535 putative active site [active] 565050002536 heme pocket [chemical binding]; other site 565050002537 PAS fold; Region: PAS_3; pfam08447 565050002538 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 565050002539 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 565050002540 PAS fold; Region: PAS_3; pfam08447 565050002541 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 565050002542 Histidine kinase; Region: HisKA_2; cl06527 565050002543 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 565050002544 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 565050002545 Walker A/P-loop; other site 565050002546 ATP binding site [chemical binding]; other site 565050002547 Q-loop/lid; other site 565050002548 ABC transporter signature motif; other site 565050002549 Walker B; other site 565050002550 D-loop; other site 565050002551 H-loop/switch region; other site 565050002552 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 565050002553 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 565050002554 S-adenosylmethionine binding site [chemical binding]; other site 565050002555 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 565050002556 putative active site [active] 565050002557 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 565050002558 aspartate kinase; Reviewed; Region: PRK06635 565050002559 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 565050002560 putative nucleotide binding site [chemical binding]; other site 565050002561 putative catalytic residues [active] 565050002562 putative Mg ion binding site [ion binding]; other site 565050002563 putative aspartate binding site [chemical binding]; other site 565050002564 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 565050002565 putative allosteric regulatory site; other site 565050002566 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 565050002567 putative allosteric regulatory residue; other site 565050002568 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 565050002569 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 565050002570 Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: LpqC; COG3509 565050002571 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; cl12031 565050002572 Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; Region: PtsP; COG3605 565050002573 GAF domain; Region: GAF; cl15785 565050002574 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 565050002575 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 565050002576 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; cl09155 565050002577 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 565050002578 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050002579 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 565050002580 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 565050002581 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 565050002582 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 565050002583 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 565050002584 RNA binding surface [nucleotide binding]; other site 565050002585 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PSSA_1; cd02555 565050002586 active site 565050002587 peptide chain release factor 1; Validated; Region: prfA; PRK00591 565050002588 RF-1 domain; Region: RF-1; cl02875 565050002589 RF-1 domain; Region: RF-1; cl02875 565050002590 CHASE4 domain; Region: CHASE4; cl01308 565050002591 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 565050002592 metal binding site [ion binding]; metal-binding site 565050002593 active site 565050002594 I-site; other site 565050002595 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 565050002596 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; cl12031 565050002597 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 565050002598 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 565050002599 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 565050002600 ligand binding site [chemical binding]; other site 565050002601 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 565050002602 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_I; cd03216 565050002603 Walker A/P-loop; other site 565050002604 ATP binding site [chemical binding]; other site 565050002605 Q-loop/lid; other site 565050002606 ABC transporter signature motif; other site 565050002607 Walker B; other site 565050002608 D-loop; other site 565050002609 H-loop/switch region; other site 565050002610 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 565050002611 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 565050002612 TM-ABC transporter signature motif; other site 565050002613 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; Region: EEP-1; cd09083 565050002614 putative catalytic site [active] 565050002615 putative metal binding site [ion binding]; other site 565050002616 putative phosphate binding site [ion binding]; other site 565050002617 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl15243 565050002618 heme binding pocket [chemical binding]; other site 565050002619 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK06816 565050002620 'initiating' condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are characterized by the...; Region: init_cond_enzymes; cd00827 565050002621 dimer interface [polypeptide binding]; other site 565050002622 active site 565050002623 Erythromycin esterase homolog [General function prediction only]; Region: COG2312 565050002624 Erythromycin esterase; Region: Erythro_esteras; pfam05139 565050002625 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050002626 AAA domain; Region: AAA_28; pfam13521 565050002627 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 565050002628 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050002629 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 565050002630 Coenzyme A binding pocket [chemical binding]; other site 565050002631 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 565050002632 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 565050002633 MOSC domain; Region: MOSC; pfam03473 565050002634 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 565050002635 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 565050002636 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 565050002637 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 565050002638 S-adenosylmethionine binding site [chemical binding]; other site 565050002639 Domain of unknown function (DUF4167); Region: DUF4167; pfam13763 565050002640 Peptidase family M48; Region: Peptidase_M48; cl12018 565050002641 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 565050002642 Clp amino terminal domain; Region: Clp_N; pfam02861 565050002643 Clp amino terminal domain; Region: Clp_N; pfam02861 565050002644 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 565050002645 Walker A motif; other site 565050002646 ATP binding site [chemical binding]; other site 565050002647 Walker B motif; other site 565050002648 arginine finger; other site 565050002649 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 565050002650 Walker A motif; other site 565050002651 ATP binding site [chemical binding]; other site 565050002652 Walker B motif; other site 565050002653 arginine finger; other site 565050002654 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 565050002655 Helix-turn-helix domains; Region: HTH; cl00088 565050002656 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 565050002657 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; cl12031 565050002658 dihydroorotase; Reviewed; Region: PRK09236 565050002659 Transcriptional regulators [Transcription]; Region: GntR; COG1802 565050002660 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050002661 DNA-binding site [nucleotide binding]; DNA binding site 565050002662 FCD domain; Region: FCD; cl11656 565050002663 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 565050002664 catalytic motif [active] 565050002665 Zn binding site [ion binding]; other site 565050002666 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; cl00161 565050002667 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 565050002668 Lumazine binding domain; Region: Lum_binding; pfam00677 565050002669 Lumazine binding domain; Region: Lum_binding; pfam00677 565050002670 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 565050002671 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 565050002672 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 565050002673 dimerization interface [polypeptide binding]; other site 565050002674 active site 565050002675 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 565050002676 homopentamer interface [polypeptide binding]; other site 565050002677 active site 565050002678 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 565050002679 M28 Zn-Peptidase Aeromonas (Vibrio) proteolytica aminopeptidase (AAP)-like; Region: M28_AAP_like; cd05642 565050002680 putative metal binding site [ion binding]; other site 565050002681 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 565050002682 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 565050002683 Predicted membrane protein (DUF2306); Region: DUF2306; cl02232 565050002684 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050002685 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 565050002686 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 565050002687 dimer interface [polypeptide binding]; other site 565050002688 active site 565050002689 Helix-turn-helix domains; Region: HTH; cl00088 565050002690 Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]; Region: COG5001 565050002691 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 565050002692 metal binding site [ion binding]; metal-binding site 565050002693 active site 565050002694 I-site; other site 565050002695 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 565050002696 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 565050002697 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 565050002698 Ligand Binding Site [chemical binding]; other site 565050002699 flagellar hook-associated protein 3; Region: flagell_flgL; TIGR02550 565050002700 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 565050002701 Flagellar hook-associated protein [Cell motility and secretion]; Region: FlgK; COG1256 565050002702 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 565050002703 Flagellar hook-associated protein [Cell motility and secretion]; Region: FlgK; COG1256 565050002704 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 565050002705 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 565050002706 Flagellar hook capping protein [Cell motility and secretion]; Region: FlgD; COG1843 565050002707 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 565050002708 FlgD Ig-like domain; Region: FlgD_ig; cl15790 565050002709 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 565050002710 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 565050002711 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 565050002712 Protein of unknown function (DUF1153); Region: DUF1153; pfam06627 565050002713 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 565050002714 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 565050002715 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 565050002716 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 565050002717 FliG C-terminal domain; Region: FliG_C; pfam01706 565050002718 flagellar assembly protein H; Validated; Region: fliH; PRK06032 565050002719 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 565050002720 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 565050002721 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 565050002722 Walker A motif; other site 565050002723 ATP binding site [chemical binding]; other site 565050002724 Walker B motif; other site 565050002725 Helix-turn-helix domains; Region: HTH; cl00088 565050002726 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 565050002727 FHIPEP family; Region: FHIPEP; pfam00771 565050002728 Phosphate-selective porin O and P; Region: Porin_O_P; cl01524 565050002729 Uncharacterized protein conserved in bacteria (DUF2236); Region: DUF2236; cl01472 565050002730 Helix-turn-helix domains; Region: HTH; cl00088 565050002731 Domain of unknown function (DUF4282); Region: DUF4282; pfam14110 565050002732 Helix-turn-helix domains; Region: HTH; cl00088 565050002733 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 565050002734 OsmC-like protein; Region: OsmC; cl00767 565050002735 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 565050002736 HSP70 interaction site [polypeptide binding]; other site 565050002737 chaperone protein DnaJ; Provisional; Region: PRK14299 565050002738 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 565050002739 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 565050002740 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 565050002741 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 565050002742 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050002743 Helix-turn-helix domains; Region: HTH; cl00088 565050002744 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 565050002745 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 565050002746 Predicted kinase [General function prediction only]; Region: COG0645 565050002747 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 565050002748 dimer interface [polypeptide binding]; other site 565050002749 phosphorylation site [posttranslational modification] 565050002750 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 565050002751 ATP binding site [chemical binding]; other site 565050002752 Mg2+ binding site [ion binding]; other site 565050002753 G-X-G motif; other site 565050002754 Response regulator receiver domain; Region: Response_reg; pfam00072 565050002755 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 565050002756 active site 565050002757 phosphorylation site [posttranslational modification] 565050002758 intermolecular recognition site; other site 565050002759 dimerization interface [polypeptide binding]; other site 565050002760 putative acyl-CoA synthetase; Provisional; Region: PRK06018 565050002761 AMP-binding enzyme; Region: AMP-binding; cl15778 565050002762 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 565050002763 Protein of unknown function (DUF1499); Region: DUF1499; cl01841 565050002764 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 565050002765 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 565050002766 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 565050002767 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 565050002768 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; cl00284 565050002769 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 565050002770 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 565050002771 oligomer interface [polypeptide binding]; other site 565050002772 tandem repeat interface [polypeptide binding]; other site 565050002773 active site residues [active] 565050002774 Transposase domain (DUF772); Region: DUF772; cl15789 565050002775 Transposase domain (DUF772); Region: DUF772; cl15789 565050002776 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 565050002777 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050002778 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050002779 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 565050002780 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 565050002781 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 565050002782 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 565050002783 Walker A/P-loop; other site 565050002784 ATP binding site [chemical binding]; other site 565050002785 Q-loop/lid; other site 565050002786 ABC transporter signature motif; other site 565050002787 Walker B; other site 565050002788 D-loop; other site 565050002789 H-loop/switch region; other site 565050002790 Predicted transcriptional regulator [Transcription]; Region: COG4957 565050002791 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 565050002792 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 565050002793 dimer interface [polypeptide binding]; other site 565050002794 phosphorylation site [posttranslational modification] 565050002795 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 565050002796 ATP binding site [chemical binding]; other site 565050002797 Mg2+ binding site [ion binding]; other site 565050002798 G-X-G motif; other site 565050002799 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 565050002800 active site 565050002801 phosphorylation site [posttranslational modification] 565050002802 intermolecular recognition site; other site 565050002803 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 565050002804 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 565050002805 Coenzyme A binding pocket [chemical binding]; other site 565050002806 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 565050002807 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; cl12031 565050002808 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 565050002809 CsbD-like; Region: CsbD; cl15799 565050002810 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 565050002811 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 565050002812 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 565050002813 catalytic residue [active] 565050002814 Predicted acyl esterases [General function prediction only]; Region: COG2936 565050002815 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; cl08482 565050002816 OsmC-like protein; Region: OsmC; cl00767 565050002817 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 565050002818 putative active site [active] 565050002819 putative catalytic site [active] 565050002820 Protein of unknown function (DUF3620); Region: DUF3620; cl02233 565050002821 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08276 565050002822 AMP-binding enzyme; Region: AMP-binding; cl15778 565050002823 AMP-binding enzyme; Region: AMP-binding; cl15778 565050002824 choline dehydrogenase; Validated; Region: PRK02106 565050002825 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050002826 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 565050002827 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; cl12078 565050002828 enoyl-CoA hydratase; Provisional; Region: PRK08260 565050002829 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 565050002830 substrate binding site [chemical binding]; other site 565050002831 oxyanion hole (OAH) forming residues; other site 565050002832 trimer interface [polypeptide binding]; other site 565050002833 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; cl15419 565050002834 Predicted transcriptional regulator [Transcription]; Region: COG4957 565050002835 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 565050002836 PAS domain; Region: PAS_5; pfam07310 565050002837 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5388 565050002838 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 565050002839 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 565050002840 substrate binding site [chemical binding]; other site 565050002841 dimer interface [polypeptide binding]; other site 565050002842 ATP binding site [chemical binding]; other site 565050002843 FliP family; Region: FliP; cl00593 565050002844 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 565050002845 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK06004 565050002846 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 565050002847 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 565050002848 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 565050002849 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 565050002850 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 565050002851 urocanate hydratase; Provisional; Region: PRK05414 565050002852 N-formylglutamate amidohydrolase; Region: FGase; cl01522 565050002853 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 565050002854 active sites [active] 565050002855 tetramer interface [polypeptide binding]; other site 565050002856 imidazolonepropionase; Validated; Region: PRK09356 565050002857 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 565050002858 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 565050002859 active site 565050002860 N-formimino-L-glutamate deiminase; Validated; Region: PRK09229 565050002861 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 565050002862 active site 565050002863 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 565050002864 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050002865 DNA-binding site [nucleotide binding]; DNA binding site 565050002866 UTRA domain; Region: UTRA; cl01230 565050002867 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 565050002868 putative deacylase active site [active] 565050002869 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 565050002870 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 565050002871 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 565050002872 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 565050002873 Copper resistance protein B precursor (CopB); Region: CopB; cl01476 565050002874 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 565050002875 AMP-binding enzyme; Region: AMP-binding; cl15778 565050002876 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 565050002877 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 565050002878 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050002879 Probable beta-xylosidase; Provisional; Region: PLN03080 565050002880 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 565050002881 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 565050002882 Fibronectin type III-like domain; Region: Fn3-like; cl15273 565050002883 Transcriptional regulators [Transcription]; Region: PurR; COG1609 565050002884 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 565050002885 DNA binding site [nucleotide binding] 565050002886 domain linker motif; other site 565050002887 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 565050002888 putative dimerization interface [polypeptide binding]; other site 565050002889 putative ligand binding site [chemical binding]; other site 565050002890 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; cl00284 565050002891 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 565050002892 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050002893 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050002894 multifunctional aminopeptidase A; Provisional; Region: PRK00913 565050002895 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 565050002896 interface (dimer of trimers) [polypeptide binding]; other site 565050002897 Substrate-binding/catalytic site; other site 565050002898 Zn-binding sites [ion binding]; other site 565050002899 Alpha-L-rhamnosidase N-terminal domain; Region: Bac_rhamnosid_N; pfam08531 565050002900 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 565050002901 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 565050002902 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 565050002903 active site 565050002904 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 565050002905 putative substrate translocation pore; other site 565050002906 metabolite-proton symporter; Region: 2A0106; TIGR00883 565050002907 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 565050002908 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050002909 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 565050002910 DNA binding residues [nucleotide binding] 565050002911 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 565050002912 FecR protein; Region: FecR; pfam04773 565050002913 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050002914 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; cl00284 565050002915 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; cl00284 565050002916 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 565050002917 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 565050002918 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_3; cd06240 565050002919 putative active site [active] 565050002920 Zn binding site [ion binding]; other site 565050002921 Transcriptional regulators [Transcription]; Region: FadR; COG2186 565050002922 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050002923 DNA-binding site [nucleotide binding]; DNA binding site 565050002924 FCD domain; Region: FCD; cl11656 565050002925 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 565050002926 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050002927 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 565050002928 D-galactonate transporter; Region: 2A0114; TIGR00893 565050002929 putative substrate translocation pore; other site 565050002930 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 565050002931 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_1; cd09000 565050002932 inhibitor binding site; inhibition site 565050002933 active site 565050002934 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050002935 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; cl00284 565050002936 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; cl00284 565050002937 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050002938 Protein of unknown function (DUF419); Region: DUF419; cl15265 565050002939 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 565050002940 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050002941 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; cl00284 565050002942 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; cl00284 565050002943 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 565050002944 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 565050002945 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 565050002946 ABC transporter; Region: ABC_tran_2; pfam12848 565050002947 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 565050002948 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; cl00284 565050002949 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; cl00284 565050002950 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; cl00284 565050002951 SapC; Region: SapC; pfam07277 565050002952 JmjC domain, hydroxylase; Region: JmjC; cl15814 565050002953 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050002954 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 565050002955 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 565050002956 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050002957 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 565050002958 non-specific DNA binding site [nucleotide binding]; other site 565050002959 salt bridge; other site 565050002960 sequence-specific DNA binding site [nucleotide binding]; other site 565050002961 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 565050002962 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050002963 Walker A/P-loop; other site 565050002964 ATP binding site [chemical binding]; other site 565050002965 Q-loop/lid; other site 565050002966 ABC transporter signature motif; other site 565050002967 Walker B; other site 565050002968 D-loop; other site 565050002969 H-loop/switch region; other site 565050002970 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 565050002971 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050002972 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050002973 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 565050002974 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 565050002975 NADP-binding site; other site 565050002976 homotetramer interface [polypeptide binding]; other site 565050002977 substrate binding site [chemical binding]; other site 565050002978 homodimer interface [polypeptide binding]; other site 565050002979 active site 565050002980 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 565050002981 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 565050002982 putative trimer interface [polypeptide binding]; other site 565050002983 putative CoA binding site [chemical binding]; other site 565050002984 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 565050002985 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 565050002986 inhibitor-cofactor binding pocket; inhibition site 565050002987 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050002988 catalytic residue [active] 565050002989 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 565050002990 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 565050002991 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 565050002992 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 565050002993 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 565050002994 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 565050002995 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050002996 Predicted methyltransferase regulatory domain; Region: MethyTransf_Reg; pfam10119 565050002997 Protein of unknown function, DUF599; Region: DUF599; cl01575 565050002998 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 565050002999 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 565050003000 putative substrate translocation pore; other site 565050003001 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 565050003002 putative substrate translocation pore; other site 565050003003 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 565050003004 Protein of unknown function (DUF983); Region: DUF983; cl02211 565050003005 Beta/Gamma crystallin; Region: Crystall; cl02528 565050003006 Beta/Gamma crystallin; Region: Crystall; cl02528 565050003007 Penicillin amidase; Region: Penicil_amidase; pfam01804 565050003008 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 565050003009 Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_CA; cd01936 565050003010 active site 565050003011 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003012 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 565050003013 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 565050003014 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; cl00025 565050003015 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 565050003016 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; cl15754 565050003017 cofactor binding site; other site 565050003018 DNA binding site [nucleotide binding] 565050003019 substrate interaction site [chemical binding]; other site 565050003020 GTP-binding protein LepA; Provisional; Region: PRK05433 565050003021 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 565050003022 G1 box; other site 565050003023 putative GEF interaction site [polypeptide binding]; other site 565050003024 GTP/Mg2+ binding site [chemical binding]; other site 565050003025 Switch I region; other site 565050003026 G2 box; other site 565050003027 G3 box; other site 565050003028 Switch II region; other site 565050003029 G4 box; other site 565050003030 G5 box; other site 565050003031 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 565050003032 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 565050003033 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 565050003034 Protein of unknown function (DUF1134); Region: DUF1134; cl02235 565050003035 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 565050003036 Uncharacterized conserved protein [Function unknown]; Region: COG5316 565050003037 N-terminal domain of unknown function (DUF4140); Region: DUF4140; pfam13600 565050003038 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 565050003039 N-terminal domain of unknown function (DUF4140); Region: DUF4140; pfam13600 565050003040 Uncharacterized conserved protein [Function unknown]; Region: COG5316 565050003041 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 565050003042 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 565050003043 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 565050003044 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 565050003045 putative tRNA-binding site [nucleotide binding]; other site 565050003046 B3/4 domain; Region: B3_4; cl11458 565050003047 tRNA synthetase B5 domain; Region: B5; cl08394 565050003048 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 565050003049 dimer interface [polypeptide binding]; other site 565050003050 motif 3; other site 565050003051 motif 2; other site 565050003052 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 565050003053 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 565050003054 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 565050003055 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 565050003056 dimer interface [polypeptide binding]; other site 565050003057 motif 1; other site 565050003058 active site 565050003059 motif 2; other site 565050003060 motif 3; other site 565050003061 ribosomal protein L20; Region: rpl20; CHL00068 565050003062 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 565050003063 23S rRNA binding site [nucleotide binding]; other site 565050003064 L21 binding site [polypeptide binding]; other site 565050003065 L13 binding site [polypeptide binding]; other site 565050003066 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 565050003067 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 565050003068 Major Facilitator Superfamily; Region: MFS_1; pfam07690 565050003069 putative substrate translocation pore; other site 565050003070 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 565050003071 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; cl12031 565050003072 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 565050003073 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 565050003074 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 565050003075 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 565050003076 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 565050003077 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 565050003078 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 565050003079 putative active site [active] 565050003080 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 565050003081 This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core; Region: GT1_WavL_like; cd03819 565050003082 putative ADP-binding pocket [chemical binding]; other site 565050003083 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 565050003084 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; cl12031 565050003085 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 565050003086 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 565050003087 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 565050003088 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 565050003089 putative NAD(P) binding site [chemical binding]; other site 565050003090 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4805 565050003091 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 565050003092 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 565050003093 substrate binding site [chemical binding]; other site 565050003094 ATP binding site [chemical binding]; other site 565050003095 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 565050003096 DnaA box-binding interface [nucleotide binding]; other site 565050003097 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 565050003098 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 565050003099 active site residue [active] 565050003100 Fe-S metabolism associated domain; Region: SufE; cl00951 565050003101 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 565050003102 dimer interface [polypeptide binding]; other site 565050003103 phosphorylation site [posttranslational modification] 565050003104 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 565050003105 ATP binding site [chemical binding]; other site 565050003106 Mg2+ binding site [ion binding]; other site 565050003107 G-X-G motif; other site 565050003108 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 565050003109 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 565050003110 dimer interface [polypeptide binding]; other site 565050003111 phosphorylation site [posttranslational modification] 565050003112 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 565050003113 ATP binding site [chemical binding]; other site 565050003114 Mg2+ binding site [ion binding]; other site 565050003115 G-X-G motif; other site 565050003116 Protein of unknown function (DUF1491); Region: DUF1491; cl11568 565050003117 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 565050003118 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 565050003119 poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA; Region: PGA_TPR_OMP; TIGR03939 565050003120 Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]; Region: PrfC; COG4108 565050003121 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 565050003122 G1 box; other site 565050003123 putative GEF interaction site [polypeptide binding]; other site 565050003124 GTP/Mg2+ binding site [chemical binding]; other site 565050003125 Switch I region; other site 565050003126 G2 box; other site 565050003127 G3 box; other site 565050003128 Switch II region; other site 565050003129 G4 box; other site 565050003130 G5 box; other site 565050003131 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 565050003132 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 565050003133 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 565050003134 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050003135 homodimer interface [polypeptide binding]; other site 565050003136 catalytic residue [active] 565050003137 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 565050003138 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 565050003139 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 565050003140 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 565050003141 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 565050003142 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 565050003143 dimer interface [polypeptide binding]; other site 565050003144 phosphorylation site [posttranslational modification] 565050003145 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 565050003146 ATP binding site [chemical binding]; other site 565050003147 Mg2+ binding site [ion binding]; other site 565050003148 G-X-G motif; other site 565050003149 Response regulator receiver domain; Region: Response_reg; pfam00072 565050003150 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 565050003151 active site 565050003152 phosphorylation site [posttranslational modification] 565050003153 intermolecular recognition site; other site 565050003154 dimerization interface [polypeptide binding]; other site 565050003155 Protein of unknown function (DUF4199); Region: DUF4199; pfam13858 565050003156 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 565050003157 DNA binding residues [nucleotide binding] 565050003158 dimerization interface [polypeptide binding]; other site 565050003159 glycosyl hydrolase family 16; Region: Glyco_hydrolase_16; cl00218 565050003160 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 565050003161 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050003162 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4805 565050003163 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 565050003164 putative active site [active] 565050003165 heme pocket [chemical binding]; other site 565050003166 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 565050003167 recombinase A; Provisional; Region: recA; PRK09354 565050003168 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 565050003169 hexamer interface [polypeptide binding]; other site 565050003170 Walker A motif; other site 565050003171 ATP binding site [chemical binding]; other site 565050003172 Walker B motif; other site 565050003173 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 565050003174 homotrimer interaction site [polypeptide binding]; other site 565050003175 putative active site [active] 565050003176 Cytochrome c; Region: Cytochrom_C; cl11414 565050003177 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 565050003178 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003179 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 565050003180 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 565050003181 Coenzyme A binding pocket [chemical binding]; other site 565050003182 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050003183 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; cl00284 565050003184 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; cl00284 565050003185 Predicted transcriptional regulator [Transcription]; Region: COG2378 565050003186 WYL domain; Region: WYL; cl14852 565050003187 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 565050003188 Chromate transporter; Region: Chromate_transp; pfam02417 565050003189 Uncharacterized conserved protein [Function unknown]; Region: COG3743 565050003190 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; cl00284 565050003191 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; cl00284 565050003192 Sulfotransferase family; Region: Sulfotransfer_2; pfam03567 565050003193 hypothetical protein; Provisional; Region: PRK07208 565050003194 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003195 UDP-galactopyranose mutase; Region: GLF; pfam03275 565050003196 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 565050003197 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; cl11420 565050003198 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 565050003199 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 565050003200 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 565050003201 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 565050003202 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 565050003203 Fibronectin type III-like domain; Region: Fn3-like; cl15273 565050003204 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 565050003205 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 565050003206 TPR motif; other site 565050003207 binding surface 565050003208 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003209 Uncharacterized conserved protein [Function unknown]; Region: COG3777 565050003210 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 565050003211 active site 2 [active] 565050003212 active site 1 [active] 565050003213 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 565050003214 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 565050003215 active site 565050003216 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 565050003217 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 565050003218 dimer interface [polypeptide binding]; other site 565050003219 active site 565050003220 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050003221 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 565050003222 N-terminal plug; other site 565050003223 ligand-binding site [chemical binding]; other site 565050003224 Mitochondrial biogenesis AIM24; Region: AIM24; cl00884 565050003225 Chorismate mutase type II; Region: CM_2; cl00693 565050003226 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 565050003227 Helix-turn-helix domains; Region: HTH; cl00088 565050003228 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 565050003229 dimerization interface [polypeptide binding]; other site 565050003230 substrate binding pocket [chemical binding]; other site 565050003231 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 565050003232 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 565050003233 Protein of unknown function (DUF2849); Region: DUF2849; pfam11011 565050003234 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 565050003235 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 565050003236 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 565050003237 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 565050003238 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 565050003239 Active Sites [active] 565050003240 Penicillin amidase; Region: Penicil_amidase; pfam01804 565050003241 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 565050003242 Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_CA; cd01936 565050003243 active site 565050003244 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 565050003245 3D domain; Region: 3D; cl01439 565050003246 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 565050003247 GST_N family, unknown subfamily 4; 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_4; cd03056 565050003248 putative C-terminal domain interface [polypeptide binding]; other site 565050003249 putative GSH binding site (G-site) [chemical binding]; other site 565050003250 putative dimer interface [polypeptide binding]; other site 565050003251 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 565050003252 N-terminal domain interface [polypeptide binding]; other site 565050003253 dimer interface [polypeptide binding]; other site 565050003254 substrate binding pocket (H-site) [chemical binding]; other site 565050003255 Contains a crystal structure of the Nudix hydrolase from Enterococcus faecalis, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes...; Region: Nudix_Hydrolase_25; cd04684 565050003256 nudix motif; other site 565050003257 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050003258 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050003259 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 565050003260 FecR protein; Region: FecR; pfam04773 565050003261 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050003262 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; cl00284 565050003263 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 565050003264 PHP domain; Region: PHP; pfam02811 565050003265 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 565050003266 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 565050003267 putative substrate translocation pore; other site 565050003268 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 565050003269 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 565050003270 Alpha amylase catalytic domain found in Amylosucrase; Region: AmyAc_Amylosucrase; cd11324 565050003271 trehalose synthase; Region: treS_nterm; TIGR02456 565050003272 active site 565050003273 catalytic site [active] 565050003274 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050003275 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; cl00284 565050003276 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; cl00284 565050003277 Transcriptional regulators [Transcription]; Region: PurR; COG1609 565050003278 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 565050003279 DNA binding site [nucleotide binding] 565050003280 domain linker motif; other site 565050003281 Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators; Region: PBP1_CelR; cd06295 565050003282 putative dimerization interface [polypeptide binding]; other site 565050003283 putative ligand binding site [chemical binding]; other site 565050003284 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050003285 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; cl00284 565050003286 Uncharacterized protein conserved in bacteria (DUF2256); Region: DUF2256; cl01792 565050003287 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 565050003288 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 565050003289 NADP binding site [chemical binding]; other site 565050003290 active site 565050003291 putative substrate binding site [chemical binding]; other site 565050003292 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 565050003293 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 565050003294 substrate binding site; other site 565050003295 tetramer interface; other site 565050003296 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 565050003297 N-terminal plug; other site 565050003298 ligand-binding site [chemical binding]; other site 565050003299 Aminopeptidase N [Amino acid transport and metabolism]; Region: PepN; COG0308 565050003300 Peptidase M1 family containing bacterial Aminopeptidase N; Region: M1_APN_5; cd09604 565050003301 Zn binding site [ion binding]; other site 565050003302 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 565050003303 N-terminal plug; other site 565050003304 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050003305 ligand-binding site [chemical binding]; other site 565050003306 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 565050003307 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 565050003308 NAD binding site [chemical binding]; other site 565050003309 putative substrate binding site 2 [chemical binding]; other site 565050003310 putative substrate binding site 1 [chemical binding]; other site 565050003311 active site 565050003312 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 565050003313 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency; Region: ABC_subfamily_A; cd03263 565050003314 Walker A/P-loop; other site 565050003315 ATP binding site [chemical binding]; other site 565050003316 Q-loop/lid; other site 565050003317 ABC transporter signature motif; other site 565050003318 Walker B; other site 565050003319 D-loop; other site 565050003320 H-loop/switch region; other site 565050003321 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 565050003322 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 565050003323 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 565050003324 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 565050003325 active site 565050003326 phosphorylation site [posttranslational modification] 565050003327 intermolecular recognition site; other site 565050003328 dimerization interface [polypeptide binding]; other site 565050003329 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 565050003330 DNA binding residues [nucleotide binding] 565050003331 dimerization interface [polypeptide binding]; other site 565050003332 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 565050003333 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; cl09108 565050003334 phosphate binding site [ion binding]; other site 565050003335 Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline; Region: PC_cytidylyltransferase; cd02523 565050003336 active site 565050003337 metal-binding site 565050003338 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 565050003339 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 565050003340 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 565050003341 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 565050003342 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 565050003343 nucleotide binding site/active site [active] 565050003344 HIT family signature motif; other site 565050003345 catalytic residue [active] 565050003346 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 565050003347 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 565050003348 active site 565050003349 metal binding site [ion binding]; metal-binding site 565050003350 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 565050003351 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 565050003352 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 565050003353 substrate-cofactor binding pocket; other site 565050003354 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050003355 catalytic residue [active] 565050003356 Phosphopantetheine attachment site; Region: PP-binding; cl09936 565050003357 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003358 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 565050003359 NAD(P) binding site [chemical binding]; other site 565050003360 active site 565050003361 acyl-CoA synthetase; Validated; Region: PRK09192 565050003362 AMP-binding enzyme; Region: AMP-binding; cl15778 565050003363 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 565050003364 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 565050003365 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 565050003366 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 565050003367 pyrimidine utilization protein A; Region: RutA; TIGR03612 565050003368 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 565050003369 active site 565050003370 dimer interface [polypeptide binding]; other site 565050003371 non-prolyl cis peptide bond; other site 565050003372 insertion regions; other site 565050003373 Isochorismatase family; Region: Isochorismatase; pfam00857 565050003374 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 565050003375 catalytic triad [active] 565050003376 conserved cis-peptide bond; other site 565050003377 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 565050003378 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 565050003379 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 565050003380 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 565050003381 putative catalytic residue [active] 565050003382 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 565050003383 Sulfatase; Region: Sulfatase; cl10460 565050003384 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl15394 565050003385 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 565050003386 haloalkane dehalogenase; Provisional; Region: PRK00870 565050003387 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; cl12031 565050003388 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 565050003389 General stress protein [General function prediction only]; Region: GsiB; COG3729 565050003390 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050003391 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 565050003392 dimer interface [polypeptide binding]; other site 565050003393 phosphorylation site [posttranslational modification] 565050003394 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 565050003395 ATP binding site [chemical binding]; other site 565050003396 Mg2+ binding site [ion binding]; other site 565050003397 G-X-G motif; other site 565050003398 osmolarity response regulator; Provisional; Region: ompR; PRK09468 565050003399 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 565050003400 active site 565050003401 phosphorylation site [posttranslational modification] 565050003402 intermolecular recognition site; other site 565050003403 dimerization interface [polypeptide binding]; other site 565050003404 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 565050003405 DNA binding site [nucleotide binding] 565050003406 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 565050003407 amino acid transporter; Region: 2A0306; TIGR00909 565050003408 Spore germination protein; Region: Spore_permease; cl15802 565050003409 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 565050003410 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 565050003411 ATP binding site [chemical binding]; other site 565050003412 putative Mg++ binding site [ion binding]; other site 565050003413 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050003414 Helicase associated domain (HA2); Region: HA2; cl04503 565050003415 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 565050003416 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 565050003417 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 565050003418 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 565050003419 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 565050003420 CESA_like_2 is a member of the cellulose synthase superfamily; Region: CESA_like_2; cd06427 565050003421 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 565050003422 DXD motif; other site 565050003423 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050003424 Helix-turn-helix domains; Region: HTH; cl00088 565050003425 WHG domain; Region: WHG; pfam13305 565050003426 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 565050003427 intersubunit interface [polypeptide binding]; other site 565050003428 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 565050003429 putative PBP binding regions; other site 565050003430 ABC-ATPase subunit interface; other site 565050003431 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 565050003432 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050003433 Walker A/P-loop; other site 565050003434 ATP binding site [chemical binding]; other site 565050003435 Q-loop/lid; other site 565050003436 ABC transporter signature motif; other site 565050003437 Walker B; other site 565050003438 D-loop; other site 565050003439 H-loop/switch region; other site 565050003440 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 565050003441 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 catalyze...; Region: LT_GEWL; cd00254 565050003442 N-acetyl-D-glucosamine binding site [chemical binding]; other site 565050003443 catalytic residue [active] 565050003444 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 565050003445 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 565050003446 dimer interface [polypeptide binding]; other site 565050003447 active site 565050003448 catalytic residue [active] 565050003449 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 565050003450 SmpB-tmRNA interface; other site 565050003451 Protein of unknown function (DUF2891); Region: DUF2891; pfam11199 565050003452 Protein of unknown function (DUF979); Region: DUF979; cl01572 565050003453 Protein of unknown function (DUF969); Region: DUF969; cl01573 565050003454 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 565050003455 intersubunit interface [polypeptide binding]; other site 565050003456 active site 565050003457 Zn2+ binding site [ion binding]; other site 565050003458 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 565050003459 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050003460 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050003461 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 565050003462 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 565050003463 TPP-binding site [chemical binding]; other site 565050003464 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 565050003465 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 565050003466 dimer interface [polypeptide binding]; other site 565050003467 PYR/PP interface [polypeptide binding]; other site 565050003468 TPP binding site [chemical binding]; other site 565050003469 Transposase domain (DUF772); Region: DUF772; cl15789 565050003470 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 565050003471 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 565050003472 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 565050003473 Cytochrome c; Region: Cytochrom_C; cl11414 565050003474 GcrA cell cycle regulator; Region: GcrA; cl11564 565050003475 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 565050003476 Helix-turn-helix domains; Region: HTH; cl00088 565050003477 RF-1 domain; Region: RF-1; cl02875 565050003478 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 565050003479 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 565050003480 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 565050003481 tetrameric interface [polypeptide binding]; other site 565050003482 NAD binding site [chemical binding]; other site 565050003483 catalytic residues [active] 565050003484 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14188 565050003485 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 565050003486 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 565050003487 homodimer interface [polypeptide binding]; other site 565050003488 NADP binding site [chemical binding]; other site 565050003489 substrate binding site [chemical binding]; other site 565050003490 Cytochrome c; Region: Cytochrom_C; cl11414 565050003491 FAD-linked oxidoreductase; Region: bact_FAD_ox; TIGR01679 565050003492 FAD binding domain; Region: FAD_binding_4; pfam01565 565050003493 D-arabinono-1,4-lactone oxidase; Region: ALO; cl04370 565050003494 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 565050003495 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; cl15419 565050003496 glycerol kinase; Region: glycerol_kin; TIGR01311 565050003497 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 565050003498 N- and C-terminal domain interface [polypeptide binding]; other site 565050003499 active site 565050003500 MgATP binding site [chemical binding]; other site 565050003501 catalytic site [active] 565050003502 metal binding site [ion binding]; metal-binding site 565050003503 glycerol binding site [chemical binding]; other site 565050003504 homotetramer interface [polypeptide binding]; other site 565050003505 homodimer interface [polypeptide binding]; other site 565050003506 FBP binding site [chemical binding]; other site 565050003507 protein IIAGlc interface [polypeptide binding]; other site 565050003508 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 565050003509 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 565050003510 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003511 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 565050003512 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 565050003513 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; cl12031 565050003514 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 565050003515 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; cl12031 565050003516 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; cl12031 565050003517 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050003518 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 565050003519 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 565050003520 putative substrate translocation pore; other site 565050003521 Protein of unknown function (DUF423); Region: DUF423; cl01008 565050003522 Phosphotransferase enzyme family; Region: APH; pfam01636 565050003523 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 565050003524 putative active site [active] 565050003525 putative substrate binding site [chemical binding]; other site 565050003526 ATP binding site [chemical binding]; other site 565050003527 Transposase domain (DUF772); Region: DUF772; cl15789 565050003528 Integral membrane protein TerC family; Region: TerC; cl10468 565050003529 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 565050003530 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 565050003531 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 565050003532 elongation factor Tu; Reviewed; Region: PRK00049 565050003533 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 565050003534 G1 box; other site 565050003535 GEF interaction site [polypeptide binding]; other site 565050003536 GTP/Mg2+ binding site [chemical binding]; other site 565050003537 Switch I region; other site 565050003538 G2 box; other site 565050003539 G3 box; other site 565050003540 Switch II region; other site 565050003541 G4 box; other site 565050003542 G5 box; other site 565050003543 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 565050003544 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 565050003545 Antibiotic Binding Site [chemical binding]; other site 565050003546 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4430 565050003547 Protein of unknown function (DUF419); Region: DUF419; cl15265 565050003548 Bacteriocin-protection, YdeI or OmpD-Associated; Region: OmdA; pfam13376 565050003549 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 565050003550 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 565050003551 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 565050003552 putative molybdopterin cofactor binding site [chemical binding]; other site 565050003553 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region...; Region: MopB_CT_ydeP; cd02787 565050003554 putative molybdopterin cofactor binding site; other site 565050003555 Protein involved in cellulose biosynthesis (CelD) [Cell envelope biogenesis, outer membrane]; Region: COG5653 565050003556 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050003557 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 565050003558 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 565050003559 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 565050003560 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 565050003561 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 565050003562 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 565050003563 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 565050003564 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 565050003565 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 565050003566 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 565050003567 putative translocon binding site; other site 565050003568 protein-rRNA interface [nucleotide binding]; other site 565050003569 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 565050003570 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 565050003571 G-X-X-G motif; other site 565050003572 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 565050003573 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 565050003574 23S rRNA interface [nucleotide binding]; other site 565050003575 5S rRNA interface [nucleotide binding]; other site 565050003576 putative antibiotic binding site [chemical binding]; other site 565050003577 L25 interface [polypeptide binding]; other site 565050003578 L27 interface [polypeptide binding]; other site 565050003579 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 565050003580 23S rRNA interface [nucleotide binding]; other site 565050003581 putative translocon interaction site; other site 565050003582 signal recognition particle (SRP54) interaction site; other site 565050003583 L23 interface [polypeptide binding]; other site 565050003584 trigger factor interaction site; other site 565050003585 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 565050003586 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 565050003587 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 565050003588 KOW motif; Region: KOW; cl00354 565050003589 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 565050003590 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 565050003591 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 565050003592 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 565050003593 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 565050003594 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 565050003595 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 565050003596 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 565050003597 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 565050003598 23S rRNA interface [nucleotide binding]; other site 565050003599 L21e interface [polypeptide binding]; other site 565050003600 5S rRNA interface [nucleotide binding]; other site 565050003601 L27 interface [polypeptide binding]; other site 565050003602 L5 interface [polypeptide binding]; other site 565050003603 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 565050003604 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 565050003605 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 565050003606 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 565050003607 23S rRNA binding site [nucleotide binding]; other site 565050003608 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 565050003609 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 565050003610 SecY translocase; Region: SecY; pfam00344 565050003611 adenylate kinase; Provisional; Region: PRK14532 565050003612 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 565050003613 AMP-binding site [chemical binding]; other site 565050003614 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 565050003615 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 565050003616 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 565050003617 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 565050003618 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 565050003619 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 565050003620 alphaNTD - beta interaction site [polypeptide binding]; other site 565050003621 alphaNTD homodimer interface [polypeptide binding]; other site 565050003622 alphaNTD - beta' interaction site [polypeptide binding]; other site 565050003623 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 565050003624 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 565050003625 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 565050003626 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 565050003627 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050003628 Walker A/P-loop; other site 565050003629 ATP binding site [chemical binding]; other site 565050003630 Q-loop/lid; other site 565050003631 ABC transporter signature motif; other site 565050003632 Walker B; other site 565050003633 D-loop; other site 565050003634 H-loop/switch region; other site 565050003635 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 565050003636 Sulfatase; Region: Sulfatase; cl10460 565050003637 choline dehydrogenase; Validated; Region: PRK02106 565050003638 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003639 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 565050003640 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 565050003641 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050003642 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 565050003643 dimerization interface [polypeptide binding]; other site 565050003644 putative DNA binding site [nucleotide binding]; other site 565050003645 putative Zn2+ binding site [ion binding]; other site 565050003646 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 565050003647 putative substrate translocation pore; other site 565050003648 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 565050003649 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 565050003650 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 565050003651 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 565050003652 protein binding site [polypeptide binding]; other site 565050003653 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 565050003654 protein binding site [polypeptide binding]; other site 565050003655 recombination factor protein RarA; Reviewed; Region: PRK13342 565050003656 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 565050003657 Walker A motif; other site 565050003658 ATP binding site [chemical binding]; other site 565050003659 Walker B motif; other site 565050003660 arginine finger; other site 565050003661 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 565050003662 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 565050003663 active site 565050003664 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 565050003665 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003666 NAD(P) binding site [chemical binding]; other site 565050003667 active site 565050003668 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 565050003669 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 565050003670 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4337 565050003671 Transposase domain (DUF772); Region: DUF772; cl15789 565050003672 Transposase domain (DUF772); Region: DUF772; cl15789 565050003673 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 565050003674 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 565050003675 active site 565050003676 phosphorylation site [posttranslational modification] 565050003677 intermolecular recognition site; other site 565050003678 dimerization interface [polypeptide binding]; other site 565050003679 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 565050003680 DNA binding site [nucleotide binding] 565050003681 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 565050003682 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050003683 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 565050003684 dimer interface [polypeptide binding]; other site 565050003685 phosphorylation site [posttranslational modification] 565050003686 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 565050003687 ATP binding site [chemical binding]; other site 565050003688 Mg2+ binding site [ion binding]; other site 565050003689 G-X-G motif; other site 565050003690 Phytase; Region: Phytase; pfam02333 565050003691 3-phytase (myo-inositol-hexaphosphate 3-phosphohydrolase) [Lipid metabolism]; Region: Phy; COG4247 565050003692 Phytase; Region: Phytase; pfam02333 565050003693 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 565050003694 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003695 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 565050003696 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 565050003697 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 565050003698 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 565050003699 putative active site [active] 565050003700 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 565050003701 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 565050003702 substrate binding site [chemical binding]; other site 565050003703 ATP binding site [chemical binding]; other site 565050003704 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; cl09108 565050003705 Acetolactate synthase [Amino acid transport and metabolism]; Region: COG3962 565050003706 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 565050003707 PYR/PP interface [polypeptide binding]; other site 565050003708 dimer interface [polypeptide binding]; other site 565050003709 TPP binding site [chemical binding]; other site 565050003710 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 565050003711 Thiamine pyrophosphate (TPP) family, IolD subfamily, TPP-binding module; composed of proteins similar to Rhizobium leguminosarum bv. viciae IolD. IolD plays an important role in myo-inositol catabolism; Region: TPP_IolD; cd02003 565050003712 TPP-binding site; other site 565050003713 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 565050003714 KduI/IolB family; Region: KduI; cl01508 565050003715 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 565050003716 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 565050003717 tetrameric interface [polypeptide binding]; other site 565050003718 NAD binding site [chemical binding]; other site 565050003719 catalytic residues [active] 565050003720 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 565050003721 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 565050003722 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 565050003723 active site 565050003724 phosphorylation site [posttranslational modification] 565050003725 intermolecular recognition site; other site 565050003726 dimerization interface [polypeptide binding]; other site 565050003727 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 565050003728 DNA binding site [nucleotide binding] 565050003729 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 565050003730 ATP binding site [chemical binding]; other site 565050003731 Mg2+ binding site [ion binding]; other site 565050003732 G-X-G motif; other site 565050003733 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 565050003734 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 565050003735 FMN binding site [chemical binding]; other site 565050003736 active site 565050003737 catalytic residues [active] 565050003738 substrate binding site [chemical binding]; other site 565050003739 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 565050003740 catalytic motif [active] 565050003741 Catalytic residue [active] 565050003742 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 565050003743 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 565050003744 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cl11435 565050003745 putative dimer interface [polypeptide binding]; other site 565050003746 active site pocket [active] 565050003747 putative cataytic base [active] 565050003748 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 565050003749 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 565050003750 active site 565050003751 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 565050003752 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 565050003753 active site 565050003754 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 565050003755 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 565050003756 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 565050003757 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050003758 Walker A/P-loop; other site 565050003759 ATP binding site [chemical binding]; other site 565050003760 Q-loop/lid; other site 565050003761 ABC transporter signature motif; other site 565050003762 Walker B; other site 565050003763 D-loop; other site 565050003764 H-loop/switch region; other site 565050003765 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050003766 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 565050003767 dimer interface [polypeptide binding]; other site 565050003768 active site 565050003769 metal binding site [ion binding]; metal-binding site 565050003770 glutathione binding site [chemical binding]; other site 565050003771 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 565050003772 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 565050003773 C-terminal domain interface [polypeptide binding]; other site 565050003774 GSH binding site (G-site) [chemical binding]; other site 565050003775 dimer interface [polypeptide binding]; other site 565050003776 C-terminal, alpha helical domain of Ure2p and related Glutathione S-transferase-like proteins; Region: GST_C_Ure2p_like; cd03178 565050003777 dimer interface [polypeptide binding]; other site 565050003778 N-terminal domain interface [polypeptide binding]; other site 565050003779 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 565050003780 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003781 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 565050003782 Protein of unknown function (DUF2497); Region: DUF2497; cl11534 565050003783 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 565050003784 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 565050003785 HIGH motif; other site 565050003786 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 565050003787 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 565050003788 active site 565050003789 KMSKS motif; other site 565050003790 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 565050003791 tRNA binding surface [nucleotide binding]; other site 565050003792 anticodon binding site; other site 565050003793 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 565050003794 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 565050003795 AMP-binding enzyme; Region: AMP-binding; cl15778 565050003796 AMP-binding enzyme; Region: AMP-binding; cl15778 565050003797 Protein of unknown function (DUF419); Region: DUF419; cl15265 565050003798 amidase; Provisional; Region: PRK07869 565050003799 Amidase; Region: Amidase; cl11426 565050003800 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 565050003801 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; cl15754 565050003802 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 565050003803 TRAM domain; Region: TRAM; cl01282 565050003804 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; cl15754 565050003805 Methyltransferase domain; Region: Methyltransf_31; pfam13847 565050003806 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 565050003807 S-adenosylmethionine binding site [chemical binding]; other site 565050003808 OpgC protein; Region: OpgC_C; cl00792 565050003809 YCII-related domain; Region: YCII; cl00999 565050003810 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]; Region: COG4941 565050003811 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050003812 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050003813 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 565050003814 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 565050003815 FeS/SAM binding site; other site 565050003816 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 catalyze...; Region: LT_GEWL; cd00254 565050003817 N-acetyl-D-glucosamine binding site [chemical binding]; other site 565050003818 catalytic residue [active] 565050003819 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 565050003820 Fe-S cluster binding site [ion binding]; other site 565050003821 active site 565050003822 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003823 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 565050003824 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 565050003825 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 565050003826 TPR motif; other site 565050003827 TPR repeat; Region: TPR_11; pfam13414 565050003828 binding surface 565050003829 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 565050003830 binding surface 565050003831 TPR motif; other site 565050003832 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14608 565050003833 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 565050003834 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 565050003835 active site 565050003836 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 565050003837 Nitrogen regulatory protein P-II; Region: P-II; cl00412 565050003838 Nitrogen regulatory protein P-II; Region: P-II; smart00938 565050003839 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 attaches...; Region: class_II_aaRS-like_core; cl00268 565050003840 motif 1; other site 565050003841 dimer interface [polypeptide binding]; other site 565050003842 active site 565050003843 motif 2; other site 565050003844 motif 3; other site 565050003845 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 565050003846 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 565050003847 GIY-YIG motif/motif A; other site 565050003848 putative active site [active] 565050003849 putative metal binding site [ion binding]; other site 565050003850 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 565050003851 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 565050003852 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_31; cd04690 565050003853 nudix motif; other site 565050003854 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 565050003855 dimer interface [polypeptide binding]; other site 565050003856 allosteric magnesium binding site [ion binding]; other site 565050003857 active site 565050003858 aspartate-rich active site metal binding site; other site 565050003859 Schiff base residues; other site 565050003860 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 565050003861 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 565050003862 Isobutyryl-CoA dehydrogenase; Region: IBD; cd01162 565050003863 substrate binding pocket [chemical binding]; other site 565050003864 FAD binding site [chemical binding]; other site 565050003865 catalytic base [active] 565050003866 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 565050003867 catalytic core [active] 565050003868 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 565050003869 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 565050003870 substrate binding site [chemical binding]; other site 565050003871 oxyanion hole (OAH) forming residues; other site 565050003872 trimer interface [polypeptide binding]; other site 565050003873 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 565050003874 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003875 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003876 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 565050003877 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 565050003878 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 565050003879 substrate-cofactor binding pocket; other site 565050003880 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050003881 catalytic residue [active] 565050003882 Predicted transcriptional regulator [Transcription]; Region: COG4957 565050003883 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 565050003884 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 565050003885 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 565050003886 dimer interface [polypeptide binding]; other site 565050003887 glycine-pyridoxal phosphate binding site [chemical binding]; other site 565050003888 active site 565050003889 folate binding site [chemical binding]; other site 565050003890 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 565050003891 ATP cone domain; Region: ATP-cone; pfam03477 565050003892 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 565050003893 homopentamer interface [polypeptide binding]; other site 565050003894 active site 565050003895 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 565050003896 putative RNA binding site [nucleotide binding]; other site 565050003897 thiamine-monophosphate kinase; Region: thiL; TIGR01379 565050003898 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 565050003899 ATP binding site [chemical binding]; other site 565050003900 dimerization interface [polypeptide binding]; other site 565050003901 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 565050003902 Inorganic pyrophosphatase [Energy production and conversion]; Region: OVP1; cl11452 565050003903 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 565050003904 Response regulator receiver domain; Region: Response_reg; pfam00072 565050003905 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 565050003906 active site 565050003907 phosphorylation site [posttranslational modification] 565050003908 intermolecular recognition site; other site 565050003909 dimerization interface [polypeptide binding]; other site 565050003910 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 565050003911 Ubiquinol-cytochrome C chaperone; Region: Ubiq_cyt_C_chap; cl12045 565050003912 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 565050003913 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 565050003914 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 565050003915 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 565050003916 dimer interface [polypeptide binding]; other site 565050003917 active site 565050003918 CoA binding pocket [chemical binding]; other site 565050003919 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 565050003920 IHF dimer interface [polypeptide binding]; other site 565050003921 IHF - DNA interface [nucleotide binding]; other site 565050003922 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 565050003923 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 565050003924 DNA binding residues [nucleotide binding] 565050003925 Protein of unknown function (DUF2842); Region: DUF2842; pfam11003 565050003926 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 565050003927 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 565050003928 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 565050003929 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 565050003930 23S rRNA interface [nucleotide binding]; other site 565050003931 L3 interface [polypeptide binding]; other site 565050003932 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 565050003933 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 565050003934 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003935 Domain of unknown function (DUF1287); Region: DUF1287; cl01519 565050003936 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 565050003937 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 565050003938 aminotransferase; Validated; Region: PRK09148 565050003939 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 565050003940 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050003941 homodimer interface [polypeptide binding]; other site 565050003942 catalytic residue [active] 565050003943 homoserine dehydrogenase; Provisional; Region: PRK06349 565050003944 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050003945 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 565050003946 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 565050003947 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 565050003948 putative active site [active] 565050003949 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 565050003950 metal binding site [ion binding]; metal-binding site 565050003951 active site 565050003952 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 565050003953 DHH family; Region: DHH; pfam01368 565050003954 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 protein; Region: CSP_CDS; cd04458 565050003955 DNA-binding site [nucleotide binding]; DNA binding site 565050003956 RNA-binding motif; other site 565050003957 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 protein; Region: CSP_CDS; cd04458 565050003958 DNA-binding site [nucleotide binding]; DNA binding site 565050003959 RNA-binding motif; other site 565050003960 Uncharacterized ACR, COG1430; Region: DUF192; cl00627 565050003961 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 565050003962 L-Lactate 2-monooxygenase (LMO) FMN-binding domain. LMO is a FMN-containing enzyme that catalyzes the conversion of L-lactate and oxygen to acetate, carbon dioxide, and water. LMO is a member of the family of alpha-hydroxy acid oxidases. It is thought...; Region: LMO_FMN; cd03332 565050003963 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 565050003964 putative active site [active] 565050003965 putative substrate binding site [chemical binding]; other site 565050003966 putative FMN binding site [chemical binding]; other site 565050003967 putative catalytic residues [active] 565050003968 NeuB family; Region: NeuB; cl00496 565050003969 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 565050003970 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050003971 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050003972 dimer interface [polypeptide binding]; other site 565050003973 putative CheW interface [polypeptide binding]; other site 565050003974 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 565050003975 Low-spin heme binding site [chemical binding]; other site 565050003976 Putative water exit pathway; other site 565050003977 Binuclear center (active site) [active] 565050003978 Putative proton exit pathway; other site 565050003979 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 565050003980 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 565050003981 Cytochrome cbb oxidase CcoQ. 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 of O2...; Region: cbb3_Oxidase_CcoQ; cd01324 565050003982 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 565050003983 Cytochrome c; Region: Cytochrom_C; cl11414 565050003984 Cytochrome c; Region: Cytochrom_C; cl11414 565050003985 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 565050003986 4Fe-4S binding domain; Region: Fer4_5; pfam12801 565050003987 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 565050003988 FixH; Region: FixH; cl01254 565050003989 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 565050003990 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 565050003991 metal-binding site [ion binding] 565050003992 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 565050003993 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050003994 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 565050003995 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 565050003996 transcriptional activator FtrB; Provisional; Region: ftrB; PRK09392 565050003997 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 565050003998 ligand binding site [chemical binding]; other site 565050003999 flexible hinge region; other site 565050004000 Helix-turn-helix domains; Region: HTH; cl00088 565050004001 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 565050004002 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 565050004003 FeS/SAM binding site; other site 565050004004 HemN C-terminal domain; Region: HemN_C; pfam06969 565050004005 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 565050004006 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 565050004007 ligand binding site [chemical binding]; other site 565050004008 flexible hinge region; other site 565050004009 Helix-turn-helix domains; Region: HTH; cl00088 565050004010 TIR domain; Region: TIR_2; cl15770 565050004011 cyclase homology domain; Region: CHD; cd07302 565050004012 nucleotidyl binding site; other site 565050004013 metal binding site [ion binding]; metal-binding site 565050004014 dimer interface [polypeptide binding]; other site 565050004015 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 565050004016 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 565050004017 active site 565050004018 catalytic residues [active] 565050004019 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 565050004020 Transcriptional regulators [Transcription]; Region: FadR; COG2186 565050004021 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050004022 DNA-binding site [nucleotide binding]; DNA binding site 565050004023 FCD domain; Region: FCD; cl11656 565050004024 Dehydratase family; Region: ILVD_EDD; cl00340 565050004025 Alpha-L-arabinofuranosidase [Carbohydrate transport and metabolism]; Region: AbfA; COG3534 565050004026 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; cl01412 565050004027 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 565050004028 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004029 cystathionine beta-lyase, bacterial; Region: cysta_beta_ly_B; TIGR01324 565050004030 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 565050004031 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 565050004032 catalytic residue [active] 565050004033 3-mercaptopyruvate sulfurtransferase; Region: PLN02723 565050004034 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 565050004035 active site residue [active] 565050004036 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 565050004037 active site residue [active] 565050004038 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 565050004039 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 565050004040 dimer interface [polypeptide binding]; other site 565050004041 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050004042 catalytic residue [active] 565050004043 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 565050004044 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 565050004045 S-adenosylmethionine binding site [chemical binding]; other site 565050004046 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 565050004047 DNA photolyase; Region: DNA_photolyase; pfam00875 565050004048 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 565050004049 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 565050004050 NeuB family; Region: NeuB; cl00496 565050004051 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 565050004052 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004053 NAD(P) binding site [chemical binding]; other site 565050004054 active site 565050004055 3-hydroxy-3-methylglutaryl CoA synthase [Lipid metabolism]; Region: PksG; COG3425 565050004056 'initiating' condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are characterized by the...; Region: init_cond_enzymes; cd00827 565050004057 dimer interface [polypeptide binding]; other site 565050004058 active site 565050004059 DUF35 OB-fold domain; Region: DUF35; pfam01796 565050004060 acetyl-CoA acetyltransferase; Validated; Region: PRK06157 565050004061 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 565050004062 active site 565050004063 Protein of unknown function (DUF3089); Region: DUF3089; pfam11288 565050004064 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 565050004065 Predicted aminoglycoside phosphotransferase [General function prediction only]; Region: COG3173 565050004066 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 565050004067 putative active site [active] 565050004068 putative substrate binding site [chemical binding]; other site 565050004069 ATP binding site [chemical binding]; other site 565050004070 Protein of unknown function (DUF808); Region: DUF808; cl01002 565050004071 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 565050004072 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 565050004073 generic binding surface II; other site 565050004074 ssDNA binding site; other site 565050004075 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 565050004076 ATP binding site [chemical binding]; other site 565050004077 putative Mg++ binding site [ion binding]; other site 565050004078 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 565050004079 nucleotide binding region [chemical binding]; other site 565050004080 ATP-binding site [chemical binding]; other site 565050004081 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 565050004082 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 565050004083 Walker A/P-loop; other site 565050004084 ATP binding site [chemical binding]; other site 565050004085 Q-loop/lid; other site 565050004086 ABC transporter signature motif; other site 565050004087 Walker B; other site 565050004088 D-loop; other site 565050004089 H-loop/switch region; other site 565050004090 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 565050004091 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 565050004092 dimer interface [polypeptide binding]; other site 565050004093 conserved gate region; other site 565050004094 putative PBP binding loops; other site 565050004095 ABC-ATPase subunit interface; other site 565050004096 cystine transporter subunit; Provisional; Region: PRK11260 565050004097 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 565050004098 substrate binding pocket [chemical binding]; other site 565050004099 membrane-bound complex binding site; other site 565050004100 hinge residues; other site 565050004101 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 565050004102 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 565050004103 dimer interface [polypeptide binding]; other site 565050004104 active site 565050004105 CoA binding pocket [chemical binding]; other site 565050004106 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 565050004107 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 565050004108 Transposase IS200 like; Region: Y1_Tnp; cl00848 565050004109 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 565050004110 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 565050004111 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 565050004112 DctM-like transporters; Region: DctM; pfam06808 565050004113 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 565050004114 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 565050004115 dimer interface [polypeptide binding]; other site 565050004116 FMN binding site [chemical binding]; other site 565050004117 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 565050004118 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 565050004119 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 565050004120 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 565050004121 Walker A motif; other site 565050004122 ATP binding site [chemical binding]; other site 565050004123 Walker B motif; other site 565050004124 arginine finger; other site 565050004125 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 565050004126 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050004127 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 565050004128 binding surface 565050004129 Tetratricopeptide repeat; Region: TPR_16; pfam13432 565050004130 TPR motif; other site 565050004131 Tetratricopeptide repeat; Region: TPR_16; pfam13432 565050004132 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 565050004133 binding surface 565050004134 TPR motif; other site 565050004135 TPR repeat; Region: TPR_11; pfam13414 565050004136 Flagellar protein FlbT; Region: FlbT; cl11455 565050004137 Flagellar protein FlaF; Region: FlaF; cl11454 565050004138 flagellin; Provisional; Region: PRK12802 565050004139 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 565050004140 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 565050004141 flagellin; Reviewed; Region: PRK12687 565050004142 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 565050004143 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 565050004144 FlaG protein; Region: FlaG; cl00591 565050004145 flagellin; Reviewed; Region: PRK12687 565050004146 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 565050004147 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 565050004148 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 565050004149 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050004150 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 565050004151 dimer interface [polypeptide binding]; other site 565050004152 ssDNA binding site [nucleotide binding]; other site 565050004153 tetramer (dimer of dimers) interface [polypeptide binding]; other site 565050004154 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 565050004155 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 565050004156 Coenzyme A binding pocket [chemical binding]; other site 565050004157 pyruvate phosphate dikinase; Provisional; Region: PRK09279 565050004158 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 565050004159 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 565050004160 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; cl09155 565050004161 Pirin-related protein [General function prediction only]; Region: COG1741 565050004162 Cupin domain; Region: Cupin_2; cl09118 565050004163 LysR family transcriptional regulator; Provisional; Region: PRK14997 565050004164 Helix-turn-helix domains; Region: HTH; cl00088 565050004165 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 565050004166 putative effector binding pocket; other site 565050004167 dimerization interface [polypeptide binding]; other site 565050004168 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 565050004169 HI0933-like protein; Region: HI0933_like; pfam03486 565050004170 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004171 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 565050004172 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050004173 ATP binding site [chemical binding]; other site 565050004174 putative Mg++ binding site [ion binding]; other site 565050004175 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 565050004176 nucleotide binding region [chemical binding]; other site 565050004177 ATP-binding site [chemical binding]; other site 565050004178 DbpA RNA binding domain; Region: DbpA; pfam03880 565050004179 methionyl-tRNA synthetase; Reviewed; Region: PRK12268 565050004180 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 565050004181 active site 565050004182 HIGH motif; other site 565050004183 KMSKS motif; other site 565050004184 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 565050004185 tRNA binding surface [nucleotide binding]; other site 565050004186 anticodon binding site; other site 565050004187 MFS_1 like family; Region: MFS_1_like; pfam12832 565050004188 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 565050004189 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 565050004190 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 565050004191 CysD dimerization site [polypeptide binding]; other site 565050004192 G1 box; other site 565050004193 putative GEF interaction site [polypeptide binding]; other site 565050004194 GTP/Mg2+ binding site [chemical binding]; other site 565050004195 Switch I region; other site 565050004196 G2 box; other site 565050004197 G3 box; other site 565050004198 Switch II region; other site 565050004199 G4 box; other site 565050004200 G5 box; other site 565050004201 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 565050004202 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 565050004203 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 important for the assimilation of...; Region: APSK; cd02027 565050004204 ligand-binding site [chemical binding]; other site 565050004205 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 565050004206 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 565050004207 Active Sites [active] 565050004208 Bacterial sugar transferase; Region: Bac_transf; cl00939 565050004209 Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism]; Region: MtlD; COG0246 565050004210 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 565050004211 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 565050004212 SAF domain; Region: SAF; cl00555 565050004213 Altronate dehydratase [Carbohydrate transport and metabolism]; Region: UxaA; COG2721 565050004214 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 565050004215 Transcriptional regulators [Transcription]; Region: PurR; COG1609 565050004216 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 565050004217 DNA binding site [nucleotide binding] 565050004218 domain linker motif; other site 565050004219 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 565050004220 putative dimerization interface [polypeptide binding]; other site 565050004221 putative ligand binding site [chemical binding]; other site 565050004222 Glucuronate isomerase; Region: UxaC; cl00829 565050004223 KduI/IolB family; Region: KduI; cl01508 565050004224 2-deoxy-D-gluconate 3-dehydrogenase; Region: kduD; TIGR01832 565050004225 gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs; Region: Ga5DH-like_SDR_c; cd05347 565050004226 NADP binding site [chemical binding]; other site 565050004227 homodimer interface [polypeptide binding]; other site 565050004228 active site 565050004229 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl14656 565050004230 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 565050004231 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]; Region: Eda; COG0800 565050004232 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 565050004233 active site 565050004234 intersubunit interface [polypeptide binding]; other site 565050004235 catalytic residue [active] 565050004236 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 565050004237 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 565050004238 substrate binding site [chemical binding]; other site 565050004239 ATP binding site [chemical binding]; other site 565050004240 Protein of unknown function (DUF1244); Region: DUF1244; cl01385 565050004241 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 565050004242 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; cl12031 565050004243 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 565050004244 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 565050004245 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 565050004246 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 565050004247 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050004248 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 565050004249 ArsC family; Region: ArsC; pfam03960 565050004250 catalytic residues [active] 565050004251 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cl00200 565050004252 amphipathic channel; other site 565050004253 Asn-Pro-Ala signature motifs; other site 565050004254 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 565050004255 dimerization interface [polypeptide binding]; other site 565050004256 putative DNA binding site [nucleotide binding]; other site 565050004257 putative Zn2+ binding site [ion binding]; other site 565050004258 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 565050004259 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 565050004260 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 565050004261 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 565050004262 D-galactonate transporter; Region: 2A0114; TIGR00893 565050004263 putative substrate translocation pore; other site 565050004264 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 565050004265 Helix-turn-helix domains; Region: HTH; cl00088 565050004266 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 565050004267 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 565050004268 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 565050004269 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 565050004270 Peptidase M15; Region: Peptidase_M15_3; cl01194 565050004271 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 565050004272 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 565050004273 Transglycosylase; Region: Transgly; cl07896 565050004274 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 565050004275 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050004276 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050004277 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 565050004278 N-terminal plug; other site 565050004279 ligand-binding site [chemical binding]; other site 565050004280 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 565050004281 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 565050004282 Walker A/P-loop; other site 565050004283 ATP binding site [chemical binding]; other site 565050004284 Q-loop/lid; other site 565050004285 ABC transporter signature motif; other site 565050004286 Walker B; other site 565050004287 D-loop; other site 565050004288 H-loop/switch region; other site 565050004289 Domain of unknown function (DUF3526); Region: DUF3526; pfam12040 565050004290 Domain of unknown function (DUF3526); Region: DUF3526; pfam12040 565050004291 OpgC protein; Region: OpgC_C; cl00792 565050004292 Ligase N family; Region: LIGANc; smart00532 565050004293 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 565050004294 nucleotide binding pocket [chemical binding]; other site 565050004295 K-X-D-G motif; other site 565050004296 catalytic site [active] 565050004297 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 565050004298 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 565050004299 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 565050004300 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 565050004301 Dimer interface [polypeptide binding]; other site 565050004302 BRCT sequence motif; other site 565050004303 an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; Region: DNA_pol_III_epsilon_like; cd06130 565050004304 active site 565050004305 substrate binding site [chemical binding]; other site 565050004306 catalytic site [active] 565050004307 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; cl01951 565050004308 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 565050004309 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 565050004310 active site 565050004311 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 565050004312 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004313 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 565050004314 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050004315 Family description; Region: UvrD_C_2; cl15862 565050004316 Ribbon-helix-helix domain; Region: RHH_4; cl01775 565050004317 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004318 Domain of unknown function (DUF4169); Region: DUF4169; pfam13770 565050004319 Methane oxygenase PmoA; Region: PmoA; pfam14100 565050004320 Uncharacterized protein conserved in bacteria (DUF2171); Region: DUF2171; cl01558 565050004321 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 565050004322 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 565050004323 C-terminal domain interface [polypeptide binding]; other site 565050004324 GSH binding site (G-site) [chemical binding]; other site 565050004325 dimer interface [polypeptide binding]; other site 565050004326 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 565050004327 dimer interface [polypeptide binding]; other site 565050004328 N-terminal domain interface [polypeptide binding]; other site 565050004329 substrate binding pocket (H-site) [chemical binding]; other site 565050004330 aspartate aminotransferase; Provisional; Region: PRK05764 565050004331 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 565050004332 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050004333 homodimer interface [polypeptide binding]; other site 565050004334 catalytic residue [active] 565050004335 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 565050004336 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 565050004337 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 565050004338 P-loop; other site 565050004339 Magnesium ion binding site [ion binding]; other site 565050004340 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 565050004341 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050004342 Helix-turn-helix domains; Region: HTH; cl00088 565050004343 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2015 565050004344 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 565050004345 SCP-2 sterol transfer family; Region: SCP2; cl01225 565050004346 2-isopropylmalate synthase; Validated; Region: PRK00915 565050004347 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 565050004348 active site 565050004349 catalytic residues [active] 565050004350 metal binding site [ion binding]; metal-binding site 565050004351 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 565050004352 rod shape-determining protein MreB; Provisional; Region: PRK13927 565050004353 Cell division protein FtsA; Region: FtsA; cl11496 565050004354 rod shape-determining protein MreC; Region: MreC; pfam04085 565050004355 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 565050004356 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 565050004357 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050004358 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 565050004359 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 565050004360 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050004361 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 565050004362 Fe-S cluster binding site [ion binding]; other site 565050004363 DNA binding site [nucleotide binding] 565050004364 active site 565050004365 Uncharacterized conserved protein [Function unknown]; Region: COG1432 565050004366 LabA_like proteins; Region: LabA; cd10911 565050004367 putative metal binding site [ion binding]; other site 565050004368 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 565050004369 catalytic center binding site [active] 565050004370 ATP binding site [chemical binding]; other site 565050004371 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 565050004372 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 565050004373 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 565050004374 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 565050004375 synthetase active site [active] 565050004376 NTP binding site [chemical binding]; other site 565050004377 metal binding site [ion binding]; metal-binding site 565050004378 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 565050004379 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 565050004380 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_20; cd04679 565050004381 nudix motif; other site 565050004382 orotate phosphoribosyltransferase; Validated; Region: pyrE; PRK00455 565050004383 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 565050004384 active site 565050004385 M20 Peptidase Aminoacylase 1-like protein 2 aminobenzoyl-glutamate utilization protein B subfamily; Region: M20_Acy1L2_AbgB; cd05673 565050004386 putative metal binding site [ion binding]; other site 565050004387 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the...; Region: PNPsynthase; cd00003 565050004388 active site 565050004389 hydrophilic channel; other site 565050004390 dimerization interface [polypeptide binding]; other site 565050004391 catalytic residues [active] 565050004392 active site lid [active] 565050004393 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 565050004394 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 565050004395 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 565050004396 Catalytic site [active] 565050004397 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 565050004398 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 565050004399 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 565050004400 dimerization interface [polypeptide binding]; other site 565050004401 active site 565050004402 metal binding site [ion binding]; metal-binding site 565050004403 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 565050004404 dsRNA binding site [nucleotide binding]; other site 565050004405 GTPase Era; Reviewed; Region: era; PRK00089 565050004406 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 565050004407 G1 box; other site 565050004408 GTP/Mg2+ binding site [chemical binding]; other site 565050004409 Switch I region; other site 565050004410 G2 box; other site 565050004411 Switch II region; other site 565050004412 G3 box; other site 565050004413 G4 box; other site 565050004414 G5 box; other site 565050004415 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 565050004416 N-acetyltransferase; Region: Acetyltransf_2; cl00949 565050004417 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 565050004418 Recombination protein O N terminal; Region: RecO_N; cl15812 565050004419 Recombination protein O C terminal; Region: RecO_C; pfam02565 565050004420 Phosphodiesterase/alkaline phosphatase D [Inorganic ion transport and metabolism]; Region: PhoD; COG3540 565050004421 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 565050004422 putative active site [active] 565050004423 putative metal binding site [ion binding]; other site 565050004424 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 565050004425 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 565050004426 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 in DNA...; Region: TOP4c; cd00187 565050004427 CAP-like domain; other site 565050004428 active site 565050004429 primary dimer interface [polypeptide binding]; other site 565050004430 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 565050004431 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 565050004432 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050004433 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 565050004434 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050004435 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 565050004436 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004437 NAD(P) binding site [chemical binding]; other site 565050004438 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 565050004439 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 565050004440 FMN binding site [chemical binding]; other site 565050004441 substrate binding site [chemical binding]; other site 565050004442 putative catalytic residue [active] 565050004443 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004444 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 565050004445 NAD(P) binding site [chemical binding]; other site 565050004446 active site 565050004447 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 565050004448 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 565050004449 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050004450 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 565050004451 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 565050004452 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 565050004453 ligand binding site [chemical binding]; other site 565050004454 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 565050004455 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004456 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050004457 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 565050004458 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 565050004459 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 565050004460 catalytic residue [active] 565050004461 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 565050004462 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 565050004463 inhibitor-cofactor binding pocket; inhibition site 565050004464 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050004465 catalytic residue [active] 565050004466 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 565050004467 EamA-like transporter family; Region: EamA; cl01037 565050004468 EamA-like transporter family; Region: EamA; cl01037 565050004469 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 565050004470 E-class dimer interface [polypeptide binding]; other site 565050004471 P-class dimer interface [polypeptide binding]; other site 565050004472 active site 565050004473 Cu2+ binding site [ion binding]; other site 565050004474 Zn2+ binding site [ion binding]; other site 565050004475 DNA gyrase, A subunit; Region: gyrA; TIGR01063 565050004476 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 in DNA...; Region: TOP4c; cd00187 565050004477 CAP-like domain; other site 565050004478 active site 565050004479 primary dimer interface [polypeptide binding]; other site 565050004480 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 565050004481 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 565050004482 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 565050004483 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 565050004484 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 565050004485 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 565050004486 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 565050004487 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 565050004488 active site 565050004489 (T/H)XGH motif; other site 565050004490 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 565050004491 active site 565050004492 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 565050004493 active site 565050004494 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 565050004495 active site 565050004496 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 565050004497 putative catalytic site [active] 565050004498 putative metal binding site [ion binding]; other site 565050004499 putative phosphate binding site [ion binding]; other site 565050004500 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 565050004501 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 565050004502 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 565050004503 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 565050004504 Potassium-transporting ATPase A subunit; Region: KdpA; cl00903 565050004505 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 565050004506 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 565050004507 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050004508 K+-transporting ATPase, c chain; Region: KdpC; cl00944 565050004509 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 565050004510 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 565050004511 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 565050004512 Ligand Binding Site [chemical binding]; other site 565050004513 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 565050004514 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 565050004515 dimer interface [polypeptide binding]; other site 565050004516 phosphorylation site [posttranslational modification] 565050004517 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 565050004518 ATP binding site [chemical binding]; other site 565050004519 G-X-G motif; other site 565050004520 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 565050004521 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 565050004522 active site 565050004523 phosphorylation site [posttranslational modification] 565050004524 intermolecular recognition site; other site 565050004525 dimerization interface [polypeptide binding]; other site 565050004526 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 565050004527 DNA binding site [nucleotide binding] 565050004528 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 565050004529 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 565050004530 dimer interface [polypeptide binding]; other site 565050004531 conserved gate region; other site 565050004532 putative PBP binding loops; other site 565050004533 ABC-ATPase subunit interface; other site 565050004534 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 565050004535 dimer interface [polypeptide binding]; other site 565050004536 conserved gate region; other site 565050004537 putative PBP binding loops; other site 565050004538 ABC-ATPase subunit interface; other site 565050004539 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 565050004540 Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a...; Region: ABC_CysA_sulfate_importer; cd03296 565050004541 Walker A/P-loop; other site 565050004542 ATP binding site [chemical binding]; other site 565050004543 Q-loop/lid; other site 565050004544 ABC transporter signature motif; other site 565050004545 Walker B; other site 565050004546 D-loop; other site 565050004547 H-loop/switch region; other site 565050004548 PilZ domain; Region: PilZ; cl01260 565050004549 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 565050004550 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 565050004551 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; cl00980 565050004552 Uncharacterized conserved protein [Function unknown]; Region: COG2308 565050004553 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl00503 565050004554 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 565050004555 Surface antigen; Region: Bac_surface_Ag; cl03097 565050004556 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 565050004557 Family of unknown function (DUF490); Region: DUF490; pfam04357 565050004558 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 565050004559 Peptidase family M20/M25/M40; Region: Peptidase_M20; pfam01546 565050004560 metal binding site [ion binding]; metal-binding site 565050004561 dimer interface [polypeptide binding]; other site 565050004562 Arginine N-succinyltransferase beta subunit; Region: AstA; cl11440 565050004563 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 565050004564 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 565050004565 NAD(P) binding site [chemical binding]; other site 565050004566 catalytic residues [active] 565050004567 Succinylarginine dihydrolase; Region: AstB; cl01511 565050004568 putative acetyltransferase YhhY; Provisional; Region: PRK10140 565050004569 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050004570 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 565050004571 LytTr DNA-binding domain; Region: LytTR; cl04498 565050004572 OpgC protein; Region: OpgC_C; cl00792 565050004573 Acyltransferase family; Region: Acyl_transf_3; pfam01757 565050004574 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 565050004575 cofactor binding site; other site 565050004576 metal binding site [ion binding]; metal-binding site 565050004577 Hemimethylated DNA-binding protein YccV like; Region: YccV-like; cl01548 565050004578 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 565050004579 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 565050004580 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; cl15754 565050004581 Ion channel; Region: Ion_trans_2; cl11596 565050004582 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 565050004583 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004584 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 565050004585 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; cl09108 565050004586 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 key...; Region: CBS_pair_IMPDH; cd04601 565050004587 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 the guanine...; Region: IMPDH; cd00381 565050004588 active site 565050004589 MAPEG family; Region: MAPEG; cl09190 565050004590 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 565050004591 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; cl15754 565050004592 GMP synthase; Reviewed; Region: guaA; PRK00074 565050004593 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 565050004594 AMP/PPi binding site [chemical binding]; other site 565050004595 candidate oxyanion hole; other site 565050004596 catalytic triad [active] 565050004597 potential glutamine specificity residues [chemical binding]; other site 565050004598 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 565050004599 ATP Binding subdomain [chemical binding]; other site 565050004600 Ligand Binding sites [chemical binding]; other site 565050004601 Dimerization subdomain; other site 565050004602 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 565050004603 Helix-turn-helix domains; Region: HTH; cl00088 565050004604 The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; Region: PBP2_LysR_opines_like; cd08415 565050004605 putative dimerization interface [polypeptide binding]; other site 565050004606 Predicted acyl esterases [General function prediction only]; Region: COG2936 565050004607 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; cl08482 565050004608 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; cl00284 565050004609 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 565050004610 ligand-binding site [chemical binding]; other site 565050004611 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 565050004612 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 565050004613 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 565050004614 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 565050004615 putative active site [active] 565050004616 putative metal binding site [ion binding]; other site 565050004617 glycosyl hydrolase family 16; Region: Glyco_hydrolase_16; cl00218 565050004618 Transcriptional regulators [Transcription]; Region: PurR; COG1609 565050004619 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 565050004620 DNA binding site [nucleotide binding] 565050004621 domain linker motif; other site 565050004622 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria; Region: PBP1_LacI_like_6; cd06284 565050004623 dimerization interface [polypeptide binding]; other site 565050004624 ligand binding site [chemical binding]; other site 565050004625 Nucleoside H+ symporter; Region: Nuc_H_symport; pfam03825 565050004626 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 565050004627 putative substrate translocation pore; other site 565050004628 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 565050004629 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 565050004630 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004631 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 565050004632 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 565050004633 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cl12060 565050004634 Metal-binding active site; metal-binding site 565050004635 AP endonuclease family 2 C terminus; Region: AP_endonuc_2_N; pfam07582 565050004636 Cytochrome c; Region: Cytochrom_C; cl11414 565050004637 glycosyl hydrolase family 16; Region: Glyco_hydrolase_16; cl00218 565050004638 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 565050004639 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004640 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 565050004641 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 565050004642 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; cl01951 565050004643 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 565050004644 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 565050004645 BlaR1 peptidase M56; Region: Peptidase_M56; cl15829 565050004646 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 565050004647 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 565050004648 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 565050004649 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 565050004650 Helix-turn-helix domains; Region: HTH; cl00088 565050004651 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 565050004652 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 565050004653 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 565050004654 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 565050004655 ArsC family; Region: ArsC; pfam03960 565050004656 putative catalytic residues [active] 565050004657 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050004658 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 565050004659 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 565050004660 motif II; other site 565050004661 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 565050004662 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050004663 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 565050004664 DNA binding residues [nucleotide binding] 565050004665 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 565050004666 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 565050004667 DNA binding residues [nucleotide binding] 565050004668 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 565050004669 oligomerization interface [polypeptide binding]; other site 565050004670 active site 565050004671 metal binding site [ion binding]; metal-binding site 565050004672 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4649 565050004673 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 565050004674 PQQ-like domain; Region: PQQ_2; pfam13360 565050004675 Trp docking motif [polypeptide binding]; other site 565050004676 active site 565050004677 GTP-binding protein Der; Reviewed; Region: PRK00093 565050004678 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 565050004679 G1 box; other site 565050004680 GTP/Mg2+ binding site [chemical binding]; other site 565050004681 Switch I region; other site 565050004682 G2 box; other site 565050004683 Switch II region; other site 565050004684 G3 box; other site 565050004685 G4 box; other site 565050004686 G5 box; other site 565050004687 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 565050004688 G1 box; other site 565050004689 GTP/Mg2+ binding site [chemical binding]; other site 565050004690 Switch I region; other site 565050004691 G2 box; other site 565050004692 G3 box; other site 565050004693 Switch II region; other site 565050004694 G4 box; other site 565050004695 G5 box; other site 565050004696 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 565050004697 PAS domain; Region: PAS_9; pfam13426 565050004698 putative active site [active] 565050004699 heme pocket [chemical binding]; other site 565050004700 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050004701 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050004702 dimer interface [polypeptide binding]; other site 565050004703 putative CheW interface [polypeptide binding]; other site 565050004704 short chain dehydrogenase; Provisional; Region: PRK08703 565050004705 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004706 NAD(P) binding site [chemical binding]; other site 565050004707 active site 565050004708 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 565050004709 Membrane transport protein; Region: Mem_trans; cl09117 565050004710 amidophosphoribosyltransferase; Provisional; Region: PRK09123 565050004711 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 565050004712 active site 565050004713 tetramer interface [polypeptide binding]; other site 565050004714 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 565050004715 active site 565050004716 Colicin V production protein; Region: Colicin_V; cl00567 565050004717 DNA repair protein RadA; Provisional; Region: PRK11823 565050004718 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 565050004719 Walker A motif/ATP binding site; other site 565050004720 ATP binding site [chemical binding]; other site 565050004721 Walker B motif; other site 565050004722 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 565050004723 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 565050004724 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 565050004725 active site 565050004726 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 565050004727 dimer interface [polypeptide binding]; other site 565050004728 substrate binding site [chemical binding]; other site 565050004729 catalytic residues [active] 565050004730 MarC family integral membrane protein; Region: MarC; cl00919 565050004731 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 565050004732 CoenzymeA binding site [chemical binding]; other site 565050004733 subunit interaction site [polypeptide binding]; other site 565050004734 PHB binding site; other site 565050004735 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050004736 Helix-turn-helix domains; Region: HTH; cl00088 565050004737 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050004738 replicative DNA helicase; Provisional; Region: PRK09165 565050004739 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 565050004740 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 565050004741 Walker A motif; other site 565050004742 ATP binding site [chemical binding]; other site 565050004743 Walker B motif; other site 565050004744 DNA binding loops [nucleotide binding] 565050004745 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050004746 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 565050004747 N-terminal plug; other site 565050004748 ligand-binding site [chemical binding]; other site 565050004749 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 565050004750 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 565050004751 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 565050004752 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 565050004753 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 565050004754 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 565050004755 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 565050004756 Helix-turn-helix domain; Region: HTH_18; pfam12833 565050004757 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 565050004758 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 565050004759 catalytic triad [active] 565050004760 Acyl transferase domain; Region: Acyl_transf_1; cl08282 565050004761 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 565050004762 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004763 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 565050004764 NAD(P) binding site [chemical binding]; other site 565050004765 active site 565050004766 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004767 Phosphopantetheine attachment site; Region: PP-binding; cl09936 565050004768 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 565050004769 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 565050004770 dimer interface [polypeptide binding]; other site 565050004771 active site 565050004772 YceG-like family; Region: YceG; pfam02618 565050004773 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 565050004774 dimerization interface [polypeptide binding]; other site 565050004775 hypothetical protein; Provisional; Region: PRK11820 565050004776 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 565050004777 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 565050004778 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 565050004779 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 565050004780 catalytic site [active] 565050004781 G-X2-G-X-G-K; other site 565050004782 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 565050004783 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 565050004784 Histidine kinase; Region: HisKA_2; cl06527 565050004785 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004786 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 565050004787 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 565050004788 SurA N-terminal domain; Region: SurA_N_3; cl07813 565050004789 PPIC-type PPIASE domain; Region: Rotamase; cl08278 565050004790 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03002 565050004791 PPIC-type PPIASE domain; Region: Rotamase; cl08278 565050004792 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 565050004793 OstA-like protein; Region: OstA; cl00844 565050004794 Organic solvent tolerance protein; Region: OstA_C; pfam04453 565050004795 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 565050004796 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 565050004797 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 565050004798 multifunctional aminopeptidase A; Provisional; Region: PRK00913 565050004799 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 565050004800 interface (dimer of trimers) [polypeptide binding]; other site 565050004801 Substrate-binding/catalytic site; other site 565050004802 Zn-binding sites [ion binding]; other site 565050004803 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 565050004804 Potato inhibitor I family; Region: potato_inhibit; cl15459 565050004805 TolB amino-terminal domain; Region: TolB_N; cl00639 565050004806 Cytochrome c; Region: Cytochrom_C; cl11414 565050004807 Domain of unkown function (DUF1901); Region: DUF1901; pfam08955 565050004808 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 565050004809 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 565050004810 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 565050004811 ABC transporter; Region: ABC_tran_2; pfam12848 565050004812 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 565050004813 peptide chain release factor 2; Validated; Region: prfB; PRK00578 565050004814 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 565050004815 active site 565050004816 multimer interface [polypeptide binding]; other site 565050004817 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 565050004818 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 565050004819 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 565050004820 active site 565050004821 substrate binding site [chemical binding]; other site 565050004822 cosubstrate binding site; other site 565050004823 catalytic site [active] 565050004824 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 565050004825 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 565050004826 dimerization interface [polypeptide binding]; other site 565050004827 putative ATP binding site [chemical binding]; other site 565050004828 ribonuclease D; Region: rnd; TIGR01388 565050004829 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 565050004830 putative active site [active] 565050004831 catalytic site [active] 565050004832 putative substrate binding site [chemical binding]; other site 565050004833 HRDC domain; Region: HRDC; cl02578 565050004834 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 565050004835 dimer interface [polypeptide binding]; other site 565050004836 phosphorylation site [posttranslational modification] 565050004837 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 565050004838 ATP binding site [chemical binding]; other site 565050004839 Mg2+ binding site [ion binding]; other site 565050004840 G-X-G motif; other site 565050004841 Response regulator receiver domain; Region: Response_reg; pfam00072 565050004842 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 565050004843 active site 565050004844 phosphorylation site [posttranslational modification] 565050004845 intermolecular recognition site; other site 565050004846 dimerization interface [polypeptide binding]; other site 565050004847 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050004848 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 565050004849 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 565050004850 polyphosphate kinase; Provisional; Region: PRK05443 565050004851 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 565050004852 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 565050004853 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 565050004854 putative domain interface [polypeptide binding]; other site 565050004855 putative active site [active] 565050004856 catalytic site [active] 565050004857 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 565050004858 putative domain interface [polypeptide binding]; other site 565050004859 putative active site [active] 565050004860 catalytic site [active] 565050004861 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050004862 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 565050004863 EcsC protein family; Region: EcsC; pfam12787 565050004864 Transposase; Region: DEDD_Tnp_IS110; pfam01548 565050004865 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 565050004866 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 565050004867 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050004868 Preprotein translocase SecG subunit; Region: SecG; cl09123 565050004869 CTP synthetase; Validated; Region: pyrG; PRK05380 565050004870 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 565050004871 Catalytic site [active] 565050004872 active site 565050004873 UTP binding site [chemical binding]; other site 565050004874 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 565050004875 active site 565050004876 putative oxyanion hole; other site 565050004877 catalytic triad [active] 565050004878 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 565050004879 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 565050004880 catalytic motif [active] 565050004881 Catalytic residue [active] 565050004882 enoyl-CoA hydratase; Provisional; Region: PRK06190 565050004883 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 565050004884 substrate binding site [chemical binding]; other site 565050004885 oxyanion hole (OAH) forming residues; other site 565050004886 trimer interface [polypeptide binding]; other site 565050004887 MutS domain I; Region: MutS_I; pfam01624 565050004888 enolase; Provisional; Region: eno; PRK00077 565050004889 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 565050004890 dimer interface [polypeptide binding]; other site 565050004891 metal binding site [ion binding]; metal-binding site 565050004892 substrate binding pocket [chemical binding]; other site 565050004893 Septum formation initiator; Region: DivIC; cl11433 565050004894 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 565050004895 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 565050004896 tetramer interface [polypeptide binding]; other site 565050004897 TPP-binding site [chemical binding]; other site 565050004898 heterodimer interface [polypeptide binding]; other site 565050004899 phosphorylation loop region [posttranslational modification] 565050004900 pyruvate dehydrogenase subunit beta; Provisional; Region: PRK11892 565050004901 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 565050004902 E3 interaction surface; other site 565050004903 lipoyl attachment site [posttranslational modification]; other site 565050004904 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 565050004905 alpha subunit interface [polypeptide binding]; other site 565050004906 TPP binding site [chemical binding]; other site 565050004907 heterodimer interface [polypeptide binding]; other site 565050004908 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 565050004909 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 565050004910 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 565050004911 E3 interaction surface; other site 565050004912 lipoyl attachment site [posttranslational modification]; other site 565050004913 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 565050004914 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 565050004915 catalytic residues [active] 565050004916 dimer interface [polypeptide binding]; other site 565050004917 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 565050004918 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050004919 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 565050004920 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 565050004921 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 565050004922 AMP-binding enzyme; Region: AMP-binding; cl15778 565050004923 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 565050004924 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; cl12031 565050004925 lipoyl synthase; Provisional; Region: PRK05481 565050004926 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 565050004927 FeS/SAM binding site; other site 565050004928 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 565050004929 putative coenzyme Q binding site [chemical binding]; other site 565050004930 Competence-damaged protein; Region: CinA; cl00666 565050004931 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 565050004932 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 565050004933 substrate binding site; other site 565050004934 dimer interface; other site 565050004935 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 565050004936 homotrimer interaction site [polypeptide binding]; other site 565050004937 zinc binding site [ion binding]; other site 565050004938 CDP-binding sites; other site 565050004939 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 565050004940 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 565050004941 FMN binding site [chemical binding]; other site 565050004942 active site 565050004943 catalytic residues [active] 565050004944 substrate binding site [chemical binding]; other site 565050004945 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 565050004946 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 565050004947 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 565050004948 dimer interface [polypeptide binding]; other site 565050004949 phosphorylation site [posttranslational modification] 565050004950 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 565050004951 ATP binding site [chemical binding]; other site 565050004952 Mg2+ binding site [ion binding]; other site 565050004953 G-X-G motif; other site 565050004954 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 565050004955 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 565050004956 active site 565050004957 phosphorylation site [posttranslational modification] 565050004958 intermolecular recognition site; other site 565050004959 dimerization interface [polypeptide binding]; other site 565050004960 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 565050004961 Walker A motif; other site 565050004962 ATP binding site [chemical binding]; other site 565050004963 Walker B motif; other site 565050004964 arginine finger; other site 565050004965 Helix-turn-helix domains; Region: HTH; cl00088 565050004966 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 565050004967 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 565050004968 dimerization interface [polypeptide binding]; other site 565050004969 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 565050004970 dimer interface [polypeptide binding]; other site 565050004971 phosphorylation site [posttranslational modification] 565050004972 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 565050004973 ATP binding site [chemical binding]; other site 565050004974 Mg2+ binding site [ion binding]; other site 565050004975 G-X-G motif; other site 565050004976 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 565050004977 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 565050004978 active site 565050004979 phosphorylation site [posttranslational modification] 565050004980 intermolecular recognition site; other site 565050004981 dimerization interface [polypeptide binding]; other site 565050004982 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 565050004983 Walker A motif; other site 565050004984 ATP binding site [chemical binding]; other site 565050004985 Walker B motif; other site 565050004986 Helix-turn-helix domains; Region: HTH; cl00088 565050004987 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 565050004988 homodimer interface [polypeptide binding]; other site 565050004989 substrate-cofactor binding pocket; other site 565050004990 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050004991 catalytic residue [active] 565050004992 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 565050004993 Sm1 motif; other site 565050004994 intra - hexamer interaction site; other site 565050004995 inter - hexamer interaction site [polypeptide binding]; other site 565050004996 nucleotide binding pocket [chemical binding]; other site 565050004997 Sm2 motif; other site 565050004998 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 565050004999 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 565050005000 HflX GTPase family; Region: HflX; cd01878 565050005001 G1 box; other site 565050005002 GTP/Mg2+ binding site [chemical binding]; other site 565050005003 Switch I region; other site 565050005004 G2 box; other site 565050005005 G3 box; other site 565050005006 Switch II region; other site 565050005007 G4 box; other site 565050005008 G5 box; other site 565050005009 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 565050005010 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 565050005011 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 565050005012 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 565050005013 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 565050005014 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 565050005015 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 565050005016 N-terminal plug; other site 565050005017 ligand-binding site [chemical binding]; other site 565050005018 cobyric acid synthase; Provisional; Region: PRK00784 565050005019 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050005020 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 565050005021 catalytic triad [active] 565050005022 Protein of unknown function (DUF2939); Region: DUF2939; pfam11159 565050005023 Transcriptional regulators [Transcription]; Region: PurR; COG1609 565050005024 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 565050005025 DNA binding site [nucleotide binding] 565050005026 domain linker motif; other site 565050005027 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 565050005028 putative dimerization interface [polypeptide binding]; other site 565050005029 putative ligand binding site [chemical binding]; other site 565050005030 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050005031 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; cl00284 565050005032 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 565050005033 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050005034 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 565050005035 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 565050005036 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 565050005037 Fibronectin type III-like domain; Region: Fn3-like; cl15273 565050005038 O-Glycosyl hydrolase [Cell envelope biogenesis, outer membrane]; Region: COG5520 565050005039 O-Glycosyl hydrolase family 30; Region: Glyco_hydro_30; pfam02055 565050005040 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 565050005041 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 565050005042 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 565050005043 Walker A/P-loop; other site 565050005044 ATP binding site [chemical binding]; other site 565050005045 Q-loop/lid; other site 565050005046 ABC transporter signature motif; other site 565050005047 Walker B; other site 565050005048 D-loop; other site 565050005049 H-loop/switch region; other site 565050005050 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 565050005051 active site 565050005052 catalytic triad [active] 565050005053 oxyanion hole [active] 565050005054 switch loop; other site 565050005055 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 565050005056 Helix-turn-helix domains; Region: HTH; cl00088 565050005057 Helix-turn-helix domains; Region: HTH; cl00088 565050005058 Integrase core domain; Region: rve; cl01316 565050005059 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 565050005060 Domain of unknown function (DUF955); Region: DUF955; cl01076 565050005061 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 565050005062 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 565050005063 tetramer interface [polypeptide binding]; other site 565050005064 active site 565050005065 Mg2+/Mn2+ binding site [ion binding]; other site 565050005066 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 565050005067 malate synthase A; Region: malate_syn_A; TIGR01344 565050005068 Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to...; Region: malate_synt_A; cd00727 565050005069 active site 565050005070 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 565050005071 DNA binding site [nucleotide binding] 565050005072 Int/Topo IB signature motif; other site 565050005073 active site 565050005074 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 565050005075 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 565050005076 active site 565050005077 phosphorylation site [posttranslational modification] 565050005078 intermolecular recognition site; other site 565050005079 dimerization interface [polypeptide binding]; other site 565050005080 Helix-turn-helix domains; Region: HTH; cl00088 565050005081 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; cl00080 565050005082 dimer interface [polypeptide binding]; other site 565050005083 phosphorylation site [posttranslational modification] 565050005084 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 565050005085 ATP binding site [chemical binding]; other site 565050005086 Mg2+ binding site [ion binding]; other site 565050005087 G-X-G motif; other site 565050005088 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 565050005089 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 565050005090 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 565050005091 Subunit I/III interface [polypeptide binding]; other site 565050005092 Subunit III/IV interface [polypeptide binding]; other site 565050005093 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 565050005094 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 565050005095 D-pathway; other site 565050005096 Putative ubiquinol binding site [chemical binding]; other site 565050005097 Low-spin heme (heme b) binding site [chemical binding]; other site 565050005098 Putative water exit pathway; other site 565050005099 Binuclear center (heme o3/CuB) [ion binding]; other site 565050005100 K-pathway; other site 565050005101 Putative proton exit pathway; other site 565050005102 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 565050005103 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 565050005104 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 565050005105 metabolite-proton symporter; Region: 2A0106; TIGR00883 565050005106 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 565050005107 putative substrate translocation pore; other site 565050005108 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050005109 Transcriptional regulators [Transcription]; Region: FadR; COG2186 565050005110 DNA-binding site [nucleotide binding]; DNA binding site 565050005111 FCD domain; Region: FCD; cl11656 565050005112 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 565050005113 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 565050005114 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 565050005115 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050005116 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 565050005117 N-terminal plug; other site 565050005118 ligand-binding site [chemical binding]; other site 565050005119 DJ-1 family protein; Region: not_thiJ; TIGR01383 565050005120 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 565050005121 conserved cys residue [active] 565050005122 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 565050005123 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 565050005124 conserved cys residue [active] 565050005125 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 565050005126 N-terminal plug; other site 565050005127 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050005128 ligand-binding site [chemical binding]; other site 565050005129 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 565050005130 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 565050005131 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 565050005132 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 565050005133 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 565050005134 Helix-turn-helix domains; Region: HTH; cl00088 565050005135 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 565050005136 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050005137 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050005138 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 565050005139 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5255 565050005140 Domain of unknown function (DUF1868); Region: 2H-phosphodiest; pfam08975 565050005141 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050005142 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; cl00284 565050005143 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 565050005144 Helix-turn-helix domains; Region: HTH; cl00088 565050005145 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 565050005146 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 565050005147 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 565050005148 Transposase domain (DUF772); Region: DUF772; cl15789 565050005149 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 565050005150 Transposase domain (DUF772); Region: DUF772; cl15789 565050005151 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 565050005152 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 565050005153 active site 565050005154 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 565050005155 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050005156 Acyl-CoA thioesterase [Lipid metabolism]; Region: TesB; COG1946 565050005157 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 565050005158 active site 2 [active] 565050005159 active site 1 [active] 565050005160 acyl-CoA synthetase; Validated; Region: PRK07798 565050005161 AMP-binding enzyme; Region: AMP-binding; cl15778 565050005162 AMP-binding enzyme; Region: AMP-binding; cl15778 565050005163 Old yellow enzyme (OYE)-related FMN binding domain, group 5. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_5_FMN; cd04747 565050005164 putative active site [active] 565050005165 putative FMN binding site [chemical binding]; other site 565050005166 putative substrate binding site [chemical binding]; other site 565050005167 putative catalytic residue [active] 565050005168 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 565050005169 classical (c) SDRs; Region: SDR_c; cd05233 565050005170 NAD(P) binding site [chemical binding]; other site 565050005171 active site 565050005172 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050005173 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 565050005174 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 565050005175 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26; Region: ACAD_fadE6_17_26; cd01152 565050005176 FAD binding site [chemical binding]; other site 565050005177 substrate binding site [chemical binding]; other site 565050005178 catalytic base [active] 565050005179 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 565050005180 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 565050005181 active site 565050005182 short chain dehydrogenase; Provisional; Region: PRK07774 565050005183 classical (c) SDRs; Region: SDR_c; cd05233 565050005184 NAD(P) binding site [chemical binding]; other site 565050005185 active site 565050005186 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; cl00284 565050005187 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; cl00284 565050005188 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050005189 Transcriptional regulator [Transcription]; Region: IclR; COG1414 565050005190 Helix-turn-helix domains; Region: HTH; cl00088 565050005191 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07008 565050005192 AMP-binding enzyme; Region: AMP-binding; cl15778 565050005193 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 565050005194 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 565050005195 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 565050005196 substrate binding site [chemical binding]; other site 565050005197 trimer interface [polypeptide binding]; other site 565050005198 oxyanion hole (OAH) forming residues; other site 565050005199 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 565050005200 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 565050005201 enoyl-CoA hydratase; Provisional; Region: PRK06495 565050005202 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 565050005203 substrate binding site [chemical binding]; other site 565050005204 oxyanion hole (OAH) forming residues; other site 565050005205 trimer interface [polypeptide binding]; other site 565050005206 short chain dehydrogenase; Validated; Region: PRK06484 565050005207 classical (c) SDRs; Region: SDR_c; cd05233 565050005208 NAD(P) binding site [chemical binding]; other site 565050005209 active site 565050005210 classical (c) SDRs; Region: SDR_c; cd05233 565050005211 NAD(P) binding site [chemical binding]; other site 565050005212 active site 565050005213 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 565050005214 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 565050005215 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050005216 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 565050005217 putative substrate translocation pore; other site 565050005218 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 565050005219 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 565050005220 active site 565050005221 DNA polymerase III subunit delta'; Validated; Region: PRK07471 565050005222 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050005223 thymidylate kinase; Validated; Region: tmk; PRK00698 565050005224 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 565050005225 TMP-binding site; other site 565050005226 ATP-binding site [chemical binding]; other site 565050005227 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 565050005228 Sporulation related domain; Region: SPOR; cl10051 565050005229 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 565050005230 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 565050005231 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 565050005232 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 565050005233 Domain of unknown function (DUF1989); Region: DUF1989; cl01474 565050005234 Domain of unknown function (DUF1989); Region: DUF1989; cl01474 565050005235 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 565050005236 urea carboxylase; Region: urea_carbox; TIGR02712 565050005237 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 565050005238 ATP-grasp domain; Region: ATP-grasp_4; cl03087 565050005239 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 565050005240 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 565050005241 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 565050005242 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 565050005243 carboxyltransferase (CT) interaction site; other site 565050005244 biotinylation site [posttranslational modification]; other site 565050005245 allophanate hydrolase; Provisional; Region: PRK08186 565050005246 Amidase; Region: Amidase; cl11426 565050005247 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 565050005248 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 565050005249 Walker A/P-loop; other site 565050005250 ATP binding site [chemical binding]; other site 565050005251 Q-loop/lid; other site 565050005252 ABC transporter signature motif; other site 565050005253 Walker B; other site 565050005254 D-loop; other site 565050005255 H-loop/switch region; other site 565050005256 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 565050005257 NMT1-like family; Region: NMT1_2; cl15260 565050005258 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 565050005259 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050005260 Putative mono-oxygenase ydhR; Region: ydhR; cl07420 565050005261 Helix-turn-helix domains; Region: HTH; cl00088 565050005262 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 565050005263 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 565050005264 S-adenosylmethionine binding site [chemical binding]; other site 565050005265 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 565050005266 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 565050005267 RNA binding surface [nucleotide binding]; other site 565050005268 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 565050005269 active site 565050005270 uracil binding [chemical binding]; other site 565050005271 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 565050005272 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 565050005273 CoA-transferase family III; Region: CoA_transf_3; pfam02515 565050005274 Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]; Region: PleD; COG3706 565050005275 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 565050005276 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 565050005277 catalytic residues [active] 565050005278 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 565050005279 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 565050005280 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 565050005281 ATP binding site [chemical binding]; other site 565050005282 putative Mg++ binding site [ion binding]; other site 565050005283 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 565050005284 nucleotide binding region [chemical binding]; other site 565050005285 ATP-binding site [chemical binding]; other site 565050005286 TRCF domain; Region: TRCF; cl04088 565050005287 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 565050005288 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 565050005289 S-adenosylmethionine binding site [chemical binding]; other site 565050005290 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 565050005291 DEAD-like helicases superfamily; Region: DEXDc; smart00487 565050005292 ATP binding site [chemical binding]; other site 565050005293 Mg++ binding site [ion binding]; other site 565050005294 motif III; other site 565050005295 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 565050005296 nucleotide binding region [chemical binding]; other site 565050005297 ATP-binding site [chemical binding]; other site 565050005298 Protein of unknown function (DUF563); Region: DUF563; cl15705 565050005299 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 565050005300 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 565050005301 NAD(P) binding site [chemical binding]; other site 565050005302 catalytic residues [active] 565050005303 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 565050005304 metal binding site [ion binding]; metal-binding site 565050005305 active site 565050005306 I-site; other site 565050005307 enoyl-CoA hydratase; Provisional; Region: PRK05981 565050005308 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 565050005309 substrate binding site [chemical binding]; other site 565050005310 oxyanion hole (OAH) forming residues; other site 565050005311 trimer interface [polypeptide binding]; other site 565050005312 ACT domain; Region: ACT_3; pfam10000 565050005313 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3602 565050005314 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 565050005315 Protein of unknown function (DUF4254); Region: DUF4254; pfam14063 565050005316 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 565050005317 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 565050005318 Helix-turn-helix domains; Region: HTH; cl00088 565050005319 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 565050005320 putative acyl-acceptor binding pocket; other site 565050005321 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 565050005322 Domain of unknown function DUF59; Region: DUF59; cl00941 565050005323 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 565050005324 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 565050005325 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 565050005326 catalytic residue [active] 565050005327 cysteine desulfurase activator complex subunit SufD; Provisional; Region: PRK10948 565050005328 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 565050005329 FeS assembly ATPase SufC; Region: sufC; TIGR01978 565050005330 ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under...; Region: ABC_FeS_Assembly; cd03217 565050005331 Walker A/P-loop; other site 565050005332 ATP binding site [chemical binding]; other site 565050005333 Q-loop/lid; other site 565050005334 ABC transporter signature motif; other site 565050005335 Walker B; other site 565050005336 D-loop; other site 565050005337 H-loop/switch region; other site 565050005338 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 565050005339 putative ABC transporter; Region: ycf24; CHL00085 565050005340 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 565050005341 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 565050005342 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 565050005343 catalytic residue [active] 565050005344 Helix-turn-helix domains; Region: HTH; cl00088 565050005345 Rrf2 family protein; Region: rrf2_super; TIGR00738 565050005346 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 565050005347 Eukaryotic protein of unknown function (DUF829); Region: DUF829; pfam05705 565050005348 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 565050005349 active site 565050005350 Uncharacterized protein family (UPF0075); Region: UPF0075; cl04217 565050005351 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 565050005352 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 565050005353 active site 565050005354 HIGH motif; other site 565050005355 dimer interface [polypeptide binding]; other site 565050005356 KMSKS motif; other site 565050005357 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 565050005358 catalytic triad [active] 565050005359 Peptidase family M23; Region: Peptidase_M23; pfam01551 565050005360 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 565050005361 peptide chain release factor 2; Validated; Region: prfB; PRK00578 565050005362 RF-1 domain; Region: RF-1; cl02875 565050005363 RF-1 domain; Region: RF-1; cl02875 565050005364 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 565050005365 Transglycosylase; Region: Transgly; cl07896 565050005366 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050005367 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 565050005368 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 565050005369 active site 565050005370 metal binding site [ion binding]; metal-binding site 565050005371 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 565050005372 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 565050005373 RNA binding site [nucleotide binding]; other site 565050005374 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 565050005375 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 565050005376 Peptidase family M48; Region: Peptidase_M48; cl12018 565050005377 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 565050005378 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 565050005379 binding surface 565050005380 TPR motif; other site 565050005381 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 565050005382 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 565050005383 catalytic residues [active] 565050005384 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 565050005385 ThiS interaction site; other site 565050005386 putative active site [active] 565050005387 tetramer interface [polypeptide binding]; other site 565050005388 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 565050005389 thiS-thiF/thiG interaction site; other site 565050005390 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 565050005391 trimer interface [polypeptide binding]; other site 565050005392 active site 565050005393 dimer interface [polypeptide binding]; other site 565050005394 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 565050005395 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 565050005396 carboxyltransferase (CT) interaction site; other site 565050005397 biotinylation site [posttranslational modification]; other site 565050005398 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 565050005399 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 565050005400 ATP-grasp domain; Region: ATP-grasp_4; cl03087 565050005401 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 565050005402 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050005403 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; cl01970 565050005404 NADH ubiquinone oxidoreductase subunit NDUFA12; Region: NDUFA12; cl01534 565050005405 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07562 565050005406 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07562 565050005407 TSCPD domain; Region: TSCPD; cl14834 565050005408 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 565050005409 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050005410 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050005411 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 565050005412 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050005413 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050005414 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 565050005415 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 565050005416 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050005417 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050005418 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050005419 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 565050005420 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 565050005421 dimer interface [polypeptide binding]; other site 565050005422 anticodon binding site; other site 565050005423 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 the...; Region: AspRS_core; cd00777 565050005424 homodimer interface [polypeptide binding]; other site 565050005425 motif 1; other site 565050005426 active site 565050005427 motif 2; other site 565050005428 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 attaches...; Region: class_II_aaRS-like_core; cl00268 565050005429 active site 565050005430 motif 3; other site 565050005431 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 565050005432 substrate binding site [chemical binding]; other site 565050005433 dimer interface [polypeptide binding]; other site 565050005434 catalytic triad [active] 565050005435 periplasmic folding chaperone; Provisional; Region: PRK10788 565050005436 SurA N-terminal domain; Region: SurA_N_3; cl07813 565050005437 PPIC-type PPIASE domain; Region: Rotamase; cl08278 565050005438 PPIC-type PPIASE domain; Region: Rotamase; cl08278 565050005439 anthranilate synthase component I; Provisional; Region: PRK13573 565050005440 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 565050005441 chorismate binding enzyme; Region: Chorismate_bind; cl10555 565050005442 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 565050005443 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 565050005444 glutamine binding [chemical binding]; other site 565050005445 catalytic triad [active] 565050005446 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 565050005447 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 565050005448 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 565050005449 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 565050005450 active site 565050005451 ribulose/triose binding site [chemical binding]; other site 565050005452 phosphate binding site [ion binding]; other site 565050005453 substrate (anthranilate) binding pocket [chemical binding]; other site 565050005454 product (indole) binding pocket [chemical binding]; other site 565050005455 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 565050005456 putative acyl-acceptor binding pocket; other site 565050005457 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 565050005458 S-adenosylmethionine binding site [chemical binding]; other site 565050005459 LexA repressor; Validated; Region: PRK00215 565050005460 Helix-turn-helix domains; Region: HTH; cl00088 565050005461 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 565050005462 Catalytic site [active] 565050005463 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 565050005464 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 565050005465 tetramer interface [polypeptide binding]; other site 565050005466 active site 565050005467 Mg2+/Mn2+ binding site [ion binding]; other site 565050005468 Competence protein; Region: Competence; cl00471 565050005469 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 565050005470 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 565050005471 active site 565050005472 HIGH motif; other site 565050005473 nucleotide binding site [chemical binding]; other site 565050005474 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 565050005475 active site 565050005476 KMSKS motif; other site 565050005477 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 565050005478 dimer interface [polypeptide binding]; other site 565050005479 Citrate synthase; Region: Citrate_synt; pfam00285 565050005480 active site 565050005481 citrylCoA binding site [chemical binding]; other site 565050005482 NADH binding [chemical binding]; other site 565050005483 cationic pore residues; other site 565050005484 oxalacetate/citrate binding site [chemical binding]; other site 565050005485 coenzyme A binding site [chemical binding]; other site 565050005486 catalytic triad [active] 565050005487 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 565050005488 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 565050005489 Lipid A disaccharide synthetase [Cell envelope biogenesis, outer membrane]; Region: LpxB; COG0763 565050005490 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 565050005491 Protein of unknown function (DUF1009); Region: DUF1009; cl09182 565050005492 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 565050005493 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 565050005494 active site 565050005495 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 565050005496 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Region: lipid_A_lpxD; TIGR01853 565050005497 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 565050005498 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 565050005499 trimer interface [polypeptide binding]; other site 565050005500 active site 565050005501 UDP-GlcNAc binding site [chemical binding]; other site 565050005502 lipid binding site [chemical binding]; lipid-binding site 565050005503 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 565050005504 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 565050005505 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 565050005506 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 565050005507 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 565050005508 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 565050005509 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 565050005510 Surface antigen; Region: Bac_surface_Ag; cl03097 565050005511 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 565050005512 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 565050005513 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 565050005514 protein binding site [polypeptide binding]; other site 565050005515 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 565050005516 putative substrate binding region [chemical binding]; other site 565050005517 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 565050005518 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 565050005519 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 565050005520 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 565050005521 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 565050005522 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 565050005523 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 565050005524 catalytic residue [active] 565050005525 putative FPP diphosphate binding site; other site 565050005526 putative FPP binding hydrophobic cleft; other site 565050005527 dimer interface [polypeptide binding]; other site 565050005528 putative IPP diphosphate binding site; other site 565050005529 ribosome recycling factor; Reviewed; Region: frr; PRK00083 565050005530 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 round of...; Region: RRF; cd00520 565050005531 hinge region; other site 565050005532 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 565050005533 putative nucleotide binding site [chemical binding]; other site 565050005534 uridine monophosphate binding site [chemical binding]; other site 565050005535 homohexameric interface [polypeptide binding]; other site 565050005536 elongation factor Ts; Provisional; Region: tsf; PRK09377 565050005537 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 565050005538 Elongation factor TS; Region: EF_TS; pfam00889 565050005539 Elongation factor TS; Region: EF_TS; pfam00889 565050005540 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 565050005541 rRNA interaction site [nucleotide binding]; other site 565050005542 S8 interaction site; other site 565050005543 putative laminin-1 binding site; other site 565050005544 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 565050005545 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050005546 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 565050005547 S-adenosylmethionine binding site [chemical binding]; other site 565050005548 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 565050005549 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 565050005550 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 565050005551 generic binding surface II; other site 565050005552 generic binding surface I; other site 565050005553 nuc_hydro_CeIAG: Nucleoside hydrolases similar to the inosine-adenosine-guanosine-preferring nucleoside hydrolase from Caenorhabditis elegans. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base; Region: nuc_hydro_CeIAG; cd02649 565050005554 active site 565050005555 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 565050005556 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 565050005557 Walker A/P-loop; other site 565050005558 ATP binding site [chemical binding]; other site 565050005559 Q-loop/lid; other site 565050005560 ABC transporter signature motif; other site 565050005561 Walker B; other site 565050005562 D-loop; other site 565050005563 H-loop/switch region; other site 565050005564 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 565050005565 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 565050005566 FtsX-like permease family; Region: FtsX; cl15850 565050005567 prolyl-tRNA synthetase; Provisional; Region: PRK12325 565050005568 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 formation of...; Region: ProRS_core_prok; cd00779 565050005569 dimer interface [polypeptide binding]; other site 565050005570 motif 1; other site 565050005571 active site 565050005572 motif 2; other site 565050005573 motif 3; other site 565050005574 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 565050005575 anticodon binding site; other site 565050005576 Protein of unknown function (DUF1467); Region: DUF1467; cl11569 565050005577 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050005578 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 565050005579 dimer interface [polypeptide binding]; other site 565050005580 substrate binding site [chemical binding]; other site 565050005581 metal binding site [ion binding]; metal-binding site 565050005582 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 565050005583 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 565050005584 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 565050005585 Type III pantothenate kinase; Region: Pan_kinase; cl09130 565050005586 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 565050005587 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 565050005588 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 565050005589 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 565050005590 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 565050005591 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 565050005592 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 565050005593 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 565050005594 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 565050005595 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 565050005596 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 565050005597 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 565050005598 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 565050005599 4Fe-4S binding domain; Region: Fer4; cl02805 565050005600 4Fe-4S binding domain; Region: Fer4; cl02805 565050005601 NADH dehydrogenase; Region: NADHdh; cl00469 565050005602 NADH dehydrogenase subunit G; Validated; Region: PRK09130 565050005603 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 565050005604 catalytic loop [active] 565050005605 iron binding site [ion binding]; other site 565050005606 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 565050005607 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase...; Region: MopB_Res-Cmplx1_Nad11; cd02773 565050005608 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 565050005609 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 565050005610 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 565050005611 SLBB domain; Region: SLBB; pfam10531 565050005612 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 565050005613 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cl11443 565050005614 NADH dehydrogenase subunit E; Provisional; Region: PRK12373 565050005615 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 565050005616 putative dimer interface [polypeptide binding]; other site 565050005617 [2Fe-2S] cluster binding site [ion binding]; other site 565050005618 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 565050005619 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 565050005620 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; pfam00346 565050005621 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl15771 565050005622 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 565050005623 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 565050005624 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 565050005625 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 565050005626 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 565050005627 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 565050005628 IHF dimer interface [polypeptide binding]; other site 565050005629 IHF - DNA interface [nucleotide binding]; other site 565050005630 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 565050005631 Found in ATP-dependent protease La (LON); Region: LON; smart00464 565050005632 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 565050005633 Walker A motif; other site 565050005634 ATP binding site [chemical binding]; other site 565050005635 Walker B motif; other site 565050005636 arginine finger; other site 565050005637 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 565050005638 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 565050005639 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 565050005640 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050005641 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 565050005642 Walker A motif; other site 565050005643 ATP binding site [chemical binding]; other site 565050005644 Walker B motif; other site 565050005645 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 565050005646 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050005647 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 565050005648 Clp protease; Region: CLP_protease; pfam00574 565050005649 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 565050005650 oligomer interface [polypeptide binding]; other site 565050005651 active site residues [active] 565050005652 trigger factor; Provisional; Region: tig; PRK01490 565050005653 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 565050005654 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 565050005655 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 565050005656 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 565050005657 putative substrate binding site [chemical binding]; other site 565050005658 putative ATP binding site [chemical binding]; other site 565050005659 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 565050005660 acetyl-CoA acetyltransferase; Validated; Region: PRK08257 565050005661 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 565050005662 active site 565050005663 Nitrogen regulatory protein P-II; Region: P-II; cl00412 565050005664 Nitrogen regulatory protein P-II; Region: P-II; smart00938 565050005665 glutamine synthetase; Provisional; Region: glnA; PRK09469 565050005666 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 565050005667 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 565050005668 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050005669 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 565050005670 N-terminal plug; other site 565050005671 ligand-binding site [chemical binding]; other site 565050005672 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 565050005673 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 565050005674 Metallo-dependent hydrolases, subgroup C is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_C; cd01309 565050005675 active site 565050005676 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 565050005677 Metallo-dependent hydrolases, subgroup C is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_C; cd01309 565050005678 active site 565050005679 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 565050005680 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 565050005681 ATP binding site [chemical binding]; other site 565050005682 Mg2+ binding site [ion binding]; other site 565050005683 G-X-G motif; other site 565050005684 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 565050005685 anchoring element; other site 565050005686 dimer interface [polypeptide binding]; other site 565050005687 ATP binding site [chemical binding]; other site 565050005688 TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands...; Region: TOPRIM_TopoIIA_like; cd01030 565050005689 active site 565050005690 putative metal-binding site [ion binding]; other site 565050005691 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 565050005692 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 565050005693 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 565050005694 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 565050005695 Uncharacterized BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 565050005696 ATP12 chaperone protein; Region: ATP12; cl02228 565050005697 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5267 565050005698 Protein of unknown function (DUF1800); Region: DUF1800; pfam08811 565050005699 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4102 565050005700 Protein of unknown function (DUF1501); Region: DUF1501; pfam07394 565050005701 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 565050005702 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 565050005703 RNA binding surface [nucleotide binding]; other site 565050005704 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 565050005705 active site 565050005706 CrcB-like protein; Region: CRCB; cl09114 565050005707 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 565050005708 Walker A/P-loop; other site 565050005709 ATP binding site [chemical binding]; other site 565050005710 Q-loop/lid; other site 565050005711 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 565050005712 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050005713 ABC transporter signature motif; other site 565050005714 Walker B; other site 565050005715 D-loop; other site 565050005716 H-loop/switch region; other site 565050005717 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 565050005718 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 565050005719 binding surface 565050005720 TPR motif; other site 565050005721 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 565050005722 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 565050005723 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 565050005724 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 565050005725 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; cl12031 565050005726 Isoprenoid Biosynthesis enzymes, Class 1; Region: Isoprenoid_Biosyn_C1; cl00210 565050005727 Protein of unknown function (DUF989); Region: DUF989; pfam06181 565050005728 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; cd00248 565050005729 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 565050005730 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 565050005731 Protein export membrane protein; Region: SecD_SecF; cl14618 565050005732 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 565050005733 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 565050005734 Protein export membrane protein; Region: SecD_SecF; cl14618 565050005735 Preprotein translocase subunit; Region: YajC; cl00806 565050005736 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 565050005737 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050005738 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 565050005739 sequence-specific DNA binding site [nucleotide binding]; other site 565050005740 salt bridge; other site 565050005741 Cupin domain; Region: Cupin_2; cl09118 565050005742 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 565050005743 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 565050005744 Coenzyme A binding pocket [chemical binding]; other site 565050005745 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 565050005746 putative peptidoglycan binding site; other site 565050005747 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 565050005748 putative peptidoglycan binding site; other site 565050005749 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 565050005750 putative peptidoglycan binding site; other site 565050005751 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 565050005752 putative peptidoglycan binding site; other site 565050005753 Peptidase family M23; Region: Peptidase_M23; pfam01551 565050005754 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 565050005755 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050005756 Survival protein SurE; Region: SurE; cl00448 565050005757 seryl-tRNA synthetase; Provisional; Region: PRK05431 565050005758 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 565050005759 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 bound...; Region: SerRS_core; cd00770 565050005760 dimer interface [polypeptide binding]; other site 565050005761 active site 565050005762 motif 1; other site 565050005763 motif 2; other site 565050005764 motif 3; other site 565050005765 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 565050005766 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 565050005767 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 565050005768 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 565050005769 ScpA/B protein; Region: ScpA_ScpB; cl00598 565050005770 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 565050005771 Sporulation related domain; Region: SPOR; cl10051 565050005772 deoxyguanosinetriphosphate triphosphohydrolase, putative; Region: dGTP_triPase; TIGR01353 565050005773 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 565050005774 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 565050005775 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 565050005776 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 565050005777 putative phosphate binding site [ion binding]; other site 565050005778 putative catalytic site [active] 565050005779 active site 565050005780 metal binding site A [ion binding]; metal-binding site 565050005781 DNA binding site [nucleotide binding] 565050005782 putative AP binding site [nucleotide binding]; other site 565050005783 putative metal binding site B [ion binding]; other site 565050005784 LysE type translocator; Region: LysE; cl00565 565050005785 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4805 565050005786 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 565050005787 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050005788 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 565050005789 Prostaglandin dehydrogenases; Region: PGDH; cd05288 565050005790 NAD(P) binding site [chemical binding]; other site 565050005791 substrate binding site [chemical binding]; other site 565050005792 dimer interface [polypeptide binding]; other site 565050005793 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 565050005794 Membrane glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: MdoH; COG2943 565050005795 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 565050005796 Ligand binding site; other site 565050005797 DXD motif; other site 565050005798 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/unknown domain fusion protein; Provisional; Region: PRK14495 565050005799 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 565050005800 MatE; Region: MatE; cl10513 565050005801 MatE; Region: MatE; cl10513 565050005802 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050005803 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_16; cd07263 565050005804 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 565050005805 Uncharacterized protein conserved in bacteria (DUF2239); Region: DUF2239; cl01461 565050005806 GIY-YIG domain of LuxR and ArsR family transcriptional regulators, and uncharacterized hypothetical proteins found in bacteria; Region: GIY-YIG_LuxR_like; cd10451 565050005807 GIY-YIG motif/motif A; other site 565050005808 outer membrane receptor FepA; Provisional; Region: PRK13524 565050005809 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 565050005810 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 565050005811 Interphotoreceptor retinoid-binding protein; serine protease family S41; Region: Peptidase_S41_IRBP; cd07563 565050005812 active site triad [active] 565050005813 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 565050005814 ThiC-associated domain; Region: ThiC-associated; pfam13667 565050005815 ThiC family; Region: ThiC; cl08031 565050005816 TPR repeat; Region: TPR_11; pfam13414 565050005817 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 565050005818 binding surface 565050005819 TPR motif; other site 565050005820 TPR repeat; Region: TPR_11; pfam13414 565050005821 D-cysteine desulfhydrase; Validated; Region: PRK03910 565050005822 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 565050005823 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 565050005824 catalytic residue [active] 565050005825 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 565050005826 aspartate racemase; Region: asp_race; TIGR00035 565050005827 Pectic acid lyase; Region: Pec_lyase; pfam09492 565050005828 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 565050005829 hydrophobic ligand binding site; other site 565050005830 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 565050005831 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050005832 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 565050005833 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050005834 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 565050005835 Sel1 repeat; Region: Sel1; cl02723 565050005836 Sel1 repeat; Region: Sel1; cl02723 565050005837 Sel1 repeat; Region: Sel1; cl02723 565050005838 Sel1 repeat; Region: Sel1; cl02723 565050005839 Sel1 repeat; Region: Sel1; cl02723 565050005840 DEXH box helicase, DNA ligase-associated; Region: DEXH_lig_assoc; TIGR04121 565050005841 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 565050005842 ATP binding site [chemical binding]; other site 565050005843 putative Mg++ binding site [ion binding]; other site 565050005844 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 565050005845 nucleotide binding region [chemical binding]; other site 565050005846 ATP-binding site [chemical binding]; other site 565050005847 DEAD/H associated; Region: DEAD_assoc; pfam08494 565050005848 Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; Region: MPP_PF1019; cd07391 565050005849 putative active site [active] 565050005850 putative metal binding site [ion binding]; other site 565050005851 Transposase domain (DUF772); Region: DUF772; cl15789 565050005852 Protein of unknown function (DUF3429); Region: DUF3429; pfam11911 565050005853 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 565050005854 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 565050005855 Sel1 repeat; Region: Sel1; cl02723 565050005856 Sel1 repeat; Region: Sel1; cl02723 565050005857 Sel1 repeat; Region: Sel1; cl02723 565050005858 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 565050005859 Uncharacterized conserved protein [Function unknown]; Region: COG2898 565050005860 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 565050005861 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 565050005862 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 565050005863 active site 565050005864 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 565050005865 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 565050005866 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 565050005867 active site 565050005868 pyruvate kinase; Provisional; Region: PRK06247 565050005869 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; cl09155 565050005870 domain interfaces; other site 565050005871 active site 565050005872 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 565050005873 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 565050005874 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 565050005875 Transcriptional regulators [Transcription]; Region: PurR; COG1609 565050005876 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 565050005877 DNA binding site [nucleotide binding] 565050005878 domain linker motif; other site 565050005879 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 565050005880 putative dimerization interface [polypeptide binding]; other site 565050005881 putative ligand binding site [chemical binding]; other site 565050005882 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 565050005883 glucokinase, proteobacterial type; Region: glk; TIGR00749 565050005884 Dehydratase family; Region: ILVD_EDD; cl00340 565050005885 6-phosphogluconate dehydratase; Region: edd; TIGR01196 565050005886 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 565050005887 putative active site [active] 565050005888 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 565050005889 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 565050005890 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 565050005891 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 565050005892 MgtE intracellular N domain; Region: MgtE_N; cl15244 565050005893 flagellar motor switch protein FliM; Reviewed; Region: fliM; PRK12795 565050005894 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 565050005895 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 565050005896 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 565050005897 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 565050005898 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12691 565050005899 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 565050005900 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 565050005901 Flagellar basal body P-ring biosynthesis protein [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]; Region: FlgA; COG1261 565050005902 SAF domain; Region: SAF; cl00555 565050005903 Flagellar L-ring protein; Region: FlgH; cl00905 565050005904 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 565050005905 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 565050005906 TPP-binding site; other site 565050005907 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 565050005908 PYR/PP interface [polypeptide binding]; other site 565050005909 dimer interface [polypeptide binding]; other site 565050005910 TPP binding site [chemical binding]; other site 565050005911 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 565050005912 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 565050005913 substrate binding pocket [chemical binding]; other site 565050005914 chain length determination region; other site 565050005915 substrate-Mg2+ binding site; other site 565050005916 catalytic residues [active] 565050005917 aspartate-rich region 1; other site 565050005918 active site lid residues [active] 565050005919 aspartate-rich region 2; other site 565050005920 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 565050005921 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 565050005922 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 565050005923 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 565050005924 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 565050005925 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 565050005926 Coenzyme A binding pocket [chemical binding]; other site 565050005927 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 565050005928 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 565050005929 non-specific DNA binding site [nucleotide binding]; other site 565050005930 salt bridge; other site 565050005931 sequence-specific DNA binding site [nucleotide binding]; other site 565050005932 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 565050005933 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 565050005934 active site 565050005935 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 565050005936 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050005937 Helix-turn-helix domains; Region: HTH; cl00088 565050005938 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 565050005939 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 565050005940 NAD binding site [chemical binding]; other site 565050005941 Phe binding site; other site 565050005942 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 565050005943 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; cl12031 565050005944 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 565050005945 putative uracil binding site [chemical binding]; other site 565050005946 putative active site [active] 565050005947 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 565050005948 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 565050005949 C-terminal domain interface [polypeptide binding]; other site 565050005950 GSH binding site (G-site) [chemical binding]; other site 565050005951 dimer interface [polypeptide binding]; other site 565050005952 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 565050005953 N-terminal domain interface [polypeptide binding]; other site 565050005954 dimer interface [polypeptide binding]; other site 565050005955 substrate binding pocket (H-site) [chemical binding]; other site 565050005956 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 565050005957 CoenzymeA binding site [chemical binding]; other site 565050005958 subunit interaction site [polypeptide binding]; other site 565050005959 PHB binding site; other site 565050005960 GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing...; Region: GST_N_GTT2_like; cd03051 565050005961 putative C-terminal domain interface [polypeptide binding]; other site 565050005962 putative GSH binding site (G-site) [chemical binding]; other site 565050005963 putative dimer interface [polypeptide binding]; other site 565050005964 C-terminal, alpha helical domain of GTT2-like Glutathione S-transferases; Region: GST_C_GTT2_like; cd03182 565050005965 putative N-terminal domain interface [polypeptide binding]; other site 565050005966 putative dimer interface [polypeptide binding]; other site 565050005967 putative substrate binding pocket (H-site) [chemical binding]; other site 565050005968 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 565050005969 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 565050005970 Nucleoside recognition; Region: Gate; cl00486 565050005971 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 565050005972 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 565050005973 FtsX-like permease family; Region: FtsX; cl15850 565050005974 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 565050005975 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 565050005976 Walker A/P-loop; other site 565050005977 ATP binding site [chemical binding]; other site 565050005978 Q-loop/lid; other site 565050005979 ABC transporter signature motif; other site 565050005980 Walker B; other site 565050005981 D-loop; other site 565050005982 H-loop/switch region; other site 565050005983 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 565050005984 E3 interaction surface; other site 565050005985 lipoyl attachment site [posttranslational modification]; other site 565050005986 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050005987 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 565050005988 (3R)-hydroxyacyl-CoA dehydrogenase-like, classical(c)-like SDRs; Region: hydroxyacyl-CoA-like_DH_SDR_c-like; cd05353 565050005989 NAD binding site [chemical binding]; other site 565050005990 homodimer interface [polypeptide binding]; other site 565050005991 active site 565050005992 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 565050005993 Domain of unknown function DUF59; Region: DUF59; cl00941 565050005994 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 565050005995 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 565050005996 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 565050005997 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050005998 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 565050005999 motif II; other site 565050006000 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 565050006001 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050006002 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 565050006003 motif II; other site 565050006004 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 565050006005 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050006006 Competence-damaged protein; Region: CinA; cl00666 565050006007 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK09107 565050006008 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 565050006009 PYR/PP interface [polypeptide binding]; other site 565050006010 dimer interface [polypeptide binding]; other site 565050006011 TPP binding site [chemical binding]; other site 565050006012 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 565050006013 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 565050006014 TPP-binding site [chemical binding]; other site 565050006015 dimer interface [polypeptide binding]; other site 565050006016 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 565050006017 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 565050006018 putative valine binding site [chemical binding]; other site 565050006019 dimer interface [polypeptide binding]; other site 565050006020 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 565050006021 Stringent starvation protein B; Region: SspB; cl01120 565050006022 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 565050006023 CoenzymeA binding site [chemical binding]; other site 565050006024 subunit interaction site [polypeptide binding]; other site 565050006025 PHB binding site; other site 565050006026 Peptidase C13 family; Region: Peptidase_C13; cl02159 565050006027 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050006028 Endodeoxyribonuclease RusA; Region: RusA; cl01885 565050006029 Protein of unknown function (DUF1697); Region: DUF1697; cl01557 565050006030 fumarate hydratase; Reviewed; Region: fumC; PRK00485 565050006031 Class II fumarases; Region: Fumarase_classII; cd01362 565050006032 active site 565050006033 tetramer interface [polypeptide binding]; other site 565050006034 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050006035 hypothetical protein; Provisional; Region: PRK11770 565050006036 Domain of unknown function (DUF307); Region: DUF307; pfam03733 565050006037 Domain of unknown function (DUF307); Region: DUF307; pfam03733 565050006038 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 565050006039 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 565050006040 substrate binding pocket [chemical binding]; other site 565050006041 chain length determination region; other site 565050006042 substrate-Mg2+ binding site; other site 565050006043 catalytic residues [active] 565050006044 aspartate-rich region 1; other site 565050006045 active site lid residues [active] 565050006046 aspartate-rich region 2; other site 565050006047 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 565050006048 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006049 Cytochrome c; Region: Cytochrom_C; cl11414 565050006050 TIR domain; Region: TIR_2; cl15770 565050006051 Uncharacterized protein with SCP/PR1 domains [Function unknown]; Region: COG2340 565050006052 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 565050006053 YceI-like domain; Region: YceI; cl01001 565050006054 ketol-acid reductoisomerase; Provisional; Region: PRK05479 565050006055 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006056 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 565050006057 Domain of unknown function (DUF3315); Region: DUF3315; cl02275 565050006058 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 565050006059 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 565050006060 dimerization interface [polypeptide binding]; other site 565050006061 active site 565050006062 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR8; cd08273 565050006063 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 565050006064 putative NAD(P) binding site [chemical binding]; other site 565050006065 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 565050006066 folate binding site [chemical binding]; other site 565050006067 NADP+ binding site [chemical binding]; other site 565050006068 Protein of unknown function (DUF3667); Region: DUF3667; pfam12412 565050006069 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 565050006070 Old yellow enzyme (OYE)-related FMN binding domain, group 5. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_5_FMN; cd04747 565050006071 putative active site [active] 565050006072 putative FMN binding site [chemical binding]; other site 565050006073 putative substrate binding site [chemical binding]; other site 565050006074 putative catalytic residue [active] 565050006075 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 565050006076 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 565050006077 active site 565050006078 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 565050006079 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 565050006080 DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]; Region: DjlA; COG1076 565050006081 putative metal binding site [ion binding]; other site 565050006082 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 565050006083 HSP70 interaction site [polypeptide binding]; other site 565050006084 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 565050006085 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Region: MetH; COG1410 565050006086 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 565050006087 substrate binding pocket [chemical binding]; other site 565050006088 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 565050006089 B12 binding site [chemical binding]; other site 565050006090 cobalt ligand [ion binding]; other site 565050006091 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 565050006092 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 565050006093 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 565050006094 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 565050006095 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 565050006096 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 565050006097 FAD binding site [chemical binding]; other site 565050006098 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 565050006099 dimerization interface [polypeptide binding]; other site 565050006100 putative DNA binding site [nucleotide binding]; other site 565050006101 putative Zn2+ binding site [ion binding]; other site 565050006102 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 565050006103 S-adenosylmethionine binding site [chemical binding]; other site 565050006104 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 565050006105 active site 565050006106 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050006107 metal binding site [ion binding]; metal-binding site 565050006108 Transcriptional regulator [Transcription]; Region: LysR; COG0583 565050006109 Helix-turn-helix domains; Region: HTH; cl00088 565050006110 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 565050006111 substrate binding pocket [chemical binding]; other site 565050006112 dimerization interface [polypeptide binding]; other site 565050006113 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 565050006114 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 565050006115 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006116 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 565050006117 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 565050006118 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050006119 Walker A/P-loop; other site 565050006120 ATP binding site [chemical binding]; other site 565050006121 Q-loop/lid; other site 565050006122 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 565050006123 ABC transporter signature motif; other site 565050006124 Walker B; other site 565050006125 D-loop; other site 565050006126 ABC transporter; Region: ABC_tran_2; pfam12848 565050006127 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 565050006128 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050006129 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 565050006130 N-terminal plug; other site 565050006131 ligand-binding site [chemical binding]; other site 565050006132 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 565050006133 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 565050006134 Catalytic site [active] 565050006135 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 565050006136 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; cl08302 565050006137 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 565050006138 active site 565050006139 catalytic triad [active] 565050006140 oxyanion hole [active] 565050006141 Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases; Region: CE4_NodB_like_1; cd10960 565050006142 NodB motif; other site 565050006143 putative active site [active] 565050006144 putative catalytic site [active] 565050006145 putative Zn binding site [ion binding]; other site 565050006146 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 565050006147 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; cl12031 565050006148 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050006149 Protein of unknown function, DUF482; Region: DUF482; pfam04339 565050006150 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases; Region: GDPD_like_3; cd08585 565050006151 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 565050006152 putative active site [active] 565050006153 catalytic site [active] 565050006154 putative metal binding site [ion binding]; other site 565050006155 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 565050006156 homotrimer interaction site [polypeptide binding]; other site 565050006157 putative active site [active] 565050006158 Phasin protein; Region: Phasin_2; cl11491 565050006159 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 565050006160 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050006161 Sporulation related domain; Region: SPOR; cl10051 565050006162 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 565050006163 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 565050006164 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050006165 homodimer interface [polypeptide binding]; other site 565050006166 catalytic residue [active] 565050006167 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 565050006168 HSP70 interaction site [polypeptide binding]; other site 565050006169 ATPase MipZ; Region: MipZ; pfam09140 565050006170 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 565050006171 P-loop; other site 565050006172 Magnesium ion binding site [ion binding]; other site 565050006173 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 565050006174 Magnesium ion binding site [ion binding]; other site 565050006175 Pantoate-beta-alanine ligase; Region: PanC; cd00560 565050006176 pantoate--beta-alanine ligase; Region: panC; TIGR00018 565050006177 active site 565050006178 ATP-binding site [chemical binding]; other site 565050006179 pantoate-binding site; other site 565050006180 HXXH motif; other site 565050006181 Protein of unknown function (DUF1489); Region: DUF1489; cl11570 565050006182 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 565050006183 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 565050006184 ATP-grasp domain; Region: ATP-grasp_4; cl03087 565050006185 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 565050006186 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 565050006187 carboxyltransferase (CT) interaction site; other site 565050006188 biotinylation site [posttranslational modification]; other site 565050006189 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 565050006190 enoyl-CoA hydratase; Provisional; Region: PRK05995 565050006191 substrate binding site [chemical binding]; other site 565050006192 oxyanion hole (OAH) forming residues; other site 565050006193 trimer interface [polypeptide binding]; other site 565050006194 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 565050006195 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 565050006196 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 565050006197 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 565050006198 ligand binding site [chemical binding]; other site 565050006199 flexible hinge region; other site 565050006200 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 565050006201 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 565050006202 active site 565050006203 nucleophile elbow; other site 565050006204 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 565050006205 isovaleryl-CoA dehydrogenase; Region: PLN02519 565050006206 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 565050006207 active site 565050006208 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 565050006209 catalytic residues [active] 565050006210 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 565050006211 MgtE intracellular N domain; Region: MgtE_N; cl15244 565050006212 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 565050006213 Divalent cation transporter; Region: MgtE; cl00786 565050006214 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 565050006215 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 565050006216 Protein of unknown function (DUF805); Region: DUF805; cl01224 565050006217 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 565050006218 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 565050006219 ATP-grasp domain; Region: ATP-grasp_4; cl03087 565050006220 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 565050006221 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 565050006222 carboxyltransferase (CT) interaction site; other site 565050006223 biotinylation site [posttranslational modification]; other site 565050006224 Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of...; Region: LamG; cl00102 565050006225 Domain of unknown function (DUF336); Region: DUF336; cl01249 565050006226 DJ-1 family protein; Region: not_thiJ; TIGR01383 565050006227 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_3; cd03140 565050006228 conserved cys residue [active] 565050006229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 565050006230 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 565050006231 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 565050006232 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 565050006233 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; cl12031 565050006234 Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of...; Region: LamG; cl00102 565050006235 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of...; Region: nylC_like; cd02252 565050006236 putative active site pocket [active] 565050006237 DmpA/OAT superfamily; composed of L-aminopeptidase D-amidase/D-esterase (DmpA), ornithine acetyltransferase (OAT) and similar proteins. DmpA is an aminopeptidase that releases N-terminal D and L amino acids from peptide substrates. This group represents...; Region: DmpA_OAT; cl00603 565050006238 Transcriptional regulators [Transcription]; Region: MarR; COG1846 565050006239 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 565050006240 transaldolase/EF-hand domain-containing protein; Provisional; Region: PRK12309 565050006241 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 565050006242 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 565050006243 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 565050006244 N-terminal plug; other site 565050006245 ligand-binding site [chemical binding]; other site 565050006246 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 565050006247 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 565050006248 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 565050006249 diiron binding motif [ion binding]; other site 565050006250 Peptidase M1 family Aminopeptidase N; Region: M1_APN_4; cd09603 565050006251 Peptidase family M1; Region: Peptidase_M1; pfam01433 565050006252 Zn binding site [ion binding]; other site 565050006253 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 565050006254 active site 565050006255 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 565050006256 minor groove reading motif; other site 565050006257 helix-hairpin-helix signature motif; other site 565050006258 substrate binding pocket [chemical binding]; other site 565050006259 active site 565050006260 transcription elongation factor regulatory protein; Validated; Region: PRK06342 565050006261 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 565050006262 Helix-turn-helix domains; Region: HTH; cl00088 565050006263 WHG domain; Region: WHG; pfam13305 565050006264 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 565050006265 active site 565050006266 HIGH motif; other site 565050006267 nucleotide binding site [chemical binding]; other site 565050006268 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 565050006269 active site 565050006270 KMSKS motif; other site 565050006271 Helix-turn-helix domains; Region: HTH; cl00088 565050006272 Acyltransferase family; Region: Acyl_transf_3; pfam01757 565050006273 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 565050006274 catalytic residues [active] 565050006275 argininosuccinate lyase; Provisional; Region: PRK00855 565050006276 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 565050006277 active sites [active] 565050006278 tetramer interface [polypeptide binding]; other site 565050006279 diaminopimelate decarboxylase; Region: lysA; TIGR01048 565050006280 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 565050006281 active site 565050006282 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 565050006283 substrate binding site [chemical binding]; other site 565050006284 catalytic residues [active] 565050006285 dimer interface [polypeptide binding]; other site 565050006286 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 565050006287 active site 565050006288 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 565050006289 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 565050006290 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 565050006291 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 565050006292 Walker A/P-loop; other site 565050006293 ATP binding site [chemical binding]; other site 565050006294 Q-loop/lid; other site 565050006295 ABC transporter signature motif; other site 565050006296 Walker B; other site 565050006297 D-loop; other site 565050006298 H-loop/switch region; other site 565050006299 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 565050006300 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 565050006301 putative active site [active] 565050006302 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 565050006303 putative acyl-acceptor binding pocket; other site 565050006304 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 565050006305 putative active site pocket [active] 565050006306 dimerization interface [polypeptide binding]; other site 565050006307 putative catalytic residue [active] 565050006308 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4093 565050006309 Uncharacterized protein conserved in bacteria (DUF2125); Region: DUF2125; pfam09898 565050006310 hypothetical protein; Provisional; Region: PRK06034 565050006311 Chorismate mutase type II; Region: CM_2; cl00693 565050006312 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 565050006313 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 565050006314 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050006315 homodimer interface [polypeptide binding]; other site 565050006316 catalytic residue [active] 565050006317 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 565050006318 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006319 transaldolase/EF-hand domain-containing protein; Provisional; Region: PRK12309 565050006320 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; cl08302 565050006321 N-terminal Early set domain associated with the catalytic domain of cellulase; Region: E_set_Cellulase_N; cd02850 565050006322 Glycosyl hydrolase family 9; Region: Glyco_hydro_9; cl02959 565050006323 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3735 565050006324 TraB family; Region: TraB; cl12050 565050006325 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050006326 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 565050006327 non-specific DNA binding site [nucleotide binding]; other site 565050006328 salt bridge; other site 565050006329 sequence-specific DNA binding site [nucleotide binding]; other site 565050006330 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 565050006331 trimer interface [polypeptide binding]; other site 565050006332 active site 565050006333 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 565050006334 O-succinylhomoserine sulfhydrylase; Region: O_suc_HS_sulf; TIGR01325 565050006335 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 565050006336 homodimer interface [polypeptide binding]; other site 565050006337 substrate-cofactor binding pocket; other site 565050006338 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050006339 catalytic residue [active] 565050006340 Protein of unknown function (DUF525); Region: DUF525; cl01119 565050006341 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]; Region: COG1281 565050006342 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 565050006343 dimerization interface [polypeptide binding]; other site 565050006344 domain crossover interface; other site 565050006345 redox-dependent activation switch; other site 565050006346 ornithine carbamoyltransferase; Provisional; Region: PRK00779 565050006347 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 565050006348 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006349 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 565050006350 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 565050006351 inhibitor-cofactor binding pocket; inhibition site 565050006352 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050006353 catalytic residue [active] 565050006354 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 565050006355 ABC-2 type transporter; Region: ABC2_membrane; cl11417 565050006356 ABC-2 type transporter; Region: ABC2_membrane; cl11417 565050006357 GcrA cell cycle regulator; Region: GcrA; cl11564 565050006358 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 565050006359 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 565050006360 generic binding surface II; other site 565050006361 generic binding surface I; other site 565050006362 Uncharacterized protein conserved in bacteria (DUF2093); Region: DUF2093; cl11535 565050006363 Peptidase family M23; Region: Peptidase_M23; pfam01551 565050006364 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 565050006365 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 565050006366 active site 565050006367 phosphorylation site [posttranslational modification] 565050006368 intermolecular recognition site; other site 565050006369 dimerization interface [polypeptide binding]; other site 565050006370 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 565050006371 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 565050006372 putative acyl-acceptor binding pocket; other site 565050006373 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050006374 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 565050006375 active site 565050006376 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 565050006377 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; cl12031 565050006378 SCP-2 sterol transfer family; Region: SCP2; cl01225 565050006379 Protein of unknown function (DUF2987); Region: DUF2987; pfam11205 565050006380 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006381 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006382 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 565050006383 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 565050006384 putative dimer interface [polypeptide binding]; other site 565050006385 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 565050006386 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050006387 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 565050006388 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050006389 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050006390 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050006391 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050006392 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 565050006393 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050006394 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050006395 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 565050006396 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050006397 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050006398 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 565050006399 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 565050006400 catalytic core [active] 565050006401 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 565050006402 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 565050006403 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 565050006404 putative active site [active] 565050006405 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 565050006406 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 565050006407 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 565050006408 active site 565050006409 substrate binding site [chemical binding]; other site 565050006410 metal binding site [ion binding]; metal-binding site 565050006411 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050006412 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 565050006413 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 565050006414 Stress responsive A/B Barrel Domain; Region: Dabb; cl15807 565050006415 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 565050006416 active site 565050006417 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 565050006418 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 565050006419 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 565050006420 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 565050006421 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 565050006422 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 565050006423 catalytic loop [active] 565050006424 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 565050006425 iron binding site [ion binding]; other site 565050006426 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 565050006427 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 565050006428 nudix motif; other site 565050006429 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 565050006430 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 565050006431 minor groove reading motif; other site 565050006432 helix-hairpin-helix signature motif; other site 565050006433 substrate binding pocket [chemical binding]; other site 565050006434 active site 565050006435 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 565050006436 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 565050006437 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 565050006438 tetrameric interface [polypeptide binding]; other site 565050006439 NAD binding site [chemical binding]; other site 565050006440 catalytic residues [active] 565050006441 Flavin Reductases; Region: FlaRed; cl00801 565050006442 mycofactocin system glycosyltransferase; Region: actino_glycTran; TIGR03965 565050006443 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 565050006444 active site 565050006445 Protein involved in cellulose biosynthesis (CelD) [Cell envelope biogenesis, outer membrane]; Region: COG5653 565050006446 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050006447 GAF domain; Region: GAF; cl15785 565050006448 Cache domain; Region: Cache_1; pfam02743 565050006449 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 565050006450 dimerization interface [polypeptide binding]; other site 565050006451 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050006452 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050006453 dimer interface [polypeptide binding]; other site 565050006454 putative CheW interface [polypeptide binding]; other site 565050006455 Glycoside hydrolase family 15, N-terminal domain; Region: GH15_N; cd07430 565050006456 Domain interface; other site 565050006457 glucan 1,4-alpha-glucosidase; Region: glucan_glucosid; TIGR01535 565050006458 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 565050006459 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 565050006460 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 565050006461 Transcriptional regulators [Transcription]; Region: PurR; COG1609 565050006462 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 565050006463 DNA binding site [nucleotide binding] 565050006464 Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators; Region: PBP1_CelR; cd06295 565050006465 putative dimerization interface [polypeptide binding]; other site 565050006466 putative ligand binding site [chemical binding]; other site 565050006467 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 565050006468 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 565050006469 active site 565050006470 catalytic site [active] 565050006471 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 565050006472 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 565050006473 active site 565050006474 catalytic site [active] 565050006475 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050006476 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; cl00284 565050006477 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 565050006478 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006479 insertion element IS2 transposase InsD; Provisional; Region: PRK14702 565050006480 HTH-like domain; Region: HTH_21; pfam13276 565050006481 Integrase core domain; Region: rve; cl01316 565050006482 Integrase core domain; Region: rve_3; cl15866 565050006483 Helix-turn-helix domains; Region: HTH; cl00088 565050006484 Protein of unknown function (DUF541); Region: SIMPL; cl01077 565050006485 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 565050006486 tetramerization interface [polypeptide binding]; other site 565050006487 active site 565050006488 Peptidase family M23; Region: Peptidase_M23; pfam01551 565050006489 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; cl12031 565050006490 substrate binding pocket [chemical binding]; other site 565050006491 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; cl12031 565050006492 long-chain-acyl-CoA synthetase; Validated; Region: PRK08279 565050006493 AMP-binding enzyme; Region: AMP-binding; cl15778 565050006494 Class-II DAHP synthetase family; Region: DAHP_synth_2; cl03230 565050006495 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 565050006496 glutathione-disulfide reductase, plant; Region: gluta_reduc_2; TIGR01424 565050006497 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 565050006498 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 565050006499 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 565050006500 tetramer (dimer of dimers) interface [polypeptide binding]; other site 565050006501 active site 565050006502 dimer interface [polypeptide binding]; other site 565050006503 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14353 565050006504 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 565050006505 Substrate binding site; other site 565050006506 Mg++ binding site; other site 565050006507 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 565050006508 active site 565050006509 substrate binding site [chemical binding]; other site 565050006510 CoA binding site [chemical binding]; other site 565050006511 phosphoglycolate phosphatase; Provisional; Region: PRK13222 565050006512 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 565050006513 motif II; other site 565050006514 short chain dehydrogenase; Provisional; Region: PRK07825 565050006515 classical (c) SDR, subgroup 7; Region: SDR_c7; cd05354 565050006516 putative NAD(P) binding site [chemical binding]; other site 565050006517 active site 565050006518 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 565050006519 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 565050006520 putative C-terminal domain interface [polypeptide binding]; other site 565050006521 putative GSH binding site (G-site) [chemical binding]; other site 565050006522 putative dimer interface [polypeptide binding]; other site 565050006523 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 565050006524 putative substrate binding pocket (H-site) [chemical binding]; other site 565050006525 N-terminal domain interface [polypeptide binding]; other site 565050006526 dimer interface [polypeptide binding]; other site 565050006527 GST_N family, Metaxin subfamily, Metaxin-like proteins; a heterogenous group of proteins, predominantly uncharacterized, with similarity to metaxins and GSTs. Metaxin 1 is a component of a preprotein import complex of the mitochondrial outer membrane. It...; Region: GST_N_Metaxin_like; cd03080 565050006528 putative C-terminal domain interface [polypeptide binding]; other site 565050006529 putative GSH binding site [chemical binding]; other site 565050006530 putative dimer interface [polypeptide binding]; other site 565050006531 C-terminal, alpha helical domain of Metaxin and related proteins; Region: GST_C_Metaxin; cd03193 565050006532 putative N-terminal domain interface [polypeptide binding]; other site 565050006533 Helix-turn-helix domains; Region: HTH; cl00088 565050006534 WYL domain; Region: WYL; cl14852 565050006535 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 565050006536 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; cl12031 565050006537 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 565050006538 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 565050006539 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 565050006540 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 565050006541 putative substrate translocation pore; other site 565050006542 Transcriptional regulators [Transcription]; Region: PurR; COG1609 565050006543 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 565050006544 DNA binding site [nucleotide binding] 565050006545 domain linker motif; other site 565050006546 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 565050006547 putative dimerization interface [polypeptide binding]; other site 565050006548 putative ligand binding site [chemical binding]; other site 565050006549 Globin domain present in Globin-Coupled-Sensors (GCS). These domains detect changes in intracellular concentrations of oxygen, carbon monoxyde, or nitrous oxide, which result in aerotaxis and/or gene regulation. One subgroup, the HemATs, are aerotactic...; Region: sensor_globin; cd01068 565050006550 heme-binding site [chemical binding]; other site 565050006551 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050006552 dimer interface [polypeptide binding]; other site 565050006553 putative CheW interface [polypeptide binding]; other site 565050006554 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 565050006555 anti sigma factor interaction site; other site 565050006556 regulatory phosphorylation site [posttranslational modification]; other site 565050006557 Permease; Region: Permease; cl00510 565050006558 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 565050006559 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 565050006560 Walker A/P-loop; other site 565050006561 ATP binding site [chemical binding]; other site 565050006562 Q-loop/lid; other site 565050006563 ABC transporter signature motif; other site 565050006564 Walker B; other site 565050006565 D-loop; other site 565050006566 H-loop/switch region; other site 565050006567 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 565050006568 mce related protein; Region: MCE; pfam02470 565050006569 Protein of unknown function (DUF330); Region: DUF330; cl01135 565050006570 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 565050006571 nudix motif; other site 565050006572 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; cl15419 565050006573 aerobic respiration control sensor protein ArcB; Provisional; Region: PRK11091 565050006574 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 565050006575 ATP binding site [chemical binding]; other site 565050006576 Mg2+ binding site [ion binding]; other site 565050006577 G-X-G motif; other site 565050006578 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 565050006579 active site 565050006580 phosphorylation site [posttranslational modification] 565050006581 intermolecular recognition site; other site 565050006582 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 565050006583 CoA-transferase family III; Region: CoA_transf_3; pfam02515 565050006584 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 565050006585 Gram-negative bacterial tonB protein; Region: TonB; cl10048 565050006586 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 565050006587 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 565050006588 active site 565050006589 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 565050006590 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 565050006591 non-specific DNA binding site [nucleotide binding]; other site 565050006592 salt bridge; other site 565050006593 sequence-specific DNA binding site [nucleotide binding]; other site 565050006594 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 565050006595 IHF - DNA interface [nucleotide binding]; other site 565050006596 IHF dimer interface [polypeptide binding]; other site 565050006597 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]; Region: COG4277 565050006598 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 565050006599 FeS/SAM binding site; other site 565050006600 Domain of unknown function (DUF4130; Region: DUF4130; cl14836 565050006601 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 565050006602 Fe-S cluster binding site [ion binding]; other site 565050006603 active site 565050006604 Gram-negative bacterial tonB protein; Region: TonB; cl10048 565050006605 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 565050006606 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 565050006607 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 565050006608 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006609 NAD(P) binding site [chemical binding]; other site 565050006610 active site 565050006611 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; cl01930 565050006612 Helix-turn-helix domains; Region: HTH; cl00088 565050006613 WHG domain; Region: WHG; pfam13305 565050006614 Domain of unknown function (DUF329); Region: DUF329; cl01144 565050006615 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 565050006616 Maf-like protein; Region: Maf; pfam02545 565050006617 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 565050006618 active site 565050006619 dimer interface [polypeptide binding]; other site 565050006620 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 565050006621 rRNA binding site [nucleotide binding]; other site 565050006622 predicted 30S ribosome binding site; other site 565050006623 Low molecular weight phosphatase family; Region: LMWPc; cd00115 565050006624 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 565050006625 active site 565050006626 Uncharacterized protein family (UPF0262); Region: UPF0262; cl11489 565050006627 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 565050006628 histidinol dehydrogenase; Region: hisD; TIGR00069 565050006629 NAD binding site [chemical binding]; other site 565050006630 dimerization interface [polypeptide binding]; other site 565050006631 product binding site; other site 565050006632 substrate binding site [chemical binding]; other site 565050006633 zinc binding site [ion binding]; other site 565050006634 catalytic residues [active] 565050006635 Sodium:solute symporter family; Region: SSF; cl00456 565050006636 Protein of unknown function (DUF2948); Region: DUF2948; pfam11164 565050006637 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 565050006638 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 565050006639 hinge; other site 565050006640 active site 565050006641 Transcriptional regulator [Transcription]; Region: LysR; COG0583 565050006642 Helix-turn-helix domains; Region: HTH; cl00088 565050006643 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 565050006644 dimerization interface [polypeptide binding]; other site 565050006645 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 565050006646 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR1; cd08267 565050006647 putative NAD(P) binding site [chemical binding]; other site 565050006648 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 565050006649 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 565050006650 putative substrate translocation pore; other site 565050006651 Transcriptional regulators [Transcription]; Region: PurR; COG1609 565050006652 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 565050006653 DNA binding site [nucleotide binding] 565050006654 domain linker motif; other site 565050006655 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 565050006656 putative dimerization interface [polypeptide binding]; other site 565050006657 putative ligand binding site [chemical binding]; other site 565050006658 Helix-turn-helix domains; Region: HTH; cl00088 565050006659 DNA binding residues [nucleotide binding] 565050006660 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; cl15381 565050006661 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 565050006662 Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoproteins. This enzyme is an amidase located inside lysosomes. Mutation of this gene in humans causes a genetic disorder known as aspartylglycosaminuria (AGU)...; Region: Glycosylasparaginase; cd04513 565050006663 active site 565050006664 dimer interface [polypeptide binding]; other site 565050006665 catalytic nucleophile [active] 565050006666 CutC family; Region: CutC; cl01218 565050006667 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl00503 565050006668 PspA/IM30 family; Region: PspA_IM30; pfam04012 565050006669 Uncharacterized protein conserved in bacteria (DUF2170); Region: DUF2170; cl01551 565050006670 Protein of unknown function (DUF2491); Region: DUF2491; pfam10679 565050006671 Predicted membrane protein [Function unknown]; Region: COG3766 565050006672 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 565050006673 Protein of unknown function (DUF1190); Region: DUF1190; cl10031 565050006674 Low molecular weight phosphatase family; Region: LMWPc; cd00115 565050006675 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 565050006676 active site 565050006677 5-oxoprolinase; Region: PLN02666 565050006678 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 565050006679 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; cl00668 565050006680 Predicted membrane protein [Function unknown]; Region: COG2119 565050006681 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 565050006682 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 565050006683 Protein of unknown function (DUF2793); Region: DUF2793; pfam10983 565050006684 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 565050006685 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 565050006686 FMN binding site [chemical binding]; other site 565050006687 substrate binding site [chemical binding]; other site 565050006688 putative catalytic residue [active] 565050006689 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Beta subunit-like subfamily; contains bacterial proteins similar to the beta subunit of MCMs from Propionbacterium shermanni and Streptomyces cinnamonensis, which are alpha/beta...; Region: MM_CoA_mutase_beta; cd03677 565050006690 heterodimer interface [polypeptide binding]; other site 565050006691 substrate interaction site [chemical binding]; other site 565050006692 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 565050006693 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 565050006694 active site 565050006695 substrate binding site [chemical binding]; other site 565050006696 coenzyme B12 binding site [chemical binding]; other site 565050006697 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 565050006698 B12 binding site [chemical binding]; other site 565050006699 cobalt ligand [ion binding]; other site 565050006700 Domain of unknown function (DUF4112); Region: DUF4112; pfam13430 565050006701 Domain of unknown function (DUF4112); Region: DUF4112; pfam13430 565050006702 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 565050006703 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 565050006704 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006705 NAD(P) binding site [chemical binding]; other site 565050006706 active site 565050006707 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 565050006708 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006709 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 565050006710 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006711 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 565050006712 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006713 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 565050006714 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006715 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 565050006716 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 565050006717 NAD binding site [chemical binding]; other site 565050006718 homodimer interface [polypeptide binding]; other site 565050006719 active site 565050006720 substrate binding site [chemical binding]; other site 565050006721 Bacterial sugar transferase; Region: Bac_transf; cl00939 565050006722 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 565050006723 HipA-like C-terminal domain; Region: HipA_C; pfam07804 565050006724 Outer membrane efflux protein; Region: OEP; pfam02321 565050006725 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 565050006726 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050006727 lipoyl-biotinyl attachment site [posttranslational modification]; other site 565050006728 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050006729 heavy metal efflux pump (cobalt-zinc-cadmium); Region: 2A0601; TIGR00914 565050006730 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 565050006731 Helix-turn-helix domains; Region: HTH; cl00088 565050006732 Transcriptional regulators [Transcription]; Region: FadR; COG2186 565050006733 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050006734 DNA-binding site [nucleotide binding]; DNA binding site 565050006735 FCD domain; Region: FCD; cl11656 565050006736 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 565050006737 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 565050006738 iron-sulfur cluster [ion binding]; other site 565050006739 [2Fe-2S] cluster binding site [ion binding]; other site 565050006740 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 565050006741 alpha subunit interface [polypeptide binding]; other site 565050006742 active site 565050006743 substrate binding site [chemical binding]; other site 565050006744 Fe binding site [ion binding]; other site 565050006745 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 565050006746 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 565050006747 FMN-binding pocket [chemical binding]; other site 565050006748 flavin binding motif; other site 565050006749 phosphate binding motif [ion binding]; other site 565050006750 beta-alpha-beta structure motif; other site 565050006751 NAD binding pocket [chemical binding]; other site 565050006752 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 565050006753 catalytic loop [active] 565050006754 iron binding site [ion binding]; other site 565050006755 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional; Region: PRK14875 565050006756 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; cl12031 565050006757 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 565050006758 Benzyl alcohol dehydrogenase; Region: benzyl_alcohol_DH; cd08278 565050006759 catalytic Zn binding site [ion binding]; other site 565050006760 NAD binding site [chemical binding]; other site 565050006761 structural Zn binding site [ion binding]; other site 565050006762 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 565050006763 NAD-dependent benzaldehyde dehydrogenase II-like; Region: ALDH_BenzADH; cd07152 565050006764 NAD(P) binding site [chemical binding]; other site 565050006765 catalytic residues [active] 565050006766 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050006767 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; cl00284 565050006768 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; cl00284 565050006769 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 565050006770 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 565050006771 acyl-CoA synthetase; Validated; Region: PRK09088 565050006772 AMP-binding enzyme; Region: AMP-binding; cl15778 565050006773 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 565050006774 p-hydroxycinnamoyl CoA hydratase/lyase; Validated; Region: PRK09120 565050006775 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 565050006776 substrate binding site [chemical binding]; other site 565050006777 oxyanion hole (OAH) forming residues; other site 565050006778 trimer interface [polypeptide binding]; other site 565050006779 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 565050006780 Salicylaldehyde dehydrogenase, DoxF-like; Region: ALDH_SaliADH; cd07105 565050006781 NAD(P) binding site [chemical binding]; other site 565050006782 catalytic residues [active] 565050006783 4-hydroxyphenylacetate catabolism regulatory protein HpaA; Region: HpaA; TIGR02297 565050006784 Cupin domain; Region: Cupin_2; cl09118 565050006785 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 565050006786 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006787 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 565050006788 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006789 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 565050006790 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 565050006791 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 565050006792 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 565050006793 dimer interface [polypeptide binding]; other site 565050006794 active site 565050006795 Protocatechuate 3,4-dioxygenase (3,4-PCD) , beta subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and...; Region: 3,4-PCD_beta; cd03464 565050006796 multimer interface [polypeptide binding]; other site 565050006797 heterodimer interface [polypeptide binding]; other site 565050006798 protocatechuate 3,4-dioxygenase, beta subunit; Region: protocat_beta; TIGR02422 565050006799 active site 565050006800 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 565050006801 Protocatechuate 3,4-dioxygenase (3,4-PCD) , alpha subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and...; Region: 3,4-PCD_alpha; cd03463 565050006802 heterodimer interface [polypeptide binding]; other site 565050006803 active site 565050006804 prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like; Region: pCLME; cd01597 565050006805 Lyase; Region: Lyase_1; pfam00206 565050006806 tetramer interface [polypeptide binding]; other site 565050006807 active site 565050006808 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 565050006809 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; cl12031 565050006810 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 565050006811 putative 3-hydroxyphenylpropionic transporter MhpT; Provisional; Region: PRK11551 565050006812 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 565050006813 putative substrate translocation pore; other site 565050006814 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4102 565050006815 Protein of unknown function (DUF1501); Region: DUF1501; pfam07394 565050006816 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5267 565050006817 Protein of unknown function (DUF1800); Region: DUF1800; pfam08811 565050006818 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 catalyze...; Region: LT_GEWL; cd00254 565050006819 N-acetyl-D-glucosamine binding site [chemical binding]; other site 565050006820 catalytic residue [active] 565050006821 TrbC/VIRB2 family; Region: TrbC; cl01583 565050006822 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 565050006823 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]; Region: VirB4; COG3451 565050006824 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 565050006825 Galactosyltransferase; Region: Galactosyl_T; cl09537 565050006826 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 565050006827 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 565050006828 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 565050006829 VirB7 interaction site; other site 565050006830 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 565050006831 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 565050006832 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 565050006833 Walker A motif; other site 565050006834 hexamer interface [polypeptide binding]; other site 565050006835 ATP binding site [chemical binding]; other site 565050006836 Walker B motif; other site 565050006837 Domain of unknown function (DUF4102); Region: DUF4102; pfam13356 565050006838 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006839 Bacterial sugar transferase; Region: Bac_transf; cl00939 565050006840 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 565050006841 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 565050006842 Putative catalytic NodB homology domain of gellan lyase and similar proteins; Region: CE4_GLA_like_6s; cd10967 565050006843 putative active site [active] 565050006844 putative metal binding site [ion binding]; other site 565050006845 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 565050006846 O-Antigen ligase; Region: Wzy_C; cl04850 565050006847 capsular exopolysaccharide family; Region: eps_fam; TIGR01007 565050006848 Chain length determinant protein; Region: Wzz; cl15801 565050006849 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 565050006850 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 565050006851 SLBB domain; Region: SLBB; pfam10531 565050006852 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 565050006853 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 565050006854 C-terminal domain interface [polypeptide binding]; other site 565050006855 GSH binding site (G-site) [chemical binding]; other site 565050006856 dimer interface [polypeptide binding]; other site 565050006857 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 565050006858 N-terminal domain interface [polypeptide binding]; other site 565050006859 putative dimer interface [polypeptide binding]; other site 565050006860 active site 565050006861 Domain of unknown function (DUF3315); Region: DUF3315; cl02275 565050006862 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 565050006863 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 565050006864 GatB domain; Region: GatB_Yqey; cl11497 565050006865 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 565050006866 Amidase; Region: Amidase; cl11426 565050006867 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 565050006868 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 includes...; Region: RuvC_resolvase; cl00243 565050006869 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 565050006870 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 565050006871 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050006872 dihydroorotase; Validated; Region: PRK09059 565050006873 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 565050006874 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 565050006875 active site 565050006876 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 565050006877 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 565050006878 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 565050006879 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 565050006880 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 565050006881 S-adenosylmethionine binding site [chemical binding]; other site 565050006882 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 565050006883 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 565050006884 active site 565050006885 interdomain interaction site; other site 565050006886 putative metal-binding site [ion binding]; other site 565050006887 nucleotide binding site [chemical binding]; other site 565050006888 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 565050006889 domain I; other site 565050006890 DNA binding groove [nucleotide binding] 565050006891 phosphate binding site [ion binding]; other site 565050006892 domain II; other site 565050006893 domain III; other site 565050006894 nucleotide binding site [chemical binding]; other site 565050006895 catalytic site [active] 565050006896 domain IV; other site 565050006897 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 565050006898 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 565050006899 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 565050006900 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 565050006901 ribonuclease R; Region: RNase_R; TIGR02063 565050006902 RNB domain; Region: RNB; pfam00773 565050006903 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 play an important...; Region: S1_RNase_R; cd04471 565050006904 RNA binding site [nucleotide binding]; other site 565050006905 Endoglucanase E-like members of the SGNH hydrolase family; Endoglucanase E catalyzes the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans; Region: Endoglucanase_E_like; cd01831 565050006906 catalytic triad [active] 565050006907 active site 565050006908 oxyanion hole [active] 565050006909 aspartate aminotransferase; Provisional; Region: PRK05764 565050006910 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 565050006911 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050006912 homodimer interface [polypeptide binding]; other site 565050006913 catalytic residue [active] 565050006914 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 565050006915 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like2; cd05667 565050006916 metal binding site [ion binding]; metal-binding site 565050006917 putative dimer interface [polypeptide binding]; other site 565050006918 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 565050006919 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 565050006920 Uncharacterized proteins of the AP superfamily [General function prediction only]; Region: COG1524 565050006921 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 565050006922 Sulfatase; Region: Sulfatase; cl10460 565050006923 Sulfatase; Region: Sulfatase; cl10460 565050006924 response regulator PleD; Reviewed; Region: pleD; PRK09581 565050006925 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 565050006926 active site 565050006927 phosphorylation site [posttranslational modification] 565050006928 intermolecular recognition site; other site 565050006929 dimerization interface [polypeptide binding]; other site 565050006930 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 565050006931 active site 565050006932 phosphorylation site [posttranslational modification] 565050006933 intermolecular recognition site; other site 565050006934 dimerization interface [polypeptide binding]; other site 565050006935 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 565050006936 metal binding site [ion binding]; metal-binding site 565050006937 active site 565050006938 I-site; other site 565050006939 Response regulator receiver domain; Region: Response_reg; pfam00072 565050006940 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 565050006941 active site 565050006942 phosphorylation site [posttranslational modification] 565050006943 intermolecular recognition site; other site 565050006944 dimerization interface [polypeptide binding]; other site 565050006945 fructokinase; Reviewed; Region: PRK09557 565050006946 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 565050006947 DNA polymerase IV; Provisional; Region: PRK02794 565050006948 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 565050006949 active site 565050006950 DNA binding site [nucleotide binding] 565050006951 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 565050006952 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 565050006953 Clp amino terminal domain; Region: Clp_N; pfam02861 565050006954 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 565050006955 Walker A motif; other site 565050006956 ATP binding site [chemical binding]; other site 565050006957 Walker B motif; other site 565050006958 arginine finger; other site 565050006959 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 565050006960 Walker A motif; other site 565050006961 ATP binding site [chemical binding]; other site 565050006962 Walker B motif; other site 565050006963 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 565050006964 Protein of unknown function (DUF1640); Region: DUF1640; pfam07798 565050006965 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 565050006966 HIT family signature motif; other site 565050006967 catalytic residue [active] 565050006968 Domain of unknown function (DUF4287); Region: DUF4287; pfam14117 565050006969 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 565050006970 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 565050006971 active site 2 [active] 565050006972 active site 1 [active] 565050006973 amidase; Provisional; Region: PRK08137 565050006974 Amidase; Region: Amidase; cl11426 565050006975 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 565050006976 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 565050006977 Sel1 repeat; Region: Sel1; cl02723 565050006978 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 565050006979 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 565050006980 active site 565050006981 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 565050006982 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 565050006983 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 565050006984 active site 565050006985 aminopeptidase N; Provisional; Region: pepN; PRK14015 565050006986 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 565050006987 active site 565050006988 Zn binding site [ion binding]; other site 565050006989 PAS fold; Region: PAS; pfam00989 565050006990 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 565050006991 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 565050006992 PAS fold; Region: PAS_7; pfam12860 565050006993 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 565050006994 dimer interface [polypeptide binding]; other site 565050006995 phosphorylation site [posttranslational modification] 565050006996 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 565050006997 ATP binding site [chemical binding]; other site 565050006998 Mg2+ binding site [ion binding]; other site 565050006999 G-X-G motif; other site 565050007000 membrane ATPase/protein kinase; Provisional; Region: PRK09435 565050007001 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 565050007002 Walker A; other site 565050007003 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050007004 G4 box; other site 565050007005 G5 box; other site 565050007006 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 565050007007 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 565050007008 putative C-terminal domain interface [polypeptide binding]; other site 565050007009 putative GSH binding site (G-site) [chemical binding]; other site 565050007010 putative dimer interface [polypeptide binding]; other site 565050007011 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 565050007012 putative N-terminal domain interface [polypeptide binding]; other site 565050007013 putative dimer interface [polypeptide binding]; other site 565050007014 putative substrate binding pocket (H-site) [chemical binding]; other site 565050007015 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 565050007016 Major Facilitator Superfamily; Region: MFS_1; pfam07690 565050007017 putative substrate translocation pore; other site 565050007018 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 565050007019 D-galactonate transporter; Region: 2A0114; TIGR00893 565050007020 putative substrate translocation pore; other site 565050007021 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 565050007022 adenylosuccinate lyase; Provisional; Region: PRK07492 565050007023 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 565050007024 tetramer interface [polypeptide binding]; other site 565050007025 active site 565050007026 Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Region: Lyase_I_like; cl00013 565050007027 Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones]; Region: EGL-9; COG3751 565050007028 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 565050007029 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 565050007030 putative active site [active] 565050007031 Domain of unknown function (DUF1476); Region: DUF1476; cl11571 565050007032 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 565050007033 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 565050007034 ATP binding site [chemical binding]; other site 565050007035 active site 565050007036 substrate binding site [chemical binding]; other site 565050007037 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; cl00789 565050007038 Bacterial transcriptional repressor; Region: TetR_C_6; cl07106 565050007039 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; cl12078 565050007040 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 565050007041 Rubredoxin; Region: Rubredoxin; pfam00301 565050007042 iron binding site [ion binding]; other site 565050007043 Domain of unknown function (DUF3291); Region: DUF3291; pfam11695 565050007044 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 565050007045 putative active site [active] 565050007046 catalytic triad [active] 565050007047 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 565050007048 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 565050007049 dimerization interface [polypeptide binding]; other site 565050007050 ATP binding site [chemical binding]; other site 565050007051 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 565050007052 dimerization interface [polypeptide binding]; other site 565050007053 ATP binding site [chemical binding]; other site 565050007054 PAS domain S-box; Region: sensory_box; TIGR00229 565050007055 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 565050007056 putative active site [active] 565050007057 heme pocket [chemical binding]; other site 565050007058 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 565050007059 dimer interface [polypeptide binding]; other site 565050007060 phosphorylation site [posttranslational modification] 565050007061 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 565050007062 ATP binding site [chemical binding]; other site 565050007063 Mg2+ binding site [ion binding]; other site 565050007064 G-X-G motif; other site 565050007065 Response regulator receiver domain; Region: Response_reg; pfam00072 565050007066 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 565050007067 active site 565050007068 phosphorylation site [posttranslational modification] 565050007069 intermolecular recognition site; other site 565050007070 dimerization interface [polypeptide binding]; other site 565050007071 M28 Zn-Peptidases; Region: M28_like_2; cd05662 565050007072 metal binding site [ion binding]; metal-binding site 565050007073 BolA-like protein; Region: BolA; cl00386 565050007074 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cl00470 565050007075 active site 565050007076 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 565050007077 putative GSH binding site [chemical binding]; other site 565050007078 catalytic residues [active] 565050007079 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 565050007080 active site 565050007081 Peptidase family M48; Region: Peptidase_M48; cl12018 565050007082 Transcription factor zinc-finger; Region: zf-TFIIB; cl01565 565050007083 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 565050007084 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 565050007085 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 565050007086 RNA binding surface [nucleotide binding]; other site 565050007087 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 565050007088 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 565050007089 Predicted esterase [General function prediction only]; Region: COG0627 565050007090 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; cl12031 565050007091 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 565050007092 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 565050007093 substrate binding site [chemical binding]; other site 565050007094 catalytic Zn binding site [ion binding]; other site 565050007095 NAD binding site [chemical binding]; other site 565050007096 structural Zn binding site [ion binding]; other site 565050007097 dimer interface [polypeptide binding]; other site 565050007098 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like_1; cd08470 565050007099 putative effector binding pocket; other site 565050007100 putative dimerization interface [polypeptide binding]; other site 565050007101 Uncharacterized conserved protein [Function unknown]; Region: COG5361 565050007102 Protein of unknown function (DUF1254); Region: DUF1254; cl02257 565050007103 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 565050007104 Protein required for attachment to host cells; Region: Host_attach; cl02398 565050007105 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 565050007106 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 565050007107 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 565050007108 dimer interface [polypeptide binding]; other site 565050007109 phosphorylation site [posttranslational modification] 565050007110 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 565050007111 ATP binding site [chemical binding]; other site 565050007112 Mg2+ binding site [ion binding]; other site 565050007113 G-X-G motif; other site 565050007114 Response regulator receiver domain; Region: Response_reg; pfam00072 565050007115 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 565050007116 active site 565050007117 phosphorylation site [posttranslational modification] 565050007118 intermolecular recognition site; other site 565050007119 dimerization interface [polypeptide binding]; other site 565050007120 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 565050007121 Protein of unknown function (DUF2939); Region: DUF2939; pfam11159 565050007122 Membrane transport protein; Region: Mem_trans; cl09117 565050007123 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 565050007124 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050007125 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 565050007126 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 565050007127 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 565050007128 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 formation of...; Region: AlaRS_core; cd00673 565050007129 motif 1; other site 565050007130 active site 565050007131 motif 2; other site 565050007132 motif 3; other site 565050007133 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 565050007134 DHHA1 domain; Region: DHHA1; pfam02272 565050007135 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; cd03467 565050007136 iron-sulfur cluster [ion binding]; other site 565050007137 [2Fe-2S] cluster binding site [ion binding]; other site 565050007138 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 565050007139 Cupin domain; Region: Cupin_2; cl09118 565050007140 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 565050007141 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 565050007142 dimer interface [polypeptide binding]; other site 565050007143 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 565050007144 active site 565050007145 Fe binding site [ion binding]; other site 565050007146 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 565050007147 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 565050007148 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050007149 homodimer interface [polypeptide binding]; other site 565050007150 catalytic residue [active] 565050007151 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 565050007152 Helix-turn-helix domains; Region: HTH; cl00088 565050007153 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 565050007154 Domain of unknown function (DUF1905); Region: DUF1905; pfam08922 565050007155 CAAX protease self-immunity; Region: Abi; cl00558 565050007156 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 565050007157 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 565050007158 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 565050007159 cell division protein FtsZ; Validated; Region: PRK09330 565050007160 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 565050007161 nucleotide binding site [chemical binding]; other site 565050007162 SulA interaction site; other site 565050007163 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 565050007164 Cell division protein FtsA; Region: FtsA; cl11496 565050007165 Cell division protein FtsA; Region: FtsA; cl11496 565050007166 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 565050007167 Cell division protein FtsQ; Region: FtsQ; pfam03799 565050007168 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 565050007169 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 565050007170 ATP-grasp domain; Region: ATP-grasp_4; cl03087 565050007171 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 565050007172 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 565050007173 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 565050007174 PA/protease or protease-like domain interface [polypeptide binding]; other site 565050007175 M28 Zn-Peptidase Plasma glutamate carboxypeptidase; Region: M28_Pgcp_like; cd03883 565050007176 metal binding site [ion binding]; metal-binding site 565050007177 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 565050007178 FAD binding domain; Region: FAD_binding_4; pfam01565 565050007179 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 565050007180 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 565050007181 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 565050007182 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 565050007183 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 565050007184 Predicted ATPase [General function prediction only]; Region: COG4637 565050007185 SOUL heme-binding protein; Region: SOUL; pfam04832 565050007186 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3533 565050007187 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 565050007188 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 565050007189 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 565050007190 active site 565050007191 homodimer interface [polypeptide binding]; other site 565050007192 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 565050007193 PAS fold; Region: PAS_4; pfam08448 565050007194 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 565050007195 Histidine kinase; Region: HisKA_2; cl06527 565050007196 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 565050007197 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 565050007198 Cl- selectivity filter; other site 565050007199 Cl- binding residues [ion binding]; other site 565050007200 pore gating glutamate residue; other site 565050007201 dimer interface [polypeptide binding]; other site 565050007202 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the metalloprotease peptidase M50. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide...; Region: CBS_pair_M50_like; cd04801 565050007203 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01390 565050007204 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 565050007205 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 565050007206 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 565050007207 Mg++ binding site [ion binding]; other site 565050007208 putative catalytic motif [active] 565050007209 putative substrate binding site [chemical binding]; other site 565050007210 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional; Region: PRK14093 565050007211 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 565050007212 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 565050007213 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 565050007214 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 565050007215 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 565050007216 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 565050007217 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 565050007218 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 565050007219 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 565050007220 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050007221 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 565050007222 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050007223 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 565050007224 MraZ protein; Region: MraZ; pfam02381 565050007225 MraZ protein; Region: MraZ; pfam02381 565050007226 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 565050007227 Helix-turn-helix domains; Region: HTH; cl00088 565050007228 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 565050007229 dimerization interface [polypeptide binding]; other site 565050007230 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050007231 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 565050007232 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 565050007233 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 565050007234 amidase catalytic site [active] 565050007235 Zn binding residues [ion binding]; other site 565050007236 substrate binding site [chemical binding]; other site 565050007237 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 565050007238 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 565050007239 EamA-like transporter family; Region: EamA; cl01037 565050007240 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 565050007241 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050007242 Uncharacterized protein conserved in bacteria (DUF2236); Region: DUF2236; cl01472 565050007243 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 565050007244 Helix-turn-helix domain; Region: HTH_18; pfam12833 565050007245 enoyl-CoA hydratase; Provisional; Region: PRK09245 565050007246 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 565050007247 substrate binding site [chemical binding]; other site 565050007248 oxyanion hole (OAH) forming residues; other site 565050007249 trimer interface [polypeptide binding]; other site 565050007250 Response regulator receiver domain; Region: Response_reg; pfam00072 565050007251 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 565050007252 active site 565050007253 phosphorylation site [posttranslational modification] 565050007254 intermolecular recognition site; other site 565050007255 dimerization interface [polypeptide binding]; other site 565050007256 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 565050007257 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 565050007258 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 565050007259 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 565050007260 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 565050007261 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 565050007262 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 565050007263 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 565050007264 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 565050007265 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 565050007266 PA/protease or protease-like domain interface [polypeptide binding]; other site 565050007267 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_2; cd05661 565050007268 metal binding site [ion binding]; metal-binding site 565050007269 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 565050007270 Class II flagellar assembly regulator; Region: FliX; cl11677 565050007271 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 565050007272 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 565050007273 Rod binding protein; Region: Rod-binding; cl01626 565050007274 Predicted methyltransferase [General function prediction only]; Region: COG3897 565050007275 Protein of unknown function (DUF3422); Region: DUF3422; cl02073 565050007276 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 565050007277 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050007278 Walker A/P-loop; other site 565050007279 ATP binding site [chemical binding]; other site 565050007280 Q-loop/lid; other site 565050007281 ABC transporter signature motif; other site 565050007282 Walker B; other site 565050007283 D-loop; other site 565050007284 H-loop/switch region; other site 565050007285 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 565050007286 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 565050007287 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 565050007288 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 565050007289 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 565050007290 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 565050007291 Transposase domain (DUF772); Region: DUF772; cl15789 565050007292 Transposase domain (DUF772); Region: DUF772; cl15789 565050007293 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 565050007294 GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing...; Region: GST_N_GTT2_like; cd03051 565050007295 putative C-terminal domain interface [polypeptide binding]; other site 565050007296 putative GSH binding site (G-site) [chemical binding]; other site 565050007297 putative dimer interface [polypeptide binding]; other site 565050007298 C-terminal, alpha helical domain of GTT2-like Glutathione S-transferases; Region: GST_C_GTT2_like; cd03182 565050007299 putative N-terminal domain interface [polypeptide binding]; other site 565050007300 putative dimer interface [polypeptide binding]; other site 565050007301 putative substrate binding pocket (H-site) [chemical binding]; other site 565050007302 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 565050007303 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050007304 Uncharacterized conserved protein [Function unknown]; Region: COG3496 565050007305 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 565050007306 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 565050007307 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050007308 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 565050007309 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 565050007310 S-adenosylmethionine binding site [chemical binding]; other site 565050007311 Predicted membrane protein (DUF2177); Region: DUF2177; cl02014 565050007312 allantoate amidohydrolase; Reviewed; Region: PRK09290 565050007313 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 565050007314 active site 565050007315 metal binding site [ion binding]; metal-binding site 565050007316 dimer interface [polypeptide binding]; other site 565050007317 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 565050007318 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 565050007319 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 565050007320 catalytic residue [active] 565050007321 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 565050007322 Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; Region: CE4_PuuE_SpCDA1; cd10977 565050007323 active site 565050007324 catalytic site [active] 565050007325 tetramer interface [polypeptide binding]; other site 565050007326 OHCU decarboxylase; Region: OHCU_decarbox; cl01251 565050007327 Predicted membrane protein [Function unknown]; Region: COG3748 565050007328 Protein of unknown function (DUF989); Region: DUF989; pfam06181 565050007329 Cytochrome c; Region: Cytochrom_C; cl11414 565050007330 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050007331 Helix-turn-helix domains; Region: HTH; cl00088 565050007332 YceI-like domain; Region: YceI; cl01001 565050007333 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 565050007334 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 565050007335 Acetamidase/Formamidase family; Region: FmdA_AmdA; cl01023 565050007336 amidase; Provisional; Region: PRK09201 565050007337 Amidase; Region: Amidase; cl11426 565050007338 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 565050007339 NH_hydro_CaPnhB: A subgroup of nucleoside hydrolases similar to Corynebacterium ammoniagenes Purine/pyrimidine nucleoside hydrolase (pnhB). Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These...; Region: nuc_hydro_CaPnhB; cd02650 565050007340 active site 565050007341 guanine deaminase; Provisional; Region: PRK09228 565050007342 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 565050007343 active site 565050007344 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 565050007345 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 565050007346 XdhC Rossmann domain; Region: XdhC_C; pfam13478 565050007347 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 565050007348 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 565050007349 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 565050007350 xanthine dehydrogenase, small subunit; Region: xanthine_xdhA; TIGR02963 565050007351 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 565050007352 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 565050007353 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 565050007354 HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU); Region: TLP_HIUase; cd05822 565050007355 active site 565050007356 homotetramer interface [polypeptide binding]; other site 565050007357 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 565050007358 Malic enzyme, N-terminal domain; Region: malic; pfam00390 565050007359 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 565050007360 putative NAD(P) binding site [chemical binding]; other site 565050007361 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 565050007362 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 protein; Region: CSP_CDS; cd04458 565050007363 DNA-binding site [nucleotide binding]; DNA binding site 565050007364 RNA-binding motif; other site 565050007365 Helix-turn-helix domains; Region: HTH; cl00088 565050007366 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 565050007367 FOG: CBS domain [General function prediction only]; Region: COG0517 565050007368 Rhomboid family; Region: Rhomboid; cl11446 565050007369 TolB amino-terminal domain; Region: TolB_N; cl00639 565050007370 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 565050007371 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 565050007372 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 565050007373 MASE1; Region: MASE1; pfam05231 565050007374 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 565050007375 dimer interface [polypeptide binding]; other site 565050007376 phosphorylation site [posttranslational modification] 565050007377 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 565050007378 ATP binding site [chemical binding]; other site 565050007379 Mg2+ binding site [ion binding]; other site 565050007380 G-X-G motif; other site 565050007381 Response regulator receiver domain; Region: Response_reg; pfam00072 565050007382 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 565050007383 active site 565050007384 phosphorylation site [posttranslational modification] 565050007385 intermolecular recognition site; other site 565050007386 dimerization interface [polypeptide binding]; other site 565050007387 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 565050007388 NMT1-like family; Region: NMT1_2; cl15260 565050007389 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 565050007390 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 565050007391 Walker A/P-loop; other site 565050007392 ATP binding site [chemical binding]; other site 565050007393 Q-loop/lid; other site 565050007394 ABC transporter signature motif; other site 565050007395 Walker B; other site 565050007396 D-loop; other site 565050007397 H-loop/switch region; other site 565050007398 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 565050007399 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; cl15419 565050007400 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 565050007401 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 565050007402 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 565050007403 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 565050007404 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 565050007405 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5388 565050007406 PAS domain; Region: PAS_5; pfam07310 565050007407 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 565050007408 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 565050007409 active site 565050007410 catalytic tetrad [active] 565050007411 choline dehydrogenase; Validated; Region: PRK02106 565050007412 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050007413 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 565050007414 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 565050007415 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 565050007416 trimer interface [polypeptide binding]; other site 565050007417 putative metal binding site [ion binding]; other site 565050007418 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050007419 OPT oligopeptide transporter protein; Region: OPT; cl14607 565050007420 OPT oligopeptide transporter protein; Region: OPT; cl14607 565050007421 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 565050007422 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 565050007423 putative C-terminal domain interface [polypeptide binding]; other site 565050007424 putative GSH binding site (G-site) [chemical binding]; other site 565050007425 putative dimer interface [polypeptide binding]; other site 565050007426 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 565050007427 putative N-terminal domain interface [polypeptide binding]; other site 565050007428 putative dimer interface [polypeptide binding]; other site 565050007429 putative substrate binding pocket (H-site) [chemical binding]; other site 565050007430 Predicted acetyltransferase [General function prediction only]; Region: COG3393 565050007431 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 565050007432 Coenzyme A binding pocket [chemical binding]; other site 565050007433 Protein of unknown function (DUF3126); Region: DUF3126; pfam11324 565050007434 Glutamine cyclotransferase; Region: Glu_cyclase_2; pfam05096 565050007435 serine acetyltransferase; Provisional; Region: cysE; PRK11132 565050007436 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 565050007437 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 565050007438 trimer interface [polypeptide binding]; other site 565050007439 active site 565050007440 substrate binding site [chemical binding]; other site 565050007441 CoA binding site [chemical binding]; other site 565050007442 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 565050007443 ADP-ribose binding site [chemical binding]; other site 565050007444 dimer interface [polypeptide binding]; other site 565050007445 active site 565050007446 nudix motif; other site 565050007447 metal binding site [ion binding]; metal-binding site 565050007448 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 565050007449 putative FMN binding site [chemical binding]; other site 565050007450 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 565050007451 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 565050007452 classical (c) SDRs; Region: SDR_c; cd05233 565050007453 NAD(P) binding site [chemical binding]; other site 565050007454 active site 565050007455 Helix-turn-helix domains; Region: HTH; cl00088 565050007456 putative transposase OrfB; Reviewed; Region: PHA02517 565050007457 Helix-turn-helix domains; Region: HTH; cl00088 565050007458 Integrase core domain; Region: rve; cl01316 565050007459 Integrase core domain; Region: rve_3; cl15866 565050007460 Helix-turn-helix domains; Region: HTH; cl00088 565050007461 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 565050007462 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050007463 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; cl00284 565050007464 Transcriptional regulators [Transcription]; Region: GntR; COG1802 565050007465 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050007466 DNA-binding site [nucleotide binding]; DNA binding site 565050007467 FCD domain; Region: FCD; cl11656 565050007468 Helix-turn-helix domains; Region: HTH; cl00088 565050007469 phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein; Region: 3A0109s03R; TIGR01098 565050007470 NMT1-like family; Region: NMT1_2; cl15260 565050007471 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 565050007472 dimer interface [polypeptide binding]; other site 565050007473 conserved gate region; other site 565050007474 ABC-ATPase subunit interface; other site 565050007475 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 565050007476 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC...; Region: ABC_MetN_methionine_transporter; cd03258 565050007477 Walker A/P-loop; other site 565050007478 ATP binding site [chemical binding]; other site 565050007479 Q-loop/lid; other site 565050007480 ABC transporter signature motif; other site 565050007481 Walker B; other site 565050007482 D-loop; other site 565050007483 H-loop/switch region; other site 565050007484 NIL domain; Region: NIL; cl09633 565050007485 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 565050007486 PAS domain S-box; Region: sensory_box; TIGR00229 565050007487 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 565050007488 putative active site [active] 565050007489 heme pocket [chemical binding]; other site 565050007490 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 565050007491 dimer interface [polypeptide binding]; other site 565050007492 phosphorylation site [posttranslational modification] 565050007493 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 565050007494 ATP binding site [chemical binding]; other site 565050007495 Mg2+ binding site [ion binding]; other site 565050007496 G-X-G motif; other site 565050007497 Response regulator receiver domain; Region: Response_reg; pfam00072 565050007498 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 565050007499 active site 565050007500 phosphorylation site [posttranslational modification] 565050007501 intermolecular recognition site; other site 565050007502 dimerization interface [polypeptide binding]; other site 565050007503 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 565050007504 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; cl12031 565050007505 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 565050007506 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 565050007507 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_A; cd01299 565050007508 active site 565050007509 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 565050007510 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 565050007511 non-specific DNA binding site [nucleotide binding]; other site 565050007512 salt bridge; other site 565050007513 sequence-specific DNA binding site [nucleotide binding]; other site 565050007514 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 565050007515 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 565050007516 putative MPT binding site; other site 565050007517 Sugar fermentation stimulation protein; Region: SfsA; cl00647 565050007518 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 565050007519 active site 565050007520 hypothetical protein; Reviewed; Region: PRK00024 565050007521 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 565050007522 MPN+ (JAMM) motif; other site 565050007523 Zinc-binding site [ion binding]; other site 565050007524 integrase; Provisional; Region: PRK09692 565050007525 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 565050007526 DNA binding site [nucleotide binding] 565050007527 Int/Topo IB signature motif; other site 565050007528 active site 565050007529 Protein of unknown function (DUF736); Region: DUF736; cl02303 565050007530 Protein of unknown function (DUF2274); Region: DUF2274; cl02406 565050007531 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 565050007532 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 565050007533 VirB7 interaction site; other site 565050007534 VirB8 protein; Region: VirB8; cl01500 565050007535 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 565050007536 conjugal transfer protein TrbL; Provisional; Region: PRK13875 565050007537 Helix-turn-helix domains; Region: HTH; cl00088 565050007538 insertion element IS2 transposase InsD; Provisional; Region: PRK14702 565050007539 HTH-like domain; Region: HTH_21; pfam13276 565050007540 Integrase core domain; Region: rve; cl01316 565050007541 Integrase core domain; Region: rve_3; cl15866 565050007542 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050007543 dimer interface [polypeptide binding]; other site 565050007544 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 565050007545 putative CheW interface [polypeptide binding]; other site 565050007546 TSC-22/dip/bun family; Region: TSC22; cl01853 565050007547 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050007548 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 565050007549 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 565050007550 catalytic triad [active] 565050007551 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 565050007552 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 565050007553 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 565050007554 putative peptidoglycan binding site; other site 565050007555 cyclase homology domain; Region: CHD; cd07302 565050007556 nucleotidyl binding site; other site 565050007557 metal binding site [ion binding]; metal-binding site 565050007558 dimer interface [polypeptide binding]; other site 565050007559 cyclase homology domain; Region: CHD; cd07302 565050007560 nucleotidyl binding site; other site 565050007561 metal binding site [ion binding]; metal-binding site 565050007562 dimer interface [polypeptide binding]; other site 565050007563 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 565050007564 ligand binding site [chemical binding]; other site 565050007565 flexible hinge region; other site 565050007566 TIR domain; Region: TIR_2; cl15770 565050007567 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 565050007568 cyclase homology domain; Region: CHD; cd07302 565050007569 nucleotidyl binding site; other site 565050007570 metal binding site [ion binding]; metal-binding site 565050007571 dimer interface [polypeptide binding]; other site 565050007572 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 565050007573 non-specific DNA binding site [nucleotide binding]; other site 565050007574 salt bridge; other site 565050007575 sequence-specific DNA binding site [nucleotide binding]; other site 565050007576 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 565050007577 non-specific DNA binding site [nucleotide binding]; other site 565050007578 salt bridge; other site 565050007579 sequence-specific DNA binding site [nucleotide binding]; other site 565050007580 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 565050007581 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050007582 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 565050007583 DNA binding residues [nucleotide binding] 565050007584 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 565050007585 FecR protein; Region: FecR; pfam04773 565050007586 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050007587 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; cl00284 565050007588 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; cl00284 565050007589 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 565050007590 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; cl12031 565050007591 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 565050007592 Ligand Binding Site [chemical binding]; other site 565050007593 Molecular Tunnel; other site 565050007594 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 565050007595 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050007596 DNA-binding site [nucleotide binding]; DNA binding site 565050007597 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050007598 non-specific DNA binding site [nucleotide binding]; other site 565050007599 salt bridge; other site 565050007600 sequence-specific DNA binding site [nucleotide binding]; other site 565050007601 Uncharacterized conserved protein (DUF2285); Region: DUF2285; cl02246 565050007602 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 565050007603 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050007604 heavy metal efflux pump (cobalt-zinc-cadmium); Region: 2A0601; TIGR00914 565050007605 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 565050007606 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 565050007607 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 565050007608 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050007609 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 565050007610 Helix-turn-helix domains; Region: HTH; cl00088 565050007611 Helix-turn-helix domains; Region: HTH; cl00088 565050007612 putative transposase OrfB; Reviewed; Region: PHA02517 565050007613 Helix-turn-helix domains; Region: HTH; cl00088 565050007614 Integrase core domain; Region: rve; cl01316 565050007615 Integrase core domain; Region: rve_3; cl15866 565050007616 HipA N-terminal domain; Region: Couple_hipA; cl11853 565050007617 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 565050007618 HipA-like N-terminal domain; Region: HipA_N; pfam07805 565050007619 HipA-like C-terminal domain; Region: HipA_C; pfam07804 565050007620 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 565050007621 non-specific DNA binding site [nucleotide binding]; other site 565050007622 salt bridge; other site 565050007623 sequence-specific DNA binding site [nucleotide binding]; other site 565050007624 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 565050007625 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 565050007626 Transposase; Region: DEDD_Tnp_IS110; pfam01548 565050007627 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 565050007628 Helix-turn-helix domains; Region: HTH; cl00088 565050007629 insertion element IS2 transposase InsD; Provisional; Region: PRK14702 565050007630 HTH-like domain; Region: HTH_21; pfam13276 565050007631 Integrase core domain; Region: rve; cl01316 565050007632 Integrase core domain; Region: rve_3; cl15866 565050007633 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 565050007634 catalytic residues [active] 565050007635 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 565050007636 MPN+ (JAMM) motif; other site 565050007637 Zinc-binding site [ion binding]; other site 565050007638 Uncharacterized protein conserved in bacteria (DUF2272); Region: DUF2272; cl01776 565050007639 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 565050007640 active site 565050007641 dimer interface [polypeptide binding]; other site 565050007642 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 565050007643 TMAO/DMSO reductase; Reviewed; Region: PRK05363 565050007644 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 565050007645 Moco binding site; other site 565050007646 metal coordination site [ion binding]; other site 565050007647 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cl01482 565050007648 RNA polymerase sigma factor; Reviewed; Region: PRK05602 565050007649 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050007650 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 565050007651 DNA binding residues [nucleotide binding] 565050007652 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; cl08302 565050007653 EF-hand domain pair; Region: EF_hand_5; pfam13499 565050007654 Glutamine synthetase adenylyltransferase [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms]; Region: GlnE; COG1391 565050007655 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 565050007656 metal binding triad; other site 565050007657 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 565050007658 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 565050007659 metal binding triad; other site 565050007660 BlaR1 peptidase M56; Region: Peptidase_M56; cl15829 565050007661 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 565050007662 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050007663 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; cl00080 565050007664 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 565050007665 ATP binding site [chemical binding]; other site 565050007666 Mg2+ binding site [ion binding]; other site 565050007667 G-X-G motif; other site 565050007668 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 565050007669 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 565050007670 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 565050007671 active site 565050007672 phosphorylation site [posttranslational modification] 565050007673 intermolecular recognition site; other site 565050007674 dimerization interface [polypeptide binding]; other site 565050007675 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 565050007676 DNA binding site [nucleotide binding] 565050007677 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 565050007678 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 565050007679 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 565050007680 protein binding site [polypeptide binding]; other site 565050007681 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 565050007682 protein binding site [polypeptide binding]; other site 565050007683 Cytochrome C biogenesis protein; Region: CcmH; cl01179 565050007684 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 565050007685 CcmE; Region: CcmE; cl00994 565050007686 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 565050007687 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 565050007688 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 565050007689 TPR motif; other site 565050007690 binding surface 565050007691 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050007692 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; cl12031 565050007693 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; cl12031 565050007694 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; cl00080 565050007695 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 565050007696 ATP binding site [chemical binding]; other site 565050007697 Mg2+ binding site [ion binding]; other site 565050007698 G-X-G motif; other site 565050007699 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 565050007700 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 565050007701 active site 565050007702 phosphorylation site [posttranslational modification] 565050007703 intermolecular recognition site; other site 565050007704 dimerization interface [polypeptide binding]; other site 565050007705 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 565050007706 DNA binding site [nucleotide binding] 565050007707 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 565050007708 HipA N-terminal domain; Region: Couple_hipA; cl11853 565050007709 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 565050007710 HipA-like N-terminal domain; Region: HipA_N; pfam07805 565050007711 HipA-like C-terminal domain; Region: HipA_C; pfam07804 565050007712 DnaJ-class molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: CbpA; COG2214 565050007713 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 565050007714 HSP70 interaction site [polypeptide binding]; other site 565050007715 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 565050007716 substrate binding site [polypeptide binding]; other site 565050007717 dimer interface [polypeptide binding]; other site 565050007718 GTA TIM-barrel-like domain; Region: GTA_TIM; pfam13547 565050007719 Putative phage tail protein; Region: Phage-tail_3; pfam13550 565050007720 NlpC/P60 family; Region: NLPC_P60; cl11438 565050007721 Uncharacterized conserved protein [Function unknown]; Region: COG5449 565050007722 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 565050007723 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 565050007724 Protein of unknown function (DUF805); Region: DUF805; cl01224 565050007725 Conserved hypothetical phage protein (DUF2376); Region: DUF2376; cl09774 565050007726 Protein of unknown function (DUF3356); Region: DUF3356; pfam11836 565050007727 Phage major tail protein 2; Region: Phage_tail_2; cl11463 565050007728 Predicted phage phi-C31 gp36 major capsid-like protein [General function prediction only]; Region: COG4653 565050007729 Phage capsid family; Region: Phage_capsid; pfam05065 565050007730 BLMT, a bleomycin resistance protein encoded on the transposon Tn5, and similar proteins; Region: BLMT_like; cd08350 565050007731 dimer interface [polypeptide binding]; other site 565050007732 ligand binding site [chemical binding]; other site 565050007733 Caudovirus prohead protease; Region: Peptidase_U35; cl01521 565050007734 Phage-related protein [Function unknown]; Region: COG4695; cl01923 565050007735 Phage portal protein; Region: Phage_portal; pfam04860 565050007736 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 565050007737 putative active site [active] 565050007738 Uncharacterized conserved protein [Function unknown]; Region: COG5323 565050007739 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 565050007740 dimer interface [polypeptide binding]; other site 565050007741 NADP binding site [chemical binding]; other site 565050007742 catalytic residues [active] 565050007743 Cytochrome c; Region: Cytochrom_C; cl11414 565050007744 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 565050007745 Helix-turn-helix domains; Region: HTH; cl00088 565050007746 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 565050007747 Isochorismatase family; Region: Isochorismatase; pfam00857 565050007748 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 565050007749 catalytic triad [active] 565050007750 conserved cis-peptide bond; other site 565050007751 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 565050007752 homotrimer interaction site [polypeptide binding]; other site 565050007753 putative active site [active] 565050007754 pyrimidine utilization protein D; Region: RutD; TIGR03611 565050007755 pyrimidine utilization protein A; Region: RutA; TIGR03612 565050007756 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 565050007757 active site 565050007758 dimer interface [polypeptide binding]; other site 565050007759 non-prolyl cis peptide bond; other site 565050007760 insertion regions; other site 565050007761 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 565050007762 Beta-galactosidase [Carbohydrate transport and metabolism]; Region: LacA; COG1874 565050007763 Beta-galactosidase; Region: Glyco_hydro_42; cl03154 565050007764 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 565050007765 Glycosyl hydrolase family 43, beta-D-xylosidase; Region: GH43_XYL_1; cd09000 565050007766 inhibitor binding site; inhibition site 565050007767 active site 565050007768 Glycosyl hydrolase family 10; Region: Glyco_hydro_10; cl01495 565050007769 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050007770 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; cl00284 565050007771 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; cl00284 565050007772 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050007773 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050007774 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050007775 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050007776 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 565050007777 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like6; cd05664 565050007778 metal binding site [ion binding]; metal-binding site 565050007779 putative dimer interface [polypeptide binding]; other site 565050007780 PAS domain; Region: PAS_9; pfam13426 565050007781 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 565050007782 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050007783 dimer interface [polypeptide binding]; other site 565050007784 putative CheW interface [polypeptide binding]; other site 565050007785 Alpha-glucuronidase [Carbohydrate transport and metabolism]; Region: AguA; COG3661 565050007786 Glycosyl hydrolase family 67 N-terminus; Region: Glyco_hydro_67N; pfam03648 565050007787 Glycosyl hydrolase family 67 C-terminus; Region: Glyco_hydro_67C; pfam07477 565050007788 bifunctional D-altronate/D-mannonate dehydratase; Provisional; Region: PRK15072 565050007789 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; cl09108 565050007790 metal binding site [ion binding]; metal-binding site 565050007791 substrate binding pocket [chemical binding]; other site 565050007792 Transcriptional regulators [Transcription]; Region: FadR; COG2186 565050007793 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050007794 DNA-binding site [nucleotide binding]; DNA binding site 565050007795 FCD domain; Region: FCD; cl11656 565050007796 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 565050007797 putative active site [active] 565050007798 OpgC protein; Region: OpgC_C; cl00792 565050007799 Transposase; Region: DEDD_Tnp_IS110; pfam01548 565050007800 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 565050007801 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 565050007802 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050007803 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 565050007804 TPR motif; other site 565050007805 binding surface 565050007806 TPR repeat; Region: TPR_11; pfam13414 565050007807 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 565050007808 TPR motif; other site 565050007809 binding surface 565050007810 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 565050007811 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; cl00284 565050007812 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; cl00284 565050007813 Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones]; Region: EGL-9; COG3751 565050007814 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 565050007815 TMAO/DMSO reductase; Reviewed; Region: PRK05363 565050007816 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 565050007817 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 565050007818 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 565050007819 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 565050007820 Domain of unknown function (DUF4159); Region: DUF4159; pfam13709 565050007821 MoxR-like ATPases [General function prediction only]; Region: COG0714 565050007822 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 565050007823 Walker A motif; other site 565050007824 ATP binding site [chemical binding]; other site 565050007825 Walker B motif; other site 565050007826 arginine finger; other site 565050007827 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 565050007828 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 565050007829 Aerotolerance regulator N-terminal; Region: BatA; cl06567 565050007830 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050007831 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; cl00284 565050007832 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; cl00284 565050007833 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3813 565050007834 Protein of unknown function (DUF1272); Region: DUF1272; pfam06906 565050007835 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 565050007836 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 565050007837 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 565050007838 catalytic site [active] 565050007839 subunit interface [polypeptide binding]; other site 565050007840 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 565050007841 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050007842 NAD(P) binding site [chemical binding]; other site 565050007843 active site 565050007844 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 2; Region: FDH_like_2; cd08284 565050007845 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 565050007846 catalytic Zn binding site [ion binding]; other site 565050007847 NAD(P) binding site [chemical binding]; other site 565050007848 structural Zn binding site [ion binding]; other site 565050007849 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 565050007850 putative active site [active] 565050007851 Flagellar hook protein FlgE [Cell motility and secretion]; Region: FlgE; COG1749 565050007852 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 565050007853 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 565050007854 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 565050007855 PA/protease or protease-like domain interface [polypeptide binding]; other site 565050007856 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_2; cd05661 565050007857 metal binding site [ion binding]; metal-binding site 565050007858 Predicted membrane protein [Function unknown]; Region: COG3371 565050007859 Protein of unknown function (DUF998); Region: DUF998; pfam06197 565050007860 Cache domain; Region: Cache_1; pfam02743 565050007861 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050007862 dimerization interface [polypeptide binding]; other site 565050007863 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050007864 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050007865 dimer interface [polypeptide binding]; other site 565050007866 putative CheW interface [polypeptide binding]; other site 565050007867 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 565050007868 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 565050007869 putative C-terminal domain interface [polypeptide binding]; other site 565050007870 putative GSH binding site (G-site) [chemical binding]; other site 565050007871 putative dimer interface [polypeptide binding]; other site 565050007872 C-terminal, alpha helical domain of GTT1-like Glutathione S-transferases; Region: GST_C_GTT1_like; cd03189 565050007873 putative N-terminal domain interface [polypeptide binding]; other site 565050007874 putative dimer interface [polypeptide binding]; other site 565050007875 putative substrate binding pocket (H-site) [chemical binding]; other site 565050007876 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 565050007877 ligand binding site [chemical binding]; other site 565050007878 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050007879 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050007880 dimer interface [polypeptide binding]; other site 565050007881 putative CheW interface [polypeptide binding]; other site 565050007882 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 565050007883 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 565050007884 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 565050007885 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 565050007886 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 565050007887 PAS fold; Region: PAS_7; pfam12860 565050007888 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 565050007889 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 565050007890 putative active site [active] 565050007891 heme pocket [chemical binding]; other site 565050007892 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 565050007893 dimer interface [polypeptide binding]; other site 565050007894 phosphorylation site [posttranslational modification] 565050007895 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 565050007896 ATP binding site [chemical binding]; other site 565050007897 Mg2+ binding site [ion binding]; other site 565050007898 G-X-G motif; other site 565050007899 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 565050007900 Response regulator receiver domain; Region: Response_reg; pfam00072 565050007901 active site 565050007902 phosphorylation site [posttranslational modification] 565050007903 intermolecular recognition site; other site 565050007904 dimerization interface [polypeptide binding]; other site 565050007905 SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat; Region: GT2_SpsF; cd02518 565050007906 ligand binding site; other site 565050007907 Spore coat polysaccharide biosynthesis protein, predicted glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: spsG; COG3980 565050007908 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 565050007909 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050007910 WbqC-like protein family; Region: WbqC; pfam08889 565050007911 Core-2/I-Branching enzyme; Region: Branch; pfam02485 565050007912 short chain dehydrogenase; Validated; Region: PRK06182 565050007913 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050007914 NAD(P) binding site [chemical binding]; other site 565050007915 active site 565050007916 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 565050007917 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases; Region: RHOD_YgaP; cd01527 565050007918 active site residue [active] 565050007919 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 565050007920 dimerization interface [polypeptide binding]; other site 565050007921 putative DNA binding site [nucleotide binding]; other site 565050007922 putative Zn2+ binding site [ion binding]; other site 565050007923 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 565050007924 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 565050007925 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050007926 pseudaminic acid synthase; Region: PseI; TIGR03586 565050007927 NeuB family; Region: NeuB; cl00496 565050007928 SAF domain; Region: SAF; cl00555 565050007929 Uncharacterized protein family (UPF0150); Region: UPF0150; cl00691 565050007930 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 565050007931 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 565050007932 Cell wall hydrolyses involved in spore germination [Cell envelope biogenesis, outer membrane]; Region: SleB; COG3773 565050007933 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 565050007934 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 565050007935 Ferritin-like domain; Region: Ferritin; pfam00210 565050007936 dimerization interface [polypeptide binding]; other site 565050007937 DPS ferroxidase diiron center [ion binding]; other site 565050007938 ion pore; other site 565050007939 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 565050007940 PAS fold; Region: PAS_3; pfam08447 565050007941 putative active site [active] 565050007942 heme pocket [chemical binding]; other site 565050007943 PAS domain S-box; Region: sensory_box; TIGR00229 565050007944 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 565050007945 putative active site [active] 565050007946 heme pocket [chemical binding]; other site 565050007947 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 565050007948 dimer interface [polypeptide binding]; other site 565050007949 phosphorylation site [posttranslational modification] 565050007950 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 565050007951 ATP binding site [chemical binding]; other site 565050007952 Mg2+ binding site [ion binding]; other site 565050007953 G-X-G motif; other site 565050007954 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 565050007955 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 565050007956 active site 565050007957 phosphorylation site [posttranslational modification] 565050007958 intermolecular recognition site; other site 565050007959 dimerization interface [polypeptide binding]; other site 565050007960 Protein of unknown function, DUF393; Region: DUF393; cl01136 565050007961 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 565050007962 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 565050007963 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 565050007964 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 565050007965 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 565050007966 GIY-YIG motif/motif A; other site 565050007967 active site 565050007968 catalytic site [active] 565050007969 putative DNA binding site [nucleotide binding]; other site 565050007970 metal binding site [ion binding]; metal-binding site 565050007971 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 565050007972 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 565050007973 RNA polymerase sigma factor; Provisional; Region: PRK12547 565050007974 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050007975 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 565050007976 DNA binding residues [nucleotide binding] 565050007977 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 565050007978 dimer interface [polypeptide binding]; other site 565050007979 phosphorylation site [posttranslational modification] 565050007980 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 565050007981 ATP binding site [chemical binding]; other site 565050007982 Mg2+ binding site [ion binding]; other site 565050007983 G-X-G motif; other site 565050007984 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 565050007985 Tryptophan 2,3-dioxygenase; Region: Trp_dioxygenase; cl03994 565050007986 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 565050007987 Helix-turn-helix domains; Region: HTH; cl00088 565050007988 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 565050007989 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 565050007990 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 565050007991 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 565050007992 Ligand binding site; other site 565050007993 Putative Catalytic site; other site 565050007994 DXD motif; other site 565050007995 GtrA-like protein; Region: GtrA; cl00971 565050007996 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 565050007997 S-adenosylmethionine binding site [chemical binding]; other site 565050007998 Bleomycin binding protein (BLMA) and similar proteins; BLMA confers bleomycin (Bm) resistance by directly binding to Bm; Region: BLMA_like; cd08349 565050007999 dimer interface [polypeptide binding]; other site 565050008000 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050008001 ligand binding site [chemical binding]; other site 565050008002 Transposase domain (DUF772); Region: DUF772; cl15789 565050008003 Predicted integral membrane protein (DUF2269); Region: DUF2269; cl02335 565050008004 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 565050008005 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 565050008006 putative NAD(P) binding site [chemical binding]; other site 565050008007 active site 565050008008 DoxX-like family; Region: DoxX_3; pfam13781 565050008009 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 565050008010 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 565050008011 ATP-grasp domain; Region: ATP-grasp_4; cl03087 565050008012 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 565050008013 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 565050008014 ATP-grasp domain; Region: ATP-grasp_4; cl03087 565050008015 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 565050008016 IMP binding site; other site 565050008017 dimer interface [polypeptide binding]; other site 565050008018 partial ornithine binding site; other site 565050008019 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 565050008020 putative C-terminal domain interface [polypeptide binding]; other site 565050008021 putative GSH binding site (G-site) [chemical binding]; other site 565050008022 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 565050008023 putative dimer interface [polypeptide binding]; other site 565050008024 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 565050008025 dimer interface [polypeptide binding]; other site 565050008026 N-terminal domain interface [polypeptide binding]; other site 565050008027 putative substrate binding pocket (H-site) [chemical binding]; other site 565050008028 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 565050008029 nucleophile elbow; other site 565050008030 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 protein; Region: CSP_CDS; cd04458 565050008031 DNA-binding site [nucleotide binding]; DNA binding site 565050008032 RNA-binding motif; other site 565050008033 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 565050008034 Protein of unknown function (DUF692); Region: DUF692; cl01263 565050008035 Predicted integral membrane protein (DUF2282); Region: DUF2282; cl02366 565050008036 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 565050008037 nitrate/nitrite sensor protein NarX; Provisional; Region: PRK10600 565050008038 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 565050008039 Histidine kinase; Region: HisKA_2; cl06527 565050008040 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050008041 Quinolinate synthetase A protein; Region: NadA; cl00420 565050008042 L-aspartate oxidase; Provisional; Region: PRK07512 565050008043 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050008044 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 565050008045 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 565050008046 putative active site [active] 565050008047 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06106 565050008048 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 565050008049 dimerization interface [polypeptide binding]; other site 565050008050 active site 565050008051 MAPEG family; Region: MAPEG; cl09190 565050008052 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 565050008053 peroxiredoxin; Region: AhpC; TIGR03137 565050008054 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 565050008055 dimer interface [polypeptide binding]; other site 565050008056 decamer (pentamer of dimers) interface [polypeptide binding]; other site 565050008057 catalytic triad [active] 565050008058 peroxidatic and resolving cysteines [active] 565050008059 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 565050008060 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 565050008061 catalytic residue [active] 565050008062 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 565050008063 catalytic residues [active] 565050008064 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 565050008065 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 565050008066 Transposase; Region: DEDD_Tnp_IS110; pfam01548 565050008067 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 565050008068 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 565050008069 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; cl00284 565050008070 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 565050008071 ligand-binding site [chemical binding]; other site 565050008072 Catalytic domain of Streptomyces antibioticus phosphatidylinositol-specific phospholipase C1-like proteins; Region: PI-PLCc_SaPLC1_like; cd08589 565050008073 putative active site [active] 565050008074 catalytic site [active] 565050008075 putative metal binding site [ion binding]; other site 565050008076 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 565050008077 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 565050008078 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 565050008079 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050008080 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 565050008081 N-terminal plug; other site 565050008082 ligand-binding site [chemical binding]; other site 565050008083 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 565050008084 homodimer interface [polypeptide binding]; other site 565050008085 substrate-cofactor binding pocket; other site 565050008086 catalytic residue [active] 565050008087 Helix-turn-helix domains; Region: HTH; cl00088 565050008088 Predicted transcriptional regulator [Transcription]; Region: COG2345 565050008089 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 565050008090 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 565050008091 active site 565050008092 phosphorylation site [posttranslational modification] 565050008093 intermolecular recognition site; other site 565050008094 dimerization interface [polypeptide binding]; other site 565050008095 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 565050008096 DNA binding site [nucleotide binding] 565050008097 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050008098 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 565050008099 dimer interface [polypeptide binding]; other site 565050008100 phosphorylation site [posttranslational modification] 565050008101 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 565050008102 ATP binding site [chemical binding]; other site 565050008103 Mg2+ binding site [ion binding]; other site 565050008104 G-X-G motif; other site 565050008105 prephenate dehydratase; Provisional; Region: PRK11899 565050008106 Prephenate dehydratase; Region: PDT; pfam00800 565050008107 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 565050008108 putative L-Phe binding site [chemical binding]; other site 565050008109 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 565050008110 Ligand binding site; other site 565050008111 oligomer interface; other site 565050008112 Cytochrome c; Region: Cytochrom_C; cl11414 565050008113 NlpC/P60 family; Region: NLPC_P60; cl11438 565050008114 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 565050008115 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 565050008116 interface (dimer of trimers) [polypeptide binding]; other site 565050008117 Substrate-binding/catalytic site; other site 565050008118 Zn-binding sites [ion binding]; other site 565050008119 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 565050008120 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 565050008121 binding surface 565050008122 TPR motif; other site 565050008123 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 565050008124 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 565050008125 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 565050008126 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 565050008127 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 565050008128 ATP binding site [chemical binding]; other site 565050008129 Walker A motif; other site 565050008130 hexamer interface [polypeptide binding]; other site 565050008131 Walker B motif; other site 565050008132 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 565050008133 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 565050008134 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 565050008135 Pilus biogenesis CpaD protein (pilus_cpaD); Region: Pilus_CpaD; pfam09476 565050008136 Type IV pili component [Cell motility and secretion]; Region: COG5461; cl02279 565050008137 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 565050008138 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 565050008139 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 565050008140 SAF domain; Region: SAF; cl00555 565050008141 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 565050008142 Flp/Fap pilin component; Region: Flp_Fap; cl01585 565050008143 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 565050008144 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 565050008145 TadE-like protein; Region: TadE; cl10688 565050008146 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 565050008147 TadE-like protein; Region: TadE; cl10688 565050008148 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 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cl00224 565050008149 homodimer interface [polypeptide binding]; other site 565050008150 substrate-cofactor binding pocket; other site 565050008151 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050008152 catalytic residue [active] 565050008153 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 565050008154 aminodeoxychorismate synthase, component I, clade 2; Region: PabB-clade2; TIGR01824 565050008155 chorismate binding enzyme; Region: Chorismate_bind; cl10555 565050008156 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 565050008157 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 565050008158 Protein tyrosine/serine phosphatase [Signal transduction mechanisms]; Region: COG2365 565050008159 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 565050008160 Tyrosine phosphatase family C-terminal region; Region: Y_phosphatase3C; pfam13348 565050008161 OpgC protein; Region: OpgC_C; cl00792 565050008162 Acyltransferase family; Region: Acyl_transf_3; pfam01757 565050008163 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 565050008164 putative active site [active] 565050008165 metal binding site [ion binding]; metal-binding site 565050008166 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 565050008167 DJ-1 family protein; Region: not_thiJ; TIGR01383 565050008168 conserved cys residue [active] 565050008169 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 565050008170 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 565050008171 conserved cys residue [active] 565050008172 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 565050008173 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 565050008174 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_9; cd07245 565050008175 dimer interface [polypeptide binding]; other site 565050008176 putative metal binding site [ion binding]; other site 565050008177 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050008178 Predicted amidohydrolase [General function prediction only]; Region: COG0388 565050008179 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 565050008180 active site 565050008181 catalytic triad [active] 565050008182 dimer interface [polypeptide binding]; other site 565050008183 Protein of unknown function (DUF1003); Region: DUF1003; cl01831 565050008184 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 565050008185 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 565050008186 classical (c) SDR, subgroup 9; Region: SDR_c9; cd08931 565050008187 putative NAD(P) binding site [chemical binding]; other site 565050008188 active site 565050008189 Cell wall hydrolyses involved in spore germination [Cell envelope biogenesis, outer membrane]; Region: SleB; COG3773 565050008190 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 565050008191 DEC-1 protein, N-terminal region; Region: DEC-1_N; pfam04625 565050008192 Helix-turn-helix domains; Region: HTH; cl00088 565050008193 Cytochrome c; Region: Cytochrom_C; cl11414 565050008194 GAF domain; Region: GAF; cl15785 565050008195 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 565050008196 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 565050008197 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 565050008198 dimer interface [polypeptide binding]; other site 565050008199 phosphorylation site [posttranslational modification] 565050008200 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 565050008201 ATP binding site [chemical binding]; other site 565050008202 Mg2+ binding site [ion binding]; other site 565050008203 G-X-G motif; other site 565050008204 Response regulator receiver domain; Region: Response_reg; pfam00072 565050008205 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 565050008206 active site 565050008207 phosphorylation site [posttranslational modification] 565050008208 intermolecular recognition site; other site 565050008209 dimerization interface [polypeptide binding]; other site 565050008210 Helix-turn-helix domains; Region: HTH; cl00088 565050008211 glutathionine S-transferase; Provisional; Region: PRK10542 565050008212 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 565050008213 C-terminal domain interface [polypeptide binding]; other site 565050008214 GSH binding site (G-site) [chemical binding]; other site 565050008215 dimer interface [polypeptide binding]; other site 565050008216 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 565050008217 dimer interface [polypeptide binding]; other site 565050008218 N-terminal domain interface [polypeptide binding]; other site 565050008219 substrate binding pocket (H-site) [chemical binding]; other site 565050008220 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 565050008221 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 565050008222 active site 1 [active] 565050008223 dimer interface [polypeptide binding]; other site 565050008224 hexamer interface [polypeptide binding]; other site 565050008225 active site 2 [active] 565050008226 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 565050008227 Flagellin and related hook-associated proteins [Cell motility and secretion]; Region: FlgL; COG1344 565050008228 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050008229 Helix-turn-helix domains; Region: HTH; cl00088 565050008230 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 565050008231 homodimer interface [polypeptide binding]; other site 565050008232 NADP binding site [chemical binding]; other site 565050008233 active site 565050008234 Helix-turn-helix domains; Region: HTH; cl00088 565050008235 excinuclease ABC subunit B; Provisional; Region: PRK05298 565050008236 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 565050008237 ATP binding site [chemical binding]; other site 565050008238 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 565050008239 nucleotide binding region [chemical binding]; other site 565050008240 ATP-binding site [chemical binding]; other site 565050008241 Ultra-violet resistance protein B; Region: UvrB; pfam12344 565050008242 UvrB/uvrC motif; Region: UVR; pfam02151 565050008243 Uncharacterized protein conserved in bacteria (DUF2191); Region: DUF2191; cl02270 565050008244 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 565050008245 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 565050008246 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 565050008247 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 565050008248 dimer interface [polypeptide binding]; other site 565050008249 phosphorylation site [posttranslational modification] 565050008250 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 565050008251 ATP binding site [chemical binding]; other site 565050008252 Mg2+ binding site [ion binding]; other site 565050008253 G-X-G motif; other site 565050008254 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 565050008255 active site 565050008256 phosphorylation site [posttranslational modification] 565050008257 intermolecular recognition site; other site 565050008258 dimerization interface [polypeptide binding]; other site 565050008259 Protein of unknown function (DUF1624); Region: DUF1624; cl01394 565050008260 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 565050008261 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 565050008262 FMN binding site [chemical binding]; other site 565050008263 substrate binding site [chemical binding]; other site 565050008264 putative catalytic residue [active] 565050008265 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 565050008266 Heme NO binding; Region: HNOB; cl15268 565050008267 GAF domain; Region: GAF_2; pfam13185 565050008268 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 565050008269 dimer interface [polypeptide binding]; other site 565050008270 phosphorylation site [posttranslational modification] 565050008271 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 565050008272 ATP binding site [chemical binding]; other site 565050008273 Mg2+ binding site [ion binding]; other site 565050008274 G-X-G motif; other site 565050008275 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 565050008276 active site 565050008277 phosphorylation site [posttranslational modification] 565050008278 intermolecular recognition site; other site 565050008279 dimerization interface [polypeptide binding]; other site 565050008280 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 565050008281 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 565050008282 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 565050008283 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; cl12078 565050008284 Cytochrome P450; Region: p450; pfam00067 565050008285 OsmC-like protein; Region: OsmC; cl00767 565050008286 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; cl09155 565050008287 Mechanosensitive ion channel; Region: MS_channel; pfam00924 565050008288 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; cl00284 565050008289 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050008290 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; cl00284 565050008291 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 565050008292 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 565050008293 active site 565050008294 catalytic tetrad [active] 565050008295 PhnA protein; Region: PhnA; pfam03831 565050008296 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 565050008297 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 565050008298 DNA binding site [nucleotide binding] 565050008299 Int/Topo IB signature motif; other site 565050008300 active site 565050008301 shikimate kinase; Provisional; Region: PRK13946 565050008302 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 565050008303 ADP binding site [chemical binding]; other site 565050008304 magnesium binding site [ion binding]; other site 565050008305 putative shikimate binding site; other site 565050008306 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 565050008307 active site 565050008308 dimer interface [polypeptide binding]; other site 565050008309 metal binding site [ion binding]; metal-binding site 565050008310 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 565050008311 HSP70 interaction site [polypeptide binding]; other site 565050008312 BolA-like protein; Region: BolA; cl00386 565050008313 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 565050008314 active site 565050008315 catalytic motif [active] 565050008316 Zn binding site [ion binding]; other site 565050008317 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; cl00284 565050008318 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050008319 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; cl00284 565050008320 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 565050008321 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 565050008322 active site 565050008323 phosphorylation site [posttranslational modification] 565050008324 intermolecular recognition site; other site 565050008325 dimerization interface [polypeptide binding]; other site 565050008326 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 565050008327 Domain of unknown function DUF21; Region: DUF21; pfam01595 565050008328 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 565050008329 Transporter associated domain; Region: CorC_HlyC; cl08393 565050008330 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 565050008331 active site 565050008332 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 565050008333 Cobaltochelatase CobS subunit N terminal; Region: CobS_N; pfam12556 565050008334 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050008335 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 565050008336 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 565050008337 putative trimer interface [polypeptide binding]; other site 565050008338 putative CoA binding site [chemical binding]; other site 565050008339 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 565050008340 Predicted integral membrane protein [Function unknown]; Region: COG5658 565050008341 SdpI/YhfL protein family; Region: SdpI; pfam13630 565050008342 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 565050008343 dimerization interface [polypeptide binding]; other site 565050008344 putative DNA binding site [nucleotide binding]; other site 565050008345 putative Zn2+ binding site [ion binding]; other site 565050008346 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 565050008347 Class III alcohol dehydrogenase; Region: Zn_ADH_class_III; cd08279 565050008348 NAD binding site [chemical binding]; other site 565050008349 catalytic Zn binding site [ion binding]; other site 565050008350 substrate binding site [chemical binding]; other site 565050008351 structural Zn binding site [ion binding]; other site 565050008352 Na+/melibiose symporter and related transporters [Carbohydrate transport and metabolism]; Region: MelB; COG2211 565050008353 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 565050008354 phospholipase C, phosphocholine-specific, Pseudomonas-type; Region: PC_PLC; TIGR03396 565050008355 Phosphoesterase family; Region: Phosphoesterase; cl15450 565050008356 Domain of unknown function (DUF756); Region: DUF756; pfam05506 565050008357 Domain of unknown function (DUF756); Region: DUF756; pfam05506 565050008358 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 565050008359 M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins; Region: M20_PAAh_like; cd03896 565050008360 putative metal binding site [ion binding]; other site 565050008361 EamA-like transporter family; Region: EamA; cl01037 565050008362 putative peptidase; Provisional; Region: PRK11649 565050008363 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 565050008364 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 565050008365 active site 565050008366 phosphorylation site [posttranslational modification] 565050008367 intermolecular recognition site; other site 565050008368 dimerization interface [polypeptide binding]; other site 565050008369 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 565050008370 DNA binding site [nucleotide binding] 565050008371 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 565050008372 LytTr DNA-binding domain; Region: LytTR; cl04498 565050008373 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050008374 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 565050008375 Predicted dienelactone hydrolase [General function prediction only]; Region: COG4188 565050008376 Platelet-activating factor acetylhydrolase, isoform II; Region: PAF-AH_p_II; pfam03403 565050008377 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08927 565050008378 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 565050008379 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 565050008380 Walker A motif/ATP binding site; other site 565050008381 Walker B motif; other site 565050008382 Glycosyl hydrolase family 10; Region: Glyco_hydro_10; cl01495 565050008383 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 565050008384 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 565050008385 dimer interface [polypeptide binding]; other site 565050008386 active site 565050008387 heme binding site [chemical binding]; other site 565050008388 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 565050008389 Dehydratase family; Region: ILVD_EDD; cl00340 565050008390 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 565050008391 Helix-turn-helix domains; Region: HTH; cl00088 565050008392 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 565050008393 putative dimerization interface [polypeptide binding]; other site 565050008394 putative substrate binding pocket [chemical binding]; other site 565050008395 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 565050008396 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 565050008397 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_2; cd04869 565050008398 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 565050008399 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 565050008400 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 565050008401 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 565050008402 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050008403 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 565050008404 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 565050008405 DNA binding residues [nucleotide binding] 565050008406 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 565050008407 putative active site [active] 565050008408 heme pocket [chemical binding]; other site 565050008409 PAS domain S-box; Region: sensory_box; TIGR00229 565050008410 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 565050008411 putative active site [active] 565050008412 heme pocket [chemical binding]; other site 565050008413 PAS domain S-box; Region: sensory_box; TIGR00229 565050008414 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 565050008415 putative active site [active] 565050008416 heme pocket [chemical binding]; other site 565050008417 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 565050008418 Histidine kinase; Region: HisKA_2; cl06527 565050008419 DNA primase; Validated; Region: dnaG; PRK05667 565050008420 CHC2 zinc finger; Region: zf-CHC2; cl15369 565050008421 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 565050008422 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 565050008423 active site 565050008424 metal binding site [ion binding]; metal-binding site 565050008425 interdomain interaction site; other site 565050008426 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 565050008427 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 565050008428 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; cd00136 565050008429 protein binding site [polypeptide binding]; other site 565050008430 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4805 565050008431 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 565050008432 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 565050008433 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 565050008434 Fibronectin type III-like domain; Region: Fn3-like; cl15273 565050008435 Domain of unknown function (DUF303); Region: DUF303; pfam03629 565050008436 Domain of unknown function (DUF303); Region: DUF303; pfam03629 565050008437 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 565050008438 apolar tunnel; other site 565050008439 heme binding site [chemical binding]; other site 565050008440 dimerization interface [polypeptide binding]; other site 565050008441 Biofilm formation and stress response factor; Region: BsmA; cl01794 565050008442 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 565050008443 hypothetical protein; Provisional; Region: PRK13559 565050008444 Histidine kinase; Region: HisKA_2; cl06527 565050008445 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 565050008446 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 565050008447 active site 565050008448 phosphorylation site [posttranslational modification] 565050008449 intermolecular recognition site; other site 565050008450 dimerization interface [polypeptide binding]; other site 565050008451 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 565050008452 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 565050008453 FlgD Ig-like domain; Region: FlgD_ig; cl15790 565050008454 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 565050008455 ApbE family; Region: ApbE; cl00643 565050008456 Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism]; Region: CysJ; COG0369 565050008457 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 565050008458 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR_like1; cd06200 565050008459 FAD binding pocket [chemical binding]; other site 565050008460 FAD binding motif [chemical binding]; other site 565050008461 catalytic residues [active] 565050008462 NAD binding pocket [chemical binding]; other site 565050008463 phosphate binding motif [ion binding]; other site 565050008464 beta-alpha-beta structure motif; other site 565050008465 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 565050008466 Transcriptional regulators [Transcription]; Region: PurR; COG1609 565050008467 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 565050008468 DNA binding site [nucleotide binding] 565050008469 domain linker motif; other site 565050008470 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 565050008471 putative dimerization interface [polypeptide binding]; other site 565050008472 putative ligand binding site [chemical binding]; other site 565050008473 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 565050008474 heterotetramer interface [polypeptide binding]; other site 565050008475 active site pocket [active] 565050008476 cleavage site 565050008477 SurA N-terminal domain; Region: SurA_N_3; cl07813 565050008478 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 565050008479 PPIC-type PPIASE domain; Region: Rotamase; cl08278 565050008480 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 565050008481 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 565050008482 hypothetical protein; Provisional; Region: PRK10396 565050008483 SEC-C motif; Region: SEC-C; pfam02810 565050008484 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 565050008485 putative substrate translocation pore; other site 565050008486 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 565050008487 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 565050008488 dimerization interface [polypeptide binding]; other site 565050008489 putative DNA binding site [nucleotide binding]; other site 565050008490 putative Zn2+ binding site [ion binding]; other site 565050008491 Bacterial SH3 domain; Region: SH3_3; cl02551 565050008492 CAAX protease self-immunity; Region: Abi; cl00558 565050008493 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 565050008494 dimer interface [polypeptide binding]; other site 565050008495 phosphorylation site [posttranslational modification] 565050008496 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 565050008497 ATP binding site [chemical binding]; other site 565050008498 Mg2+ binding site [ion binding]; other site 565050008499 G-X-G motif; other site 565050008500 Response regulator receiver domain; Region: Response_reg; pfam00072 565050008501 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 565050008502 active site 565050008503 phosphorylation site [posttranslational modification] 565050008504 intermolecular recognition site; other site 565050008505 dimerization interface [polypeptide binding]; other site 565050008506 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 565050008507 classical (c) SDRs; Region: SDR_c; cd05233 565050008508 NAD(P) binding site [chemical binding]; other site 565050008509 active site 565050008510 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_3; cd08896 565050008511 putative hydrophobic ligand binding site [chemical binding]; other site 565050008512 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 565050008513 putative substrate translocation pore; other site 565050008514 Protein of unknown function DUF86; Region: DUF86; cl01031 565050008515 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 565050008516 active site 565050008517 NTP binding site [chemical binding]; other site 565050008518 metal binding triad [ion binding]; metal-binding site 565050008519 antibiotic binding site [chemical binding]; other site 565050008520 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of...; Region: MM_CoA_mutase; cl00817 565050008521 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 565050008522 B12 binding site [chemical binding]; other site 565050008523 cobalt ligand [ion binding]; other site 565050008524 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 565050008525 DNA binding residues [nucleotide binding] 565050008526 Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_2_FMN; cd04733 565050008527 putative active site [active] 565050008528 putative FMN binding site [chemical binding]; other site 565050008529 putative substrate binding site [chemical binding]; other site 565050008530 putative catalytic residue [active] 565050008531 enoyl-CoA hydratase; Provisional; Region: PRK07658 565050008532 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 565050008533 substrate binding site [chemical binding]; other site 565050008534 oxyanion hole (OAH) forming residues; other site 565050008535 trimer interface [polypeptide binding]; other site 565050008536 crotonyl-CoA reductase; Region: crotonyl_coA_red; cd08246 565050008537 crotonyl-CoA reductase; Region: crot-CoA-red; TIGR01751 565050008538 putative NAD(P) binding site [chemical binding]; other site 565050008539 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 565050008540 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050008541 Domain of unknown function (DUF3471); Region: DUF3471; pfam11954 565050008542 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 565050008543 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 565050008544 active site 565050008545 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 565050008546 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 565050008547 putative C-terminal domain interface [polypeptide binding]; other site 565050008548 putative GSH binding site (G-site) [chemical binding]; other site 565050008549 putative dimer interface [polypeptide binding]; other site 565050008550 C-terminal, alpha helical domain of GTT1-like Glutathione S-transferases; Region: GST_C_GTT1_like; cd03189 565050008551 putative N-terminal domain interface [polypeptide binding]; other site 565050008552 putative dimer interface [polypeptide binding]; other site 565050008553 putative substrate binding pocket (H-site) [chemical binding]; other site 565050008554 Protein of unknown function (DUF2855); Region: DUF2855; pfam11017 565050008555 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 565050008556 EamA-like transporter family; Region: EamA; cl01037 565050008557 Epoxide hydrolase N terminus; Region: EHN; pfam06441 565050008558 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 565050008559 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 565050008560 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 565050008561 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 565050008562 tetramer interface [polypeptide binding]; other site 565050008563 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050008564 catalytic residue [active] 565050008565 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 565050008566 PAS domain S-box; Region: sensory_box; TIGR00229 565050008567 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 565050008568 putative active site [active] 565050008569 heme pocket [chemical binding]; other site 565050008570 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 565050008571 metal binding site [ion binding]; metal-binding site 565050008572 active site 565050008573 I-site; other site 565050008574 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 565050008575 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 565050008576 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 565050008577 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050008578 Zn binding site [ion binding]; other site 565050008579 Membrane protein of unknown function; Region: DUF360; cl00850 565050008580 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 565050008581 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 565050008582 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050008583 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 565050008584 DNA binding residues [nucleotide binding] 565050008585 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050008586 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; cl12031 565050008587 Response regulator receiver domain; Region: Response_reg; pfam00072 565050008588 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 565050008589 active site 565050008590 phosphorylation site [posttranslational modification] 565050008591 intermolecular recognition site; other site 565050008592 dimerization interface [polypeptide binding]; other site 565050008593 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 565050008594 dimer interface [polypeptide binding]; other site 565050008595 phosphorylation site [posttranslational modification] 565050008596 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 565050008597 ATP binding site [chemical binding]; other site 565050008598 Mg2+ binding site [ion binding]; other site 565050008599 G-X-G motif; other site 565050008600 Response regulator receiver domain; Region: Response_reg; pfam00072 565050008601 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 565050008602 active site 565050008603 phosphorylation site [posttranslational modification] 565050008604 intermolecular recognition site; other site 565050008605 dimerization interface [polypeptide binding]; other site 565050008606 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 565050008607 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 565050008608 GDP-binding site [chemical binding]; other site 565050008609 ACT binding site; other site 565050008610 IMP binding site; other site 565050008611 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 565050008612 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 565050008613 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 565050008614 tetramer interface [polypeptide binding]; other site 565050008615 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050008616 catalytic residue [active] 565050008617 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 565050008618 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 565050008619 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 565050008620 catalytic residue [active] 565050008621 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 565050008622 PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain; Region: PA; cl08238 565050008623 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 565050008624 PA/protease or protease-like domain interface [polypeptide binding]; other site 565050008625 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 565050008626 metal binding site [ion binding]; metal-binding site 565050008627 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 565050008628 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 565050008629 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 565050008630 Protein of unknown function DUF72; Region: DUF72; cl00777 565050008631 Phospholipid methyltransferase; Region: PEMT; cl00763 565050008632 acetyl-CoA acetyltransferase; Provisional; Region: PRK06289 565050008633 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 565050008634 active site 565050008635 Helix-turn-helix domains; Region: HTH; cl00088 565050008636 Helix-turn-helix domains; Region: HTH; cl00088 565050008637 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 565050008638 L-Ala-D/L-Glu epimerase; Provisional; Region: PRK15129 565050008639 active site 565050008640 Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); Region: PHA_gran_rgn; cl09865 565050008641 Protein of unknown function (DUF983); Region: DUF983; cl02211 565050008642 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 565050008643 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050008644 DNA-binding site [nucleotide binding]; DNA binding site 565050008645 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 565050008646 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050008647 homodimer interface [polypeptide binding]; other site 565050008648 catalytic residue [active] 565050008649 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050008650 Helix-turn-helix domains; Region: HTH; cl00088 565050008651 WHG domain; Region: WHG; pfam13305 565050008652 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 565050008653 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050008654 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050008655 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 565050008656 Protein export membrane protein; Region: SecD_SecF; cl14618 565050008657 Protein export membrane protein; Region: SecD_SecF; cl14618 565050008658 Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG1233 565050008659 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050008660 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 565050008661 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 565050008662 [2Fe-2S] cluster binding site [ion binding]; other site 565050008663 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 565050008664 alpha subunit interface [polypeptide binding]; other site 565050008665 active site 565050008666 substrate binding site [chemical binding]; other site 565050008667 Fe binding site [ion binding]; other site 565050008668 Helix-turn-helix domains; Region: HTH; cl00088 565050008669 Bacterial transcriptional repressor; Region: TetR_C_6; cl07106 565050008670 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 565050008671 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 565050008672 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_A; cd01299 565050008673 active site 565050008674 transporter, basic amino acid/polyamine antiporter (APA) family; Region: 2A0302; TIGR00905 565050008675 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050008676 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 565050008677 N-terminal plug; other site 565050008678 ligand-binding site [chemical binding]; other site 565050008679 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 565050008680 TPR motif; other site 565050008681 binding surface 565050008682 TPR repeat; Region: TPR_11; pfam13414 565050008683 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 565050008684 binding surface 565050008685 TPR motif; other site 565050008686 TPR repeat; Region: TPR_11; pfam13414 565050008687 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 565050008688 binding surface 565050008689 TPR motif; other site 565050008690 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 565050008691 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050008692 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 565050008693 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 565050008694 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 565050008695 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 565050008696 putative aminotransferase; Validated; Region: PRK07480 565050008697 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 565050008698 inhibitor-cofactor binding pocket; inhibition site 565050008699 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050008700 catalytic residue [active] 565050008701 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 565050008702 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 565050008703 catalytic triad [active] 565050008704 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 565050008705 PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required...; Region: ABC_PotA_N; cd03300 565050008706 Walker A/P-loop; other site 565050008707 ATP binding site [chemical binding]; other site 565050008708 Q-loop/lid; other site 565050008709 ABC transporter signature motif; other site 565050008710 Walker B; other site 565050008711 D-loop; other site 565050008712 H-loop/switch region; other site 565050008713 TOBE domain; Region: TOBE_2; cl01440 565050008714 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 565050008715 dimer interface [polypeptide binding]; other site 565050008716 conserved gate region; other site 565050008717 putative PBP binding loops; other site 565050008718 ABC-ATPase subunit interface; other site 565050008719 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 565050008720 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 565050008721 dimer interface [polypeptide binding]; other site 565050008722 conserved gate region; other site 565050008723 putative PBP binding loops; other site 565050008724 ABC-ATPase subunit interface; other site 565050008725 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 565050008726 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 565050008727 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 565050008728 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 565050008729 aminotransferase; Validated; Region: PRK07046 565050008730 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 565050008731 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 565050008732 catalytic residue [active] 565050008733 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 565050008734 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 565050008735 tetramerization interface [polypeptide binding]; other site 565050008736 NAD(P) binding site [chemical binding]; other site 565050008737 catalytic residues [active] 565050008738 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 565050008739 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 565050008740 NAD(P) binding site [chemical binding]; other site 565050008741 catalytic residues [active] 565050008742 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 565050008743 FCD domain; Region: FCD; cl11656 565050008744 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 565050008745 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 565050008746 inhibitor-cofactor binding pocket; inhibition site 565050008747 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050008748 catalytic residue [active] 565050008749 Uncharacterized protein conserved in bacteria (DUF2332); Region: DUF2332; cl01837 565050008750 CHASE3 domain; Region: CHASE3; cl05000 565050008751 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050008752 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050008753 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050008754 dimer interface [polypeptide binding]; other site 565050008755 putative CheW interface [polypeptide binding]; other site 565050008756 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; cl00284 565050008757 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050008758 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; cl00284 565050008759 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; cl00284 565050008760 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050008761 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; cl00284 565050008762 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 565050008763 Helix-turn-helix domains; Region: HTH; cl00088 565050008764 BlaR1 peptidase M56; Region: Peptidase_M56; cl15829 565050008765 Pectate lyase; Region: Pec_lyase_C; cl01593 565050008766 PemK-like protein; Region: PemK; cl00995 565050008767 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 565050008768 Tetramer interface [polypeptide binding]; other site 565050008769 active site 565050008770 FMN-binding site [chemical binding]; other site 565050008771 Response regulator receiver domain; Region: Response_reg; pfam00072 565050008772 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 565050008773 active site 565050008774 phosphorylation site [posttranslational modification] 565050008775 intermolecular recognition site; other site 565050008776 dimerization interface [polypeptide binding]; other site 565050008777 Cupin domain; Region: Cupin_2; cl09118 565050008778 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 565050008779 active site 565050008780 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 565050008781 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 565050008782 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 565050008783 Ligand Binding Site [chemical binding]; other site 565050008784 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; cl00284 565050008785 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; cl00284 565050008786 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; cl00284 565050008787 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 565050008788 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 565050008789 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 565050008790 ATP binding site [chemical binding]; other site 565050008791 Mg2+ binding site [ion binding]; other site 565050008792 G-X-G motif; other site 565050008793 Response regulator receiver domain; Region: Response_reg; pfam00072 565050008794 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 565050008795 active site 565050008796 phosphorylation site [posttranslational modification] 565050008797 intermolecular recognition site; other site 565050008798 dimerization interface [polypeptide binding]; other site 565050008799 Protein of unknown function (DUF962); Region: DUF962; cl01879 565050008800 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 565050008801 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 565050008802 non-specific DNA binding site [nucleotide binding]; other site 565050008803 salt bridge; other site 565050008804 sequence-specific DNA binding site [nucleotide binding]; other site 565050008805 PilZ domain; Region: PilZ; cl01260 565050008806 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 565050008807 glucokinase, proteobacterial type; Region: glk; TIGR00749 565050008808 methionine gamma-lyase; Provisional; Region: PRK07503 565050008809 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 565050008810 homodimer interface [polypeptide binding]; other site 565050008811 substrate-cofactor binding pocket; other site 565050008812 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050008813 catalytic residue [active] 565050008814 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 565050008815 Helix-turn-helix domains; Region: HTH; cl00088 565050008816 PAS fold; Region: PAS_4; pfam08448 565050008817 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 565050008818 PAS domain; Region: PAS_9; pfam13426 565050008819 putative active site [active] 565050008820 heme pocket [chemical binding]; other site 565050008821 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 565050008822 Histidine kinase; Region: HisKA_2; cl06527 565050008823 Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins; Region: GDPD_AtGDE_like; cd08566 565050008824 putative active site [active] 565050008825 catalytic site [active] 565050008826 putative metal binding site [ion binding]; other site 565050008827 oligomer interface [polypeptide binding]; other site 565050008828 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 565050008829 putative ADP-binding pocket [chemical binding]; other site 565050008830 Predicted dehydrogenase [General function prediction only]; Region: COG0579 565050008831 short chain dehydrogenase; Provisional; Region: PRK06181 565050008832 classical (c) SDRs; Region: SDR_c; cd05233 565050008833 NAD(P) binding site [chemical binding]; other site 565050008834 active site 565050008835 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 565050008836 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 565050008837 dimer interface [polypeptide binding]; other site 565050008838 PYR/PP interface [polypeptide binding]; other site 565050008839 TPP binding site [chemical binding]; other site 565050008840 substrate binding site [chemical binding]; other site 565050008841 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 565050008842 TPP-binding site [chemical binding]; other site 565050008843 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 565050008844 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 565050008845 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 565050008846 putative DNA binding site [nucleotide binding]; other site 565050008847 putative Zn2+ binding site [ion binding]; other site 565050008848 Helix-turn-helix domains; Region: HTH; cl00088 565050008849 Pirin-related protein [General function prediction only]; Region: COG1741 565050008850 Cupin domain; Region: Cupin_2; cl09118 565050008851 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 565050008852 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 565050008853 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 565050008854 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 565050008855 active site 565050008856 purine riboside binding site [chemical binding]; other site 565050008857 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 565050008858 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 565050008859 Helix-turn-helix domains; Region: HTH; cl00088 565050008860 YcfA-like protein; Region: YcfA; cl00752 565050008861 Uncharacterized protein family (UPF0150); Region: UPF0150; cl00691 565050008862 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 565050008863 Uncharacterized protein conserved in bacteria (DUF2199); Region: DUF2199; cl02048 565050008864 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 565050008865 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 565050008866 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 565050008867 AMP-binding enzyme; Region: AMP-binding; cl15778 565050008868 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 565050008869 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 565050008870 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 565050008871 substrate binding site [chemical binding]; other site 565050008872 oxyanion hole (OAH) forming residues; other site 565050008873 trimer interface [polypeptide binding]; other site 565050008874 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050008875 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 565050008876 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 565050008877 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 565050008878 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050008879 PAS domain; Region: PAS_9; pfam13426 565050008880 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 565050008881 putative active site [active] 565050008882 heme pocket [chemical binding]; other site 565050008883 PAS fold; Region: PAS_3; pfam08447 565050008884 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 565050008885 dimer interface [polypeptide binding]; other site 565050008886 phosphorylation site [posttranslational modification] 565050008887 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 565050008888 ATP binding site [chemical binding]; other site 565050008889 Mg2+ binding site [ion binding]; other site 565050008890 G-X-G motif; other site 565050008891 Response regulator receiver domain; Region: Response_reg; pfam00072 565050008892 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 565050008893 active site 565050008894 phosphorylation site [posttranslational modification] 565050008895 intermolecular recognition site; other site 565050008896 dimerization interface [polypeptide binding]; other site 565050008897 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050008898 Helix-turn-helix domains; Region: HTH; cl00088 565050008899 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050008900 Helix-turn-helix domains; Region: HTH; cl00088 565050008901 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; cl00284 565050008902 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 565050008903 ligand-binding site [chemical binding]; other site 565050008904 multidrug resistance outer membrane protein MdtQ; Provisional; Region: PRK11459 565050008905 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 565050008906 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 565050008907 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050008908 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 565050008909 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 565050008910 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 565050008911 Histidine kinase; Region: HisKA_2; cl06527 565050008912 elongation factor Tu; Reviewed; Region: PRK00049 565050008913 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 565050008914 G1 box; other site 565050008915 GEF interaction site [polypeptide binding]; other site 565050008916 GTP/Mg2+ binding site [chemical binding]; other site 565050008917 Switch I region; other site 565050008918 G2 box; other site 565050008919 G3 box; other site 565050008920 Switch II region; other site 565050008921 G4 box; other site 565050008922 G5 box; other site 565050008923 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 565050008924 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 565050008925 Antibiotic Binding Site [chemical binding]; other site 565050008926 elongation factor G; Reviewed; Region: PRK00007 565050008927 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 565050008928 G1 box; other site 565050008929 putative GEF interaction site [polypeptide binding]; other site 565050008930 GTP/Mg2+ binding site [chemical binding]; other site 565050008931 Switch I region; other site 565050008932 G2 box; other site 565050008933 G3 box; other site 565050008934 Switch II region; other site 565050008935 G4 box; other site 565050008936 G5 box; other site 565050008937 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 565050008938 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 565050008939 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 565050008940 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 565050008941 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 565050008942 S17 interaction site [polypeptide binding]; other site 565050008943 S8 interaction site; other site 565050008944 16S rRNA interaction site [nucleotide binding]; other site 565050008945 streptomycin interaction site [chemical binding]; other site 565050008946 23S rRNA interaction site [nucleotide binding]; other site 565050008947 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 565050008948 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; cl12031 565050008949 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 565050008950 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 565050008951 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 565050008952 putative homodimer interface [polypeptide binding]; other site 565050008953 KOW motif; Region: KOW; cl00354 565050008954 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 565050008955 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 565050008956 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 565050008957 FAD binding pocket [chemical binding]; other site 565050008958 FAD binding motif [chemical binding]; other site 565050008959 phosphate binding motif [ion binding]; other site 565050008960 beta-alpha-beta structure motif; other site 565050008961 NAD binding pocket [chemical binding]; other site 565050008962 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 565050008963 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 565050008964 dimer interface [polypeptide binding]; other site 565050008965 putative functional site; other site 565050008966 putative MPT binding site; other site 565050008967 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 565050008968 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 565050008969 NAD(P) binding site [chemical binding]; other site 565050008970 homodimer interface [polypeptide binding]; other site 565050008971 substrate binding site [chemical binding]; other site 565050008972 active site 565050008973 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 565050008974 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 565050008975 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 565050008976 generic binding surface I; other site 565050008977 generic binding surface II; other site 565050008978 DNA Polymerase Y-family; Region: PolY_like; cd03468 565050008979 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 565050008980 DNA binding site [nucleotide binding] 565050008981 Cell division inhibitor SulA; Region: SulA; cl01880 565050008982 pyruvate carboxylase; Reviewed; Region: PRK12999 565050008983 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 565050008984 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 565050008985 Biotin carboxyl carrier protein [Lipid metabolism]; Region: AccB; COG0511 565050008986 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 565050008987 carboxyltransferase (CT) interaction site; other site 565050008988 biotinylation site [posttranslational modification]; other site 565050008989 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 565050008990 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 565050008991 VanZ like family; Region: VanZ; cl01971 565050008992 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 565050008993 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050008994 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 565050008995 putative L-serine binding site [chemical binding]; other site 565050008996 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; cd01494 565050008997 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 565050008998 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 565050008999 catalytic residue [active] 565050009000 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050009001 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 565050009002 dimer interface [polypeptide binding]; other site 565050009003 phosphorylation site [posttranslational modification] 565050009004 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 565050009005 ATP binding site [chemical binding]; other site 565050009006 Mg2+ binding site [ion binding]; other site 565050009007 G-X-G motif; other site 565050009008 Response regulator receiver domain; Region: Response_reg; pfam00072 565050009009 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 565050009010 active site 565050009011 phosphorylation site [posttranslational modification] 565050009012 intermolecular recognition site; other site 565050009013 dimerization interface [polypeptide binding]; other site 565050009014 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 565050009015 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 565050009016 Bacterial protein of unknown function (DUF925); Region: DUF925; cl01435 565050009017 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 565050009018 dimer interface [polypeptide binding]; other site 565050009019 substrate binding site [chemical binding]; other site 565050009020 ATP binding site [chemical binding]; other site 565050009021 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 565050009022 dihydropteroate synthase; Region: DHPS; TIGR01496 565050009023 substrate binding pocket [chemical binding]; other site 565050009024 dimer interface [polypeptide binding]; other site 565050009025 inhibitor binding site; inhibition site 565050009026 PAS domain; Region: PAS_9; pfam13426 565050009027 sensory histidine kinase AtoS; Provisional; Region: PRK11360 565050009028 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 565050009029 ATP binding site [chemical binding]; other site 565050009030 Mg2+ binding site [ion binding]; other site 565050009031 G-X-G motif; other site 565050009032 Response regulator receiver domain; Region: Response_reg; pfam00072 565050009033 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 565050009034 active site 565050009035 phosphorylation site [posttranslational modification] 565050009036 intermolecular recognition site; other site 565050009037 dimerization interface [polypeptide binding]; other site 565050009038 FtsH Extracellular; Region: FtsH_ext; pfam06480 565050009039 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 565050009040 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 565050009041 Walker A motif; other site 565050009042 ATP binding site [chemical binding]; other site 565050009043 Walker B motif; other site 565050009044 arginine finger; other site 565050009045 Peptidase family M41; Region: Peptidase_M41; pfam01434 565050009046 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 565050009047 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 565050009048 Tetratricopeptide repeat; Region: TPR_6; pfam13174 565050009049 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 565050009050 ligand binding site [chemical binding]; other site 565050009051 translocation protein TolB; Provisional; Region: tolB; PRK05137 565050009052 TolB amino-terminal domain; Region: TolB_N; cl00639 565050009053 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 565050009054 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 565050009055 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 565050009056 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 565050009057 Gram-negative bacterial tonB protein; Region: TonB; cl10048 565050009058 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 565050009059 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 565050009060 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 565050009061 active site 565050009062 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 565050009063 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 565050009064 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 565050009065 Walker A motif; other site 565050009066 ATP binding site [chemical binding]; other site 565050009067 Walker B motif; other site 565050009068 arginine finger; other site 565050009069 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 565050009070 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 565050009071 RuvA N terminal domain; Region: RuvA_N; pfam01330 565050009072 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 includes...; Region: RuvC_resolvase; cd00529 565050009073 active site 565050009074 putative DNA-binding cleft [nucleotide binding]; other site 565050009075 dimer interface [polypeptide binding]; other site 565050009076 hypothetical protein; Provisional; Region: PRK09133 565050009077 M20 Peptidase, carboxypeptidase yscS-like; Region: M20_yscS_like; cd05675 565050009078 putative metal binding site [ion binding]; other site 565050009079 NlpC/P60 family; Region: NLPC_P60; cl11438 565050009080 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 565050009081 ATP binding site [chemical binding]; other site 565050009082 active site 565050009083 substrate binding site [chemical binding]; other site 565050009084 Transcriptional regulator; Region: Transcrip_reg; cl00361 565050009085 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 565050009086 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 565050009087 putative active site [active] 565050009088 metal binding site [ion binding]; metal-binding site 565050009089 homodimer binding site [polypeptide binding]; other site 565050009090 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 565050009091 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 565050009092 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; cl12031 565050009093 Cell division protein ZapA; Region: ZapA; cl01146 565050009094 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009095 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 565050009096 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 565050009097 Phosphoglycerate kinase; Region: PGK; pfam00162 565050009098 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 565050009099 substrate binding site [chemical binding]; other site 565050009100 hinge regions; other site 565050009101 ADP binding site [chemical binding]; other site 565050009102 catalytic site [active] 565050009103 hypothetical protein; Provisional; Region: PRK08185 565050009104 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 565050009105 intersubunit interface [polypeptide binding]; other site 565050009106 active site 565050009107 zinc binding site [ion binding]; other site 565050009108 Na+ binding site [ion binding]; other site 565050009109 Protein of unknown function (DUF1109); Region: DUF1109; cl02071 565050009110 RNA polymerase sigma factor; Provisional; Region: PRK12536 565050009111 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050009112 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 565050009113 DNA binding residues [nucleotide binding] 565050009114 Predicted integral membrane protein (DUF2282); Region: DUF2282; cl02366 565050009115 Protein of unknown function (DUF692); Region: DUF692; cl01263 565050009116 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 565050009117 DoxX; Region: DoxX; cl00976 565050009118 Response regulator receiver domain; Region: Response_reg; pfam00072 565050009119 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 565050009120 active site 565050009121 phosphorylation site [posttranslational modification] 565050009122 intermolecular recognition site; other site 565050009123 dimerization interface [polypeptide binding]; other site 565050009124 TspO/MBR family; Region: TspO_MBR; cl01379 565050009125 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 565050009126 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 565050009127 Coenzyme A binding pocket [chemical binding]; other site 565050009128 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 565050009129 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 565050009130 heme binding site [chemical binding]; other site 565050009131 ferroxidase pore; other site 565050009132 ferroxidase diiron center [ion binding]; other site 565050009133 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 565050009134 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 565050009135 thiamine phosphate binding site [chemical binding]; other site 565050009136 active site 565050009137 pyrophosphate binding site [ion binding]; other site 565050009138 RNA polymerase sigma factor SigJ; Provisional; Region: PRK09636 565050009139 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050009140 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050009141 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 565050009142 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 565050009143 active site 565050009144 dimerization interface [polypeptide binding]; other site 565050009145 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050009146 Protein of unknown function (DUF2975); Region: DUF2975; pfam11188 565050009147 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 565050009148 Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins; Region: GDPD_ScGlpQ1_like; cd08602 565050009149 putative active site [active] 565050009150 catalytic site [active] 565050009151 putative metal binding site [ion binding]; other site 565050009152 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 565050009153 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 565050009154 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the...; Region: ABC_MTABC3_MDL1_MDL2; cd03249 565050009155 Walker A/P-loop; other site 565050009156 ATP binding site [chemical binding]; other site 565050009157 Q-loop/lid; other site 565050009158 ABC transporter signature motif; other site 565050009159 Walker B; other site 565050009160 D-loop; other site 565050009161 H-loop/switch region; other site 565050009162 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 565050009163 Flagellin N-methylase; Region: FliB; cl00497 565050009164 Transglycosylase; Region: Transgly; cl07896 565050009165 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 565050009166 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050009167 aspartate racemase; Region: asp_race; TIGR00035 565050009168 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 565050009169 ABC-2 type transporter; Region: ABC2_membrane; cl11417 565050009170 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 565050009171 The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance. Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme...; Region: ABC_BcrA_bacitracin_resist; cd03268 565050009172 Walker A/P-loop; other site 565050009173 ATP binding site [chemical binding]; other site 565050009174 Q-loop/lid; other site 565050009175 ABC transporter signature motif; other site 565050009176 Walker B; other site 565050009177 D-loop; other site 565050009178 H-loop/switch region; other site 565050009179 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050009180 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 565050009181 ATP-grasp domain; Region: ATP-grasp_4; cl03087 565050009182 AIR carboxylase; Region: AIRC; cl00310 565050009183 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 565050009184 metal binding site [ion binding]; metal-binding site 565050009185 active site 565050009186 I-site; other site 565050009187 Response regulator receiver domain; Region: Response_reg; pfam00072 565050009188 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 565050009189 active site 565050009190 phosphorylation site [posttranslational modification] 565050009191 intermolecular recognition site; other site 565050009192 dimerization interface [polypeptide binding]; other site 565050009193 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 565050009194 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 565050009195 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 565050009196 protein binding site [polypeptide binding]; other site 565050009197 Protein of unknown function (DUF465); Region: DUF465; cl01070 565050009198 Protein of unknown function (DUF2390); Region: DUF2390; cl02376 565050009199 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 565050009200 Flavoprotein; Region: Flavoprotein; cl08021 565050009201 Protein of unknown function (DUF465); Region: DUF465; cl01070 565050009202 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 565050009203 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 565050009204 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 565050009205 NAD(P) binding site [chemical binding]; other site 565050009206 Protein of unknown function (DUF1192); Region: DUF1192; cl11573 565050009207 Protein of unknown function (DUF1465); Region: DUF1465; cl11562 565050009208 Uncharacterized conserved protein [Function unknown]; Region: COG5590 565050009209 Helix-turn-helix domains; Region: HTH; cl00088 565050009210 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 565050009211 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 565050009212 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4152 565050009213 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050009214 Walker A/P-loop; other site 565050009215 ATP binding site [chemical binding]; other site 565050009216 Q-loop/lid; other site 565050009217 ABC transporter signature motif; other site 565050009218 Walker B; other site 565050009219 D-loop; other site 565050009220 H-loop/switch region; other site 565050009221 Domain of unknown function (DUF4162); Region: DUF4162; pfam13732 565050009222 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050009223 Peptidase family M23; Region: Peptidase_M23; pfam01551 565050009224 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 565050009225 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 565050009226 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 565050009227 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 565050009228 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 565050009229 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009230 Bacterial aa3 type cytochrome c oxidase subunit IV; Region: COX4_pro_2; pfam07835 565050009231 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 565050009232 putative active site [active] 565050009233 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050009234 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; cl12031 565050009235 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 565050009236 CoenzymeA binding site [chemical binding]; other site 565050009237 subunit interaction site [polypeptide binding]; other site 565050009238 PHB binding site; other site 565050009239 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 565050009240 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050009241 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050009242 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 565050009243 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 565050009244 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 565050009245 active site 565050009246 Zn binding site [ion binding]; other site 565050009247 Protein of unknown function (DUF419); Region: DUF419; cl15265 565050009248 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 565050009249 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 565050009250 active site 565050009251 phosphorylation site [posttranslational modification] 565050009252 intermolecular recognition site; other site 565050009253 dimerization interface [polypeptide binding]; other site 565050009254 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 565050009255 Walker A motif; other site 565050009256 ATP binding site [chemical binding]; other site 565050009257 Walker B motif; other site 565050009258 arginine finger; other site 565050009259 Helix-turn-helix domains; Region: HTH; cl00088 565050009260 Helix-turn-helix domains; Region: HTH; cl00088 565050009261 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; cl11480 565050009262 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 565050009263 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 565050009264 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 565050009265 lytic murein transglycosylase; Region: MltB_2; TIGR02283 565050009266 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 565050009267 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 565050009268 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 565050009269 aldose 1-epimerase, similar to Escherichia coli YphB; Region: Aldose_epim_Ec_YphB; cd09021 565050009270 active site 565050009271 catalytic residues [active] 565050009272 Protein of unknown function (DUF1006); Region: DUF1006; cl15826 565050009273 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 565050009274 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 565050009275 active site 565050009276 phosphorylation site [posttranslational modification] 565050009277 intermolecular recognition site; other site 565050009278 dimerization interface [polypeptide binding]; other site 565050009279 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 565050009280 DNA binding site [nucleotide binding] 565050009281 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4254 565050009282 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 565050009283 putative peptidoglycan binding site; other site 565050009284 FecR protein; Region: FecR; pfam04773 565050009285 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 565050009286 CHASE2 domain; Region: CHASE2; cl01732 565050009287 PAS fold; Region: PAS_4; pfam08448 565050009288 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 565050009289 putative active site [active] 565050009290 heme pocket [chemical binding]; other site 565050009291 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 565050009292 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 565050009293 ATP binding site [chemical binding]; other site 565050009294 Mg2+ binding site [ion binding]; other site 565050009295 G-X-G motif; other site 565050009296 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 565050009297 Transposase domain (DUF772); Region: DUF772; cl15789 565050009298 Transposase domain (DUF772); Region: DUF772; cl15789 565050009299 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 565050009300 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050009301 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 565050009302 N-terminal plug; other site 565050009303 ligand-binding site [chemical binding]; other site 565050009304 M28 Zn-peptidase Endoplasmic reticulum metallopeptidase 1; Region: M28_Fxna_like; cd03875 565050009305 metal binding site [ion binding]; metal-binding site 565050009306 acyl-CoA synthetase; Provisional; Region: PRK12582 565050009307 AMP-binding enzyme; Region: AMP-binding; cl15778 565050009308 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009309 Predicted methyltransferase regulatory domain; Region: MethyTransf_Reg; pfam10119 565050009310 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050009311 Helix-turn-helix domains; Region: HTH; cl00088 565050009312 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 565050009313 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 565050009314 putative active site [active] 565050009315 putative metal binding site [ion binding]; other site 565050009316 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 565050009317 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 565050009318 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 565050009319 Vitamin K-dependent gamma-carboxylase; Region: VKG_Carbox; cl02773 565050009320 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 565050009321 PAS domain; Region: PAS_9; pfam13426 565050009322 putative active site [active] 565050009323 heme pocket [chemical binding]; other site 565050009324 PAS domain; Region: PAS_9; pfam13426 565050009325 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 565050009326 putative active site [active] 565050009327 heme pocket [chemical binding]; other site 565050009328 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050009329 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050009330 dimer interface [polypeptide binding]; other site 565050009331 putative CheW interface [polypeptide binding]; other site 565050009332 Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG1003 565050009333 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 565050009334 tetramer interface [polypeptide binding]; other site 565050009335 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050009336 catalytic residue [active] 565050009337 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 565050009338 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 565050009339 tetramer interface [polypeptide binding]; other site 565050009340 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050009341 catalytic residue [active] 565050009342 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 565050009343 lipoyl attachment site [posttranslational modification]; other site 565050009344 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 565050009345 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 565050009346 ORF6N domain; Region: ORF6N; pfam10543 565050009347 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 565050009348 active site 565050009349 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050009350 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 565050009351 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 565050009352 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 565050009353 dimer interface [polypeptide binding]; other site 565050009354 putative CheW interface [polypeptide binding]; other site 565050009355 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 565050009356 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 565050009357 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 565050009358 active site 565050009359 HIGH motif; other site 565050009360 nucleotide binding site [chemical binding]; other site 565050009361 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 565050009362 KMSK motif region; other site 565050009363 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 565050009364 tRNA binding surface [nucleotide binding]; other site 565050009365 anticodon binding site; other site 565050009366 LytB protein; Region: LYTB; cl00507 565050009367 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 565050009368 Fic/DOC family; Region: Fic; cl00960 565050009369 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 565050009370 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 565050009371 Phosphotransferase enzyme family; Region: APH; pfam01636 565050009372 putative active site [active] 565050009373 putative substrate binding site [chemical binding]; other site 565050009374 ATP binding site [chemical binding]; other site 565050009375 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 565050009376 RNA/DNA hybrid binding site [nucleotide binding]; other site 565050009377 active site 565050009378 Member of the Rhodanese Homology Domain superfamily. This CD includes the putative rhodanese-like protein, Psp2, of Yersinia pestis biovar Medievalis and other similar uncharacterized proteins; Region: RHOD_PspE2; cd01521 565050009379 active site residue [active] 565050009380 transcriptional activator FtrA; Provisional; Region: ftrA; PRK09393 565050009381 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 565050009382 conserved cys residue [active] 565050009383 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 565050009384 Helix-turn-helix domains; Region: HTH; cl00088 565050009385 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 565050009386 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 565050009387 NADP binding site [chemical binding]; other site 565050009388 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 565050009389 catalytic residues [active] 565050009390 catalytic nucleophile [active] 565050009391 Presynaptic Site I dimer interface [polypeptide binding]; other site 565050009392 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 565050009393 Synaptic Flat tetramer interface [polypeptide binding]; other site 565050009394 Synaptic Site I dimer interface [polypeptide binding]; other site 565050009395 ABC-2 type transporter; Region: ABC2_membrane; cl11417 565050009396 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 565050009397 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency; Region: ABC_subfamily_A; cd03263 565050009398 Walker A/P-loop; other site 565050009399 ATP binding site [chemical binding]; other site 565050009400 Q-loop/lid; other site 565050009401 ABC transporter signature motif; other site 565050009402 Walker B; other site 565050009403 D-loop; other site 565050009404 H-loop/switch region; other site 565050009405 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 565050009406 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 565050009407 Protein of unknown function (DUF2385); Region: DUF2385; cl11490 565050009408 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050009409 Nitronate monooxygenase; Region: NMO; pfam03060 565050009410 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 565050009411 FMN binding site [chemical binding]; other site 565050009412 substrate binding site [chemical binding]; other site 565050009413 putative catalytic residue [active] 565050009414 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009415 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 565050009416 NAD(P) binding site [chemical binding]; other site 565050009417 active site 565050009418 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 565050009419 active site 565050009420 putative substrate binding region [chemical binding]; other site 565050009421 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_15; cd04673 565050009422 nudix motif; other site 565050009423 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 565050009424 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 565050009425 active site 565050009426 nucleophile elbow; other site 565050009427 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009428 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 565050009429 NAD(P) binding site [chemical binding]; other site 565050009430 active site 565050009431 Protein of unknown function (DUF328); Region: DUF328; cl01143 565050009432 Helix-turn-helix domains; Region: HTH; cl00088 565050009433 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 565050009434 FAD binding domain; Region: FAD_binding_4; pfam01565 565050009435 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 565050009436 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 565050009437 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 565050009438 YceI-like domain; Region: YceI; cl01001 565050009439 YceI-like domain; Region: YceI; cl01001 565050009440 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 565050009441 putative acyl-CoA dehydrogenase; Provisional; Region: PRK12341 565050009442 active site 565050009443 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 565050009444 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 565050009445 catalytic triad [active] 565050009446 dimer interface [polypeptide binding]; other site 565050009447 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 565050009448 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 565050009449 metal binding site [ion binding]; metal-binding site 565050009450 active site 565050009451 I-site; other site 565050009452 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 565050009453 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 565050009454 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050009455 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 565050009456 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 565050009457 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 565050009458 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, cyanobacteria; Region: Thr-synth_2; cd01560 565050009459 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050009460 catalytic residue [active] 565050009461 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 565050009462 Protein of unknown function (DUF983); Region: DUF983; cl02211 565050009463 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 565050009464 Subunit III/VIIa interface [polypeptide binding]; other site 565050009465 Phospholipid binding site [chemical binding]; other site 565050009466 Subunit I/III interface [polypeptide binding]; other site 565050009467 Subunit III/VIb interface [polypeptide binding]; other site 565050009468 Subunit III/VIa interface; other site 565050009469 Subunit III/Vb interface [polypeptide binding]; other site 565050009470 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 565050009471 UbiA prenyltransferase family; Region: UbiA; cl00337 565050009472 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 565050009473 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 565050009474 Subunit I/III interface [polypeptide binding]; other site 565050009475 D-pathway; other site 565050009476 Subunit I/VIIc interface [polypeptide binding]; other site 565050009477 Subunit I/IV interface [polypeptide binding]; other site 565050009478 Subunit I/II interface [polypeptide binding]; other site 565050009479 Low-spin heme (heme a) binding site [chemical binding]; other site 565050009480 Subunit I/VIIa interface [polypeptide binding]; other site 565050009481 Subunit I/VIa interface [polypeptide binding]; other site 565050009482 Dimer interface; other site 565050009483 Putative water exit pathway; other site 565050009484 Binuclear center (heme a3/CuB) [ion binding]; other site 565050009485 K-pathway; other site 565050009486 Subunit I/Vb interface [polypeptide binding]; other site 565050009487 Putative proton exit pathway; other site 565050009488 Subunit I/VIb interface; other site 565050009489 Subunit I/VIc interface [polypeptide binding]; other site 565050009490 Electron transfer pathway; other site 565050009491 Subunit I/VIIIb interface [polypeptide binding]; other site 565050009492 Subunit I/VIIb interface [polypeptide binding]; other site 565050009493 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 565050009494 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 565050009495 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 565050009496 Helix-turn-helix domains; Region: HTH; cl00088 565050009497 Protein of unknown function (DUF1700); Region: DUF1700; cl01933 565050009498 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 565050009499 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 565050009500 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 565050009501 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 565050009502 Coenzyme A binding pocket [chemical binding]; other site 565050009503 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; cl11420 565050009504 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; cl11420 565050009505 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 565050009506 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 565050009507 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 565050009508 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050009509 active site 565050009510 Protein of unknown function (DUF419); Region: DUF419; cl15265 565050009511 Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism]; Region: COG2939 565050009512 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 565050009513 Domain of unknown function (DUF4153); Region: DUF4153; pfam13687 565050009514 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 565050009515 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 565050009516 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 565050009517 Walker A/P-loop; other site 565050009518 ATP binding site [chemical binding]; other site 565050009519 Q-loop/lid; other site 565050009520 ABC transporter signature motif; other site 565050009521 Walker B; other site 565050009522 D-loop; other site 565050009523 H-loop/switch region; other site 565050009524 UbiA prenyltransferase family; Region: UbiA; cl00337 565050009525 Fatty acid desaturase [Lipid metabolism]; Region: DesA; COG3239 565050009526 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 565050009527 putative di-iron ligands [ion binding]; other site 565050009528 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 565050009529 Predicted methyltransferase [General function prediction only]; Region: COG3897 565050009530 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009531 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 565050009532 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 565050009533 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009534 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009535 Protein of unknown function (DUF419); Region: DUF419; cl15265 565050009536 FAR-17a/AIG1-like protein; Region: Far-17a_AIG1; pfam04750 565050009537 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 565050009538 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 565050009539 active site 565050009540 catalytic tetrad [active] 565050009541 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 565050009542 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 565050009543 putative catalytic cysteine [active] 565050009544 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 565050009545 active site 565050009546 (T/H)XGH motif; other site 565050009547 Oligomerisation domain; Region: Oligomerisation; cl00519 565050009548 Uncharacterized conserved protein [Function unknown]; Region: COG1576; cl00679 565050009549 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; pfam02590 565050009550 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 565050009551 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 565050009552 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 565050009553 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 565050009554 protein binding site [polypeptide binding]; other site 565050009555 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 565050009556 Catalytic dyad [active] 565050009557 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050009558 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; cl00284 565050009559 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 565050009560 NodB motif; other site 565050009561 putative active site [active] 565050009562 putative catalytic site [active] 565050009563 Zn binding site [ion binding]; other site 565050009564 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 565050009565 putative active site [active] 565050009566 Ap4A binding site [chemical binding]; other site 565050009567 nudix motif; other site 565050009568 putative metal binding site [ion binding]; other site 565050009569 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; cl12031 565050009570 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050009571 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050009572 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; cl12031 565050009573 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 565050009574 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 565050009575 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 565050009576 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 565050009577 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 565050009578 alpha subunit interaction interface [polypeptide binding]; other site 565050009579 Walker A motif; other site 565050009580 ATP binding site [chemical binding]; other site 565050009581 Walker B motif; other site 565050009582 inhibitor binding site; inhibition site 565050009583 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 565050009584 ATP synthase; Region: ATP-synt; cl00365 565050009585 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 565050009586 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 565050009587 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 565050009588 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 565050009589 beta subunit interaction interface [polypeptide binding]; other site 565050009590 Walker A motif; other site 565050009591 ATP binding site [chemical binding]; other site 565050009592 Walker B motif; other site 565050009593 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 565050009594 Plant ATP synthase F0; Region: YMF19; cl07975 565050009595 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 565050009596 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 565050009597 CoenzymeA binding site [chemical binding]; other site 565050009598 subunit interaction site [polypeptide binding]; other site 565050009599 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 565050009600 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 565050009601 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 565050009602 active site 565050009603 LemA family; Region: LemA; cl00742 565050009604 Repair protein; Region: Repair_PSII; cl01535 565050009605 Repair protein; Region: Repair_PSII; cl01535 565050009606 CAAX protease self-immunity; Region: Abi; cl00558 565050009607 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 565050009608 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 565050009609 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 565050009610 active site 565050009611 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 565050009612 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 565050009613 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 565050009614 N-terminal plug; other site 565050009615 ligand-binding site [chemical binding]; other site 565050009616 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 565050009617 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 565050009618 dimer interface [polypeptide binding]; other site 565050009619 active site 565050009620 DNA polymerase I; Provisional; Region: PRK05755 565050009621 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 565050009622 active site 565050009623 metal binding site 1 [ion binding]; metal-binding site 565050009624 putative 5' ssDNA interaction site; other site 565050009625 metal binding site 3; metal-binding site 565050009626 metal binding site 2 [ion binding]; metal-binding site 565050009627 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 565050009628 putative DNA binding site [nucleotide binding]; other site 565050009629 putative metal binding site [ion binding]; other site 565050009630 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 565050009631 active site 565050009632 catalytic site [active] 565050009633 substrate binding site [chemical binding]; other site 565050009634 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 565050009635 active site 565050009636 DNA binding site [nucleotide binding] 565050009637 catalytic site [active] 565050009638 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 565050009639 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 565050009640 ATP binding site [chemical binding]; other site 565050009641 putative Mg++ binding site [ion binding]; other site 565050009642 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 565050009643 nucleotide binding region [chemical binding]; other site 565050009644 ATP-binding site [chemical binding]; other site 565050009645 RQC domain; Region: RQC; cl09632 565050009646 HRDC domain; Region: HRDC; cl02578 565050009647 Protein of unknown function (DUF1052); Region: DUF1052; cl02197 565050009648 Threonine/homoserine efflux transporter [Amino acid transport and metabolism]; Region: rhtA; COG5006 565050009649 EamA-like transporter family; Region: EamA; cl01037 565050009650 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 cysteine...; Region: CysQ; cd01638 565050009651 active site 565050009652 Protein of unknown function (DUF3553); Region: DUF3553; pfam12073 565050009653 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5385 565050009654 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 565050009655 Response regulator receiver domain; Region: Response_reg; pfam00072 565050009656 active site 565050009657 phosphorylation site [posttranslational modification] 565050009658 intermolecular recognition site; other site 565050009659 dimerization interface [polypeptide binding]; other site 565050009660 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 565050009661 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 565050009662 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009663 Entericidin EcnA/B family; Region: Entericidin; cl02322 565050009664 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 565050009665 Histidine kinase; Region: HisKA_2; cl06527 565050009666 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 565050009667 ATP binding site [chemical binding]; other site 565050009668 Mg2+ binding site [ion binding]; other site 565050009669 G-X-G motif; other site 565050009670 RNA polymerase sigma factor; Provisional; Region: PRK12547 565050009671 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 565050009672 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050009673 two-component response regulator; Provisional; Region: PRK09191 565050009674 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050009675 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 565050009676 active site 565050009677 phosphorylation site [posttranslational modification] 565050009678 intermolecular recognition site; other site 565050009679 dimerization interface [polypeptide binding]; other site 565050009680 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 565050009681 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 565050009682 dinuclear metal binding motif [ion binding]; other site 565050009683 NAD-dependent deacetylase; Provisional; Region: PRK00481 565050009684 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 565050009685 NAD+ binding site [chemical binding]; other site 565050009686 substrate binding site [chemical binding]; other site 565050009687 Zn binding site [ion binding]; other site 565050009688 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 565050009689 Uncharacterized conserved protein [Function unknown]; Region: COG4715 565050009690 SWIM zinc finger; Region: SWIM; cl15408 565050009691 Possibl zinc metallo-peptidase; Region: DUF1025; cl01577 565050009692 PAS fold; Region: PAS_7; pfam12860 565050009693 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 565050009694 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 565050009695 dimer interface [polypeptide binding]; other site 565050009696 phosphorylation site [posttranslational modification] 565050009697 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 565050009698 ATP binding site [chemical binding]; other site 565050009699 Mg2+ binding site [ion binding]; other site 565050009700 G-X-G motif; other site 565050009701 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009702 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 565050009703 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 565050009704 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 565050009705 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 565050009706 Haemolysin-III related; Region: HlyIII; cl03831 565050009707 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 565050009708 nucleophile elbow; other site 565050009709 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050009710 Domain of unknown function (DUF3471); Region: DUF3471; pfam11954 565050009711 Domain of unknown function (DUF3471); Region: DUF3471; pfam11954 565050009712 Uncharacterized protein conserved in bacteria (DUF2219); Region: DUF2219; cl01409 565050009713 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 565050009714 Class I ribonucleotide reductase; Region: RNR_I; cd01679 565050009715 active site 565050009716 dimer interface [polypeptide binding]; other site 565050009717 catalytic residues [active] 565050009718 effector binding site; other site 565050009719 R2 peptide binding site; other site 565050009720 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 565050009721 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 565050009722 ligand binding site [chemical binding]; other site 565050009723 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 565050009724 S-adenosylmethionine binding site [chemical binding]; other site 565050009725 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 565050009726 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 565050009727 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009728 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 565050009729 (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. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 565050009730 dimer interaction site [polypeptide binding]; other site 565050009731 substrate-binding tunnel; other site 565050009732 active site 565050009733 catalytic site [active] 565050009734 substrate binding site [chemical binding]; other site 565050009735 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 565050009736 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 565050009737 N-terminal plug; other site 565050009738 ligand-binding site [chemical binding]; other site 565050009739 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 565050009740 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 565050009741 Protein of unknown function (DUF461); Region: DUF461; cl01071 565050009742 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 565050009743 Cu(I) binding site [ion binding]; other site 565050009744 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 565050009745 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 565050009746 active site 565050009747 Zn binding site [ion binding]; other site 565050009748 Helix-turn-helix domain; Region: HTH_18; pfam12833 565050009749 Helix-turn-helix domains; Region: HTH; cl00088 565050009750 BlaR1 peptidase M56; Region: Peptidase_M56; cl15829 565050009751 Gram-negative bacterial tonB protein; Region: TonB; cl10048 565050009752 Domain of unknown function (DUF897); Region: DUF897; cl01312 565050009753 Transcriptional regulator [Transcription]; Region: LysR; COG0583 565050009754 Helix-turn-helix domains; Region: HTH; cl00088 565050009755 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 565050009756 dimerization interface [polypeptide binding]; other site 565050009757 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 565050009758 ATP phosphoribosyltransferase; Region: HisG; cl15266 565050009759 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12295 565050009760 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 attaches...; Region: class_II_aaRS-like_core; cl00268 565050009761 active site 565050009762 dimer interface [polypeptide binding]; other site 565050009763 motif 2; other site 565050009764 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 attaches...; Region: class_II_aaRS-like_core; cl00268 565050009765 active site 565050009766 motif 3; other site 565050009767 histidyl-tRNA synthetase; Region: hisS; TIGR00442 565050009768 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 ATP-dependent...; Region: HisRS-like_core; cd00773 565050009769 dimer interface [polypeptide binding]; other site 565050009770 motif 1; other site 565050009771 motif 2; other site 565050009772 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 attaches...; Region: class_II_aaRS-like_core; cl00268 565050009773 motif 3; other site 565050009774 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 565050009775 anticodon binding site; other site 565050009776 Protein of unknown function (DUF4065); Region: DUF4065; cl01445 565050009777 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 565050009778 GIY-YIG motif/motif A; other site 565050009779 putative active site [active] 565050009780 putative metal binding site [ion binding]; other site 565050009781 DoxX; Region: DoxX; cl00976 565050009782 biotin synthase; Region: bioB; TIGR00433 565050009783 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 565050009784 FeS/SAM binding site; other site 565050009785 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 565050009786 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 565050009787 putative active site [active] 565050009788 putative metal binding residues [ion binding]; other site 565050009789 signature motif; other site 565050009790 putative triphosphate binding site [ion binding]; other site 565050009791 CHAD domain; Region: CHAD; cl10506 565050009792 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 565050009793 catalytic loop [active] 565050009794 iron binding site [ion binding]; other site 565050009795 phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional; Region: PRK09754 565050009796 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 565050009797 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 565050009798 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 565050009799 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 565050009800 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009801 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 565050009802 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 565050009803 putative SdhC subunit interface [polypeptide binding]; other site 565050009804 putative proximal heme binding site [chemical binding]; other site 565050009805 putative Iron-sulfur protein interface [polypeptide binding]; other site 565050009806 putative proximal quinone binding site; other site 565050009807 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 565050009808 Iron-sulfur protein interface; other site 565050009809 proximal quinone binding site [chemical binding]; other site 565050009810 SdhD (CybS) interface [polypeptide binding]; other site 565050009811 proximal heme binding site [chemical binding]; other site 565050009812 GDP-mannose pyrophosphatase NudK; Provisional; Region: PRK15009 565050009813 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 565050009814 dimer interface [polypeptide binding]; other site 565050009815 ADP-ribose binding site [chemical binding]; other site 565050009816 active site 565050009817 nudix motif; other site 565050009818 metal binding site [ion binding]; metal-binding site 565050009819 AFG1-like ATPase; Region: AFG1_ATPase; pfam03969 565050009820 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050009821 putative acyl-acceptor binding pocket; other site 565050009822 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 565050009823 Phosphotransferase enzyme family; Region: APH; pfam01636 565050009824 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 565050009825 substrate binding site [chemical binding]; other site 565050009826 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 565050009827 Substrate binding site; other site 565050009828 metal-binding site 565050009829 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 565050009830 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 565050009831 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 565050009832 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 565050009833 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050009834 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 565050009835 catalytic residues [active] 565050009836 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 565050009837 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 565050009838 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 565050009839 tryptophan synthase subunit alpha; Provisional; Region: trpA; PRK13111 565050009840 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 565050009841 substrate binding site [chemical binding]; other site 565050009842 active site 565050009843 catalytic residues [active] 565050009844 heterodimer interface [polypeptide binding]; other site 565050009845 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 565050009846 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 565050009847 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050009848 catalytic residue [active] 565050009849 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 monomeric; Region: PRAI; cd00405 565050009850 active site 565050009851 Usg-like family; Region: Usg; cl11567 565050009852 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 565050009853 Malic enzyme, N-terminal domain; Region: malic; pfam00390 565050009854 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 565050009855 putative NAD(P) binding site [chemical binding]; other site 565050009856 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 565050009857 dihydrodipicolinate reductase; Provisional; Region: PRK00048 565050009858 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009859 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 565050009860 Dicarboxylate transport; Region: DctA-YdbH; cl14674 565050009861 YnbE-like lipoprotein; Region: Lipoprotein_19; pfam13617 565050009862 Protein of unknown function (DUF1318); Region: DUF1318; cl01547 565050009863 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 565050009864 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 565050009865 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 565050009866 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 565050009867 active site 565050009868 metal binding site [ion binding]; metal-binding site 565050009869 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 565050009870 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 565050009871 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 565050009872 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 565050009873 PAS fold; Region: PAS_3; pfam08447 565050009874 putative active site [active] 565050009875 heme pocket [chemical binding]; other site 565050009876 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 565050009877 Histidine kinase; Region: HisKA_2; cl06527 565050009878 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 565050009879 Coenzyme A binding pocket [chemical binding]; other site 565050009880 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 565050009881 CoA-transferase family III; Region: CoA_transf_3; pfam02515 565050009882 Domain of unknown function (DUF305); Region: DUF305; cl15795 565050009883 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 565050009884 CoenzymeA binding site [chemical binding]; other site 565050009885 subunit interaction site [polypeptide binding]; other site 565050009886 PHB binding site; other site 565050009887 ABC-2 type transporter; Region: ABC2_membrane; cl11417 565050009888 Aminopeptidase N [Amino acid transport and metabolism]; Region: PepN; COG0308 565050009889 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 565050009890 Zn binding site [ion binding]; other site 565050009891 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 565050009892 ABC-type multidrug transport system, ATPase component. The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the...; Region: ABC_drug_resistance_like; cd03264 565050009893 Walker A/P-loop; other site 565050009894 ATP binding site [chemical binding]; other site 565050009895 Q-loop/lid; other site 565050009896 ABC transporter signature motif; other site 565050009897 Walker B; other site 565050009898 D-loop; other site 565050009899 H-loop/switch region; other site 565050009900 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 565050009901 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 565050009902 C-terminal domain interface [polypeptide binding]; other site 565050009903 GSH binding site (G-site) [chemical binding]; other site 565050009904 putative dimer interface [polypeptide binding]; other site 565050009905 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 565050009906 dimer interface [polypeptide binding]; other site 565050009907 N-terminal domain interface [polypeptide binding]; other site 565050009908 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 565050009909 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 565050009910 active site clefts [active] 565050009911 zinc binding site [ion binding]; other site 565050009912 dimer interface [polypeptide binding]; other site 565050009913 Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane]; Region: PbpC; COG4953 565050009914 Transglycosylase; Region: Transgly; cl07896 565050009915 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050009916 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 565050009917 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 565050009918 MG2 domain; Region: A2M_N; pfam01835 565050009919 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 565050009920 Alpha-2-macroglobulin family; Region: A2M; pfam00207 565050009921 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 565050009922 surface patch; other site 565050009923 thioester region; other site 565050009924 specificity defining residues; other site 565050009925 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_cladeC; cd03378 565050009926 active site clefts [active] 565050009927 zinc binding site [ion binding]; other site 565050009928 dimer interface [polypeptide binding]; other site 565050009929 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 565050009930 Helix-turn-helix domains; Region: HTH; cl00088 565050009931 Helix-turn-helix domains; Region: HTH; cl00088 565050009932 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 565050009933 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 565050009934 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050009935 SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat; Region: GT2_SpsF; cd02518 565050009936 ligand binding site; other site 565050009937 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cl00470 565050009938 active site 565050009939 catalytic tetrad [active] 565050009940 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 565050009941 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 565050009942 XdhC Rossmann domain; Region: XdhC_C; pfam13478 565050009943 Creatinine amidohydrolase; Region: Creatininase; cl00618 565050009944 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 565050009945 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 565050009946 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 565050009947 NAD(P) binding site [chemical binding]; other site 565050009948 catalytic residues [active] 565050009949 acetyl-CoA synthetase; Provisional; Region: PRK00174 565050009950 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 565050009951 AMP-binding enzyme; Region: AMP-binding; cl15778 565050009952 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 565050009953 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 565050009954 hydrophobic ligand binding site; other site 565050009955 Protein of unknown function, DUF393; Region: DUF393; cl01136 565050009956 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 565050009957 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 565050009958 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 565050009959 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 565050009960 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 565050009961 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 565050009962 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 565050009963 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 565050009964 IHF dimer interface [polypeptide binding]; other site 565050009965 IHF - DNA interface [nucleotide binding]; other site 565050009966 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 565050009967 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 consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 565050009968 RNA binding site [nucleotide binding]; other site 565050009969 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 consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 565050009970 RNA binding site [nucleotide binding]; other site 565050009971 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 of...; Region: S1_RPS1_repeat_ec3; cd05688 565050009972 RNA binding site [nucleotide binding]; other site 565050009973 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 of...; Region: S1_RPS1_repeat_ec4; cd05689 565050009974 RNA binding site [nucleotide binding]; other site 565050009975 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 of...; Region: S1_RPS1_repeat_ec5; cd05690 565050009976 RNA binding site [nucleotide binding]; other site 565050009977 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 565050009978 RNA binding site [nucleotide binding]; other site 565050009979 cytidylate kinase; Provisional; Region: cmk; PRK00023 565050009980 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 565050009981 CMP-binding site; other site 565050009982 The sites determining sugar specificity; other site 565050009983 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 565050009984 3-phosphoshikimate 1-carboxyvinyltransferase; Region: aroA; TIGR01356 565050009985 hinge; other site 565050009986 active site 565050009987 TIGR02300 family protein; Region: FYDLN_acid 565050009988 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 565050009989 putative dimer interface [polypeptide binding]; other site 565050009990 Protein of unknown function (DUF1150); Region: DUF1150; cl11577 565050009991 Transposase domain (DUF772); Region: DUF772; cl15789 565050009992 Transposase domain (DUF772); Region: DUF772; cl15789 565050009993 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 565050009994 active site 565050009995 phosphorylation site [posttranslational modification] 565050009996 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 A site; Region: RaiA; cd00552 565050009997 30S subunit binding site; other site 565050009998 Exopolysaccharide synthesis, ExoD; Region: ExoD; cl01617 565050009999 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 565050010000 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 565050010001 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 565050010002 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 565050010003 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 565050010004 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 565050010005 Walker A/P-loop; other site 565050010006 ATP binding site [chemical binding]; other site 565050010007 Q-loop/lid; other site 565050010008 ABC transporter signature motif; other site 565050010009 Walker B; other site 565050010010 D-loop; other site 565050010011 H-loop/switch region; other site 565050010012 OstA-like protein; Region: OstA; cl00844 565050010013 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 565050010014 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 565050010015 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 565050010016 putative active site [active] 565050010017 catalytic site [active] 565050010018 putative substrate binding site [chemical binding]; other site 565050010019 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 565050010020 putative NAD(P) binding site [chemical binding]; other site 565050010021 active site 565050010022 Bacitracin resistance protein BacA; Region: BacA; cl00858 565050010023 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 565050010024 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050010025 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 565050010026 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 565050010027 active site 565050010028 dimer interface [polypeptide binding]; other site 565050010029 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 565050010030 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 565050010031 active site 565050010032 FMN binding site [chemical binding]; other site 565050010033 substrate binding site [chemical binding]; other site 565050010034 3Fe-4S cluster binding site [ion binding]; other site 565050010035 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 565050010036 domain interface; other site 565050010037 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 565050010038 CoenzymeA binding site [chemical binding]; other site 565050010039 subunit interaction site [polypeptide binding]; other site 565050010040 PHB binding site; other site 565050010041 DNA ligase, ATP-dependent, PP_1105 family; Region: DNA_lig_bact; TIGR04120 565050010042 Adenylation domain of putative bacterial ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_Bac1; cd07897 565050010043 active site 565050010044 DNA binding site [nucleotide binding] 565050010045 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 565050010046 DNA binding site [nucleotide binding] 565050010047 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 565050010048 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 565050010049 inhibitor-cofactor binding pocket; inhibition site 565050010050 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050010051 catalytic residue [active] 565050010052 Mechanosensitive ion channel; Region: MS_channel; pfam00924 565050010053 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 565050010054 active site 565050010055 intersubunit interactions; other site 565050010056 catalytic residue [active] 565050010057 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 565050010058 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 565050010059 NADP binding site [chemical binding]; other site 565050010060 active site 565050010061 putative substrate binding site [chemical binding]; other site 565050010062 Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism]; Region: HisB; COG0241 565050010063 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 565050010064 active site 565050010065 motif I; other site 565050010066 motif II; other site 565050010067 N-acyl-D-glucosamine 2-epimerase [Carbohydrate transport and metabolism]; Region: COG2942 565050010068 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cd00249 565050010069 putative active cleft [active] 565050010070 dimerization interface [polypeptide binding]; other site 565050010071 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 565050010072 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 565050010073 Substrate binding site; other site 565050010074 Cupin domain; Region: Cupin_2; cl09118 565050010075 NAD synthetase; Reviewed; Region: nadE; PRK02628 565050010076 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 565050010077 multimer interface [polypeptide binding]; other site 565050010078 active site 565050010079 catalytic triad [active] 565050010080 protein interface 1 [polypeptide binding]; other site 565050010081 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 565050010082 homodimer interface [polypeptide binding]; other site 565050010083 NAD binding pocket [chemical binding]; other site 565050010084 ATP binding pocket [chemical binding]; other site 565050010085 Mg binding site [ion binding]; other site 565050010086 active-site loop [active] 565050010087 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 565050010088 dimer interface [polypeptide binding]; other site 565050010089 TPP-binding site [chemical binding]; other site 565050010090 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 565050010091 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]; Region: COG3958 565050010092 PYR/PP interface [polypeptide binding]; other site 565050010093 dimer interface [polypeptide binding]; other site 565050010094 TPP binding site [chemical binding]; other site 565050010095 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 565050010096 YGGT family; Region: YGGT; cl00508 565050010097 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 565050010098 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 565050010099 dimer interface [polypeptide binding]; other site 565050010100 phosphorylation site [posttranslational modification] 565050010101 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 565050010102 ATP binding site [chemical binding]; other site 565050010103 Mg2+ binding site [ion binding]; other site 565050010104 G-X-G motif; other site 565050010105 Response regulator receiver domain; Region: Response_reg; pfam00072 565050010106 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 565050010107 active site 565050010108 phosphorylation site [posttranslational modification] 565050010109 intermolecular recognition site; other site 565050010110 dimerization interface [polypeptide binding]; other site 565050010111 Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches; Region: Vsr; cd00221 565050010112 additional DNA contacts [nucleotide binding]; other site 565050010113 mismatch recognition site; other site 565050010114 active site 565050010115 zinc binding site [ion binding]; other site 565050010116 DNA intercalation site [nucleotide binding]; other site 565050010117 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 565050010118 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 565050010119 dimer interface [polypeptide binding]; other site 565050010120 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050010121 catalytic residue [active] 565050010122 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 565050010123 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; cl15754 565050010124 cofactor binding site; other site 565050010125 DNA binding site [nucleotide binding] 565050010126 substrate interaction site [chemical binding]; other site 565050010127 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; cl15754 565050010128 Predicted membrane protein [Function unknown]; Region: COG3650 565050010129 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 565050010130 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 565050010131 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 565050010132 NAD binding site [chemical binding]; other site 565050010133 substrate binding site [chemical binding]; other site 565050010134 homodimer interface [polypeptide binding]; other site 565050010135 active site 565050010136 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 565050010137 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 565050010138 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 565050010139 putative active site [active] 565050010140 putative substrate binding site [chemical binding]; other site 565050010141 putative cosubstrate binding site; other site 565050010142 catalytic site [active] 565050010143 acetylornithine deacetylase (ArgE); Region: AcOrn-deacetyl; TIGR01892 565050010144 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 565050010145 metal binding site [ion binding]; metal-binding site 565050010146 putative dimer interface [polypeptide binding]; other site 565050010147 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 565050010148 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 565050010149 Probable Catalytic site; other site 565050010150 metal-binding site 565050010151 Cupin domain; Region: Cupin_2; cl09118 565050010152 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; cl12031 565050010153 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050010154 threonine dehydratase; Provisional; Region: PRK07334 565050010155 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 565050010156 tetramer interface [polypeptide binding]; other site 565050010157 pyridoxal 5'-phosphate binding site [chemical binding]; other site 565050010158 catalytic residue [active] 565050010159 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 565050010160 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 565050010161 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 565050010162 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 565050010163 active site 565050010164 tetramer interface; other site 565050010165 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 565050010166 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 565050010167 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 565050010168 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 565050010169 C-terminal domain interface [polypeptide binding]; other site 565050010170 GSH binding site (G-site) [chemical binding]; other site 565050010171 dimer interface [polypeptide binding]; other site 565050010172 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 565050010173 N-terminal domain interface [polypeptide binding]; other site 565050010174 dimer interface [polypeptide binding]; other site 565050010175 substrate binding pocket (H-site) [chemical binding]; other site 565050010176 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 565050010177 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 565050010178 putative ribose interaction site [chemical binding]; other site 565050010179 putative ADP binding site [chemical binding]; other site 565050010180 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 565050010181 active site 565050010182 nucleotide binding site [chemical binding]; other site 565050010183 HIGH motif; other site 565050010184 KMSKS motif; other site 565050010185 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 565050010186 Cation efflux family; Region: Cation_efflux; cl00316 565050010187 Bacillus subtilis (Bs) citrate synthase CS-I_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). 2MCS catalyzes the...; Region: BsCS-I_like; cd06109 565050010188 dimer interface [polypeptide binding]; other site 565050010189 Citrate synthase; Region: Citrate_synt; pfam00285 565050010190 active site 565050010191 citrylCoA binding site [chemical binding]; other site 565050010192 oxalacetate/citrate binding site [chemical binding]; other site 565050010193 coenzyme A binding site [chemical binding]; other site 565050010194 catalytic triad [active] 565050010195 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 565050010196 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 565050010197 Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A; Region: CS_ACL-C_CCL; cl00416 565050010198 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate...; Region: citrate_synt_like_2; cd06102 565050010199 dimer interface [polypeptide binding]; other site 565050010200 active site 565050010201 oxalacetate/citrate binding site [chemical binding]; other site 565050010202 citrylCoA binding site [chemical binding]; other site 565050010203 coenzyme A binding site [chemical binding]; other site 565050010204 catalytic triad [active] 565050010205 putative exonuclease, DNA ligase-associated; Region: Xnuc_lig_assoc; TIGR04122 565050010206 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 565050010207 CoenzymeA binding site [chemical binding]; other site 565050010208 subunit interaction site [polypeptide binding]; other site 565050010209 PHB binding site; other site 565050010210 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 565050010211 CoenzymeA binding site [chemical binding]; other site 565050010212 subunit interaction site [polypeptide binding]; other site 565050010213 PHB binding site; other site 565050010214 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06466 565050010215 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 565050010216 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 565050010217 Acyl-CoA thioesterase [Lipid metabolism]; Region: TesB; COG1946 565050010218 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 565050010219 active site 565050010220 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat1; cd03444 565050010221 catalytic triad [active] 565050010222 dimer interface [polypeptide binding]; other site 565050010223 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 565050010224 dimer interface [polypeptide binding]; other site 565050010225 ADP-ribose binding site [chemical binding]; other site 565050010226 active site 565050010227 nudix motif; other site 565050010228 metal binding site [ion binding]; metal-binding site 565050010229 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK13828 565050010230 RimM N-terminal domain; Region: RimM; pfam01782 565050010231 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 565050010232 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 565050010233 signal recognition particle protein; Provisional; Region: PRK10867 565050010234 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 565050010235 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 565050010236 P loop; other site 565050010237 GTP binding site [chemical binding]; other site 565050010238 Signal peptide binding domain; Region: SRP_SPB; pfam02978 565050010239 Domain of unknown function (DUF1993); Region: DUF1993; cl01567 565050010240 malate dehydrogenase; Reviewed; Region: PRK06223 565050010241 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 565050010242 NAD(P) binding site [chemical binding]; other site 565050010243 dimer interface [polypeptide binding]; other site 565050010244 tetramer (dimer of dimers) interface [polypeptide binding]; other site 565050010245 substrate binding site [chemical binding]; other site 565050010246 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 565050010247 putative active site [active] 565050010248 putative catalytic site [active] 565050010249 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 565050010250 putative active site [active] 565050010251 putative catalytic site [active] 565050010252 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 565050010253 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; cl09155 565050010254 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; cl01467 565050010255 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 565050010256 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 565050010257 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 565050010258 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 565050010259 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 565050010260 active site 565050010261 catalytic tetrad [active] 565050010262 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 565050010263 Protein of unknown function (DUF2794); Region: DUF2794; pfam10984 565050010264 Protein of unknown function (DUF1223); Region: DUF1223; cl10501 565050010265 aconitate hydratase; Validated; Region: PRK09277 565050010266 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 565050010267 substrate binding site [chemical binding]; other site 565050010268 ligand binding site [chemical binding]; other site 565050010269 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 565050010270 substrate binding site [chemical binding]; other site 565050010271 ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]; Region: CcmA; COG4133 565050010272 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050010273 Walker A/P-loop; other site 565050010274 ATP binding site [chemical binding]; other site 565050010275 Q-loop/lid; other site 565050010276 ABC transporter signature motif; other site 565050010277 Walker B; other site 565050010278 D-loop; other site 565050010279 H-loop/switch region; other site 565050010280 CcmB protein; Region: CcmB; cl01016 565050010281 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 565050010282 Heme exporter protein D (CcmD); Region: CcmD; cl11475 565050010283 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 565050010284 catalytic residues [active] 565050010285 central insert; other site 565050010286 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 565050010287 Helix-turn-helix domains; Region: HTH; cl00088 565050010288 Intracellular septation protein A; Region: IspA; cl01098 565050010289 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 565050010290 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 565050010291 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 565050010292 P loop; other site 565050010293 GTP binding site [chemical binding]; other site 565050010294 Predicted membrane protein [Function unknown]; Region: COG2860 565050010295 UPF0126 domain; Region: UPF0126; pfam03458 565050010296 UPF0126 domain; Region: UPF0126; pfam03458 565050010297 tellurium resistance terB-like protein; Region: terB_like; cl11965 565050010298 Integral membrane protein TerC family; Region: TerC; cl10468 565050010299 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 565050010300 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 565050010301 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 565050010302 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 565050010303 FeS/SAM binding site; other site 565050010304 hypothetical protein; Provisional; Region: PRK06194 565050010305 classical (c) SDRs; Region: SDR_c; cd05233 565050010306 NAD(P) binding site [chemical binding]; other site 565050010307 active site 565050010308 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 565050010309 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 565050010310 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 565050010311 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 565050010312 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; cl12031 565050010313 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 565050010314 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; cl12031 565050010315 Protein involved in cellulose biosynthesis (CelD) [Cell envelope biogenesis, outer membrane]; Region: COG5653 565050010316 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 565050010317 Uncharacterized protein conserved in bacteria (DUF2218); Region: DUF2218; cl01424 565050010318 Helix-turn-helix domains; Region: HTH; cl00088 565050010319 VacJ like lipoprotein; Region: VacJ; cl01073 565050010320 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 565050010321 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 565050010322 mce related protein; Region: MCE; pfam02470 565050010323 Permease; Region: Permease; cl00510 565050010324 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 565050010325 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 565050010326 Walker A/P-loop; other site 565050010327 ATP binding site [chemical binding]; other site 565050010328 Q-loop/lid; other site 565050010329 ABC transporter signature motif; other site 565050010330 Walker B; other site 565050010331 D-loop; other site 565050010332 H-loop/switch region; other site 565050010333 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 565050010334 Helix-turn-helix domains; Region: HTH; cl00088 565050010335 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 565050010336 dimerization interface [polypeptide binding]; other site 565050010337 alkylhydroperoxidase, AhpD family; Region: ahpD; TIGR00777 565050010338 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 565050010339 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 565050010340 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 565050010341 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3735 565050010342 TraB family; Region: TraB; cl12050 565050010343 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 565050010344 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 565050010345 active site 565050010346 Zn binding site [ion binding]; other site 565050010347 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 565050010348 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 565050010349 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050010350 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 565050010351 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 565050010352 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 565050010353 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 565050010354 putative phosphate binding site [ion binding]; other site 565050010355 putative catalytic site [active] 565050010356 active site 565050010357 metal binding site A [ion binding]; metal-binding site 565050010358 DNA binding site [nucleotide binding] 565050010359 putative AP binding site [nucleotide binding]; other site 565050010360 putative metal binding site B [ion binding]; other site 565050010361 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 565050010362 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 565050010363 DNA binding site [nucleotide binding] 565050010364 catalytic residue [active] 565050010365 H2TH interface [polypeptide binding]; other site 565050010366 putative catalytic residues [active] 565050010367 turnover-facilitating residue; other site 565050010368 intercalation triad [nucleotide binding]; other site 565050010369 8OG recognition residue [nucleotide binding]; other site 565050010370 putative reading head residues; other site 565050010371 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 565050010372 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 565050010373 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 565050010374 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050010375 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 565050010376 Pyocin large subunit [General function prediction only]; Region: COG5529 565050010377 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 565050010378 Flavoprotein; Region: Flavoprotein; cl08021 565050010379 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 565050010380 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 565050010381 trimer interface [polypeptide binding]; other site 565050010382 active site 565050010383 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 565050010384 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050010385 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 565050010386 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 565050010387 Major Facilitator Superfamily; Region: MFS_1; pfam07690 565050010388 putative substrate translocation pore; other site 565050010389 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 565050010390 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 565050010391 Helix-turn-helix domains; Region: HTH; cl00088 565050010392 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 565050010393 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 565050010394 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 565050010395 NAD binding site [chemical binding]; other site 565050010396 homotetramer interface [polypeptide binding]; other site 565050010397 homodimer interface [polypeptide binding]; other site 565050010398 substrate binding site [chemical binding]; other site 565050010399 active site 565050010400 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 565050010401 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 565050010402 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 565050010403 dimer interface [polypeptide binding]; other site 565050010404 active site 565050010405 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 565050010406 active site 1 [active] 565050010407 dimer interface [polypeptide binding]; other site 565050010408 active site 2 [active] 565050010409 Bacterial SH3 domain; Region: SH3_3; cl02551 565050010410 Bacterial SH3 domain; Region: SH3_3; cl02551 565050010411 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 565050010412 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050010413 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 565050010414 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; cl12031 565050010415 succinate CoA transferases; Region: YgfH_subfam; TIGR03458 565050010416 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 565050010417 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 565050010418 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; cl12031 565050010419 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 565050010420 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 565050010421 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 565050010422 ATP binding site [chemical binding]; other site 565050010423 substrate interface [chemical binding]; other site 565050010424 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 565050010425 active site 565050010426 HslU subunit interaction site [polypeptide binding]; other site 565050010427 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 565050010428 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 565050010429 Walker A motif; other site 565050010430 ATP binding site [chemical binding]; other site 565050010431 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050010432 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 565050010433 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 565050010434 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 565050010435 DNA binding site [nucleotide binding] 565050010436 active site 565050010437 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 565050010438 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 565050010439 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 565050010440 minor groove reading motif; other site 565050010441 helix-hairpin-helix signature motif; other site 565050010442 substrate binding pocket [chemical binding]; other site 565050010443 active site 565050010444 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 565050010445 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 565050010446 ATP-grasp domain; Region: ATP-grasp_4; cl03087 565050010447 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 adenosine...; Region: adenosine_kinase; cd01168 565050010448 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 565050010449 substrate binding site [chemical binding]; other site 565050010450 ATP binding site [chemical binding]; other site 565050010451 imidazoleglycerol-phosphate dehydratase; Validated; Region: hisB; PRK00951 565050010452 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 565050010453 putative active site pocket [active] 565050010454 4-fold oligomerization interface [polypeptide binding]; other site 565050010455 metal binding residues [ion binding]; metal-binding site 565050010456 3-fold/trimer interface [polypeptide binding]; other site 565050010457 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 565050010458 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 565050010459 putative active site [active] 565050010460 oxyanion strand; other site 565050010461 catalytic triad [active] 565050010462 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]; Region: HisA; COG0106 565050010463 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 565050010464 catalytic residues [active] 565050010465 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 565050010466 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 565050010467 substrate binding site [chemical binding]; other site 565050010468 glutamase interaction surface [polypeptide binding]; other site 565050010469 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 565050010470 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 565050010471 Smr domain; Region: Smr; cl02619 565050010472 MltA specific insert domain; Region: MltA; cl08398 565050010473 3D domain; Region: 3D; cl01439 565050010474 Tim44-like domain; Region: Tim44; cl09208 565050010475 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cl00251 565050010476 SecA binding site; other site 565050010477 Preprotein binding site; other site 565050010478 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 565050010479 active site 565050010480 phosphorylation site [posttranslational modification] 565050010481 intermolecular recognition site; other site 565050010482 dimerization interface [polypeptide binding]; other site 565050010483 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 565050010484 DNA binding site [nucleotide binding] 565050010485 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 565050010486 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 565050010487 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 565050010488 catalytic residue [active] 565050010489 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 565050010490 thiamine phosphate binding site [chemical binding]; other site 565050010491 active site 565050010492 pyrophosphate binding site [ion binding]; other site 565050010493 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 565050010494 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 565050010495 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 565050010496 HIGH motif; other site 565050010497 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 565050010498 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 565050010499 active site 565050010500 KMSKS motif; other site 565050010501 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 565050010502 tRNA binding surface [nucleotide binding]; other site 565050010503 Lipopolysaccharide-assembly; Region: LptE; cl01125 565050010504 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 565050010505 ParB-like nuclease domain; Region: ParBc; cl02129 565050010506 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 565050010507 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 565050010508 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; cl15754 565050010509 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 565050010510 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 565050010511 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 565050010512 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 565050010513 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 565050010514 trmE is a tRNA modification GTPase; Region: trmE; cd04164 565050010515 G1 box; other site 565050010516 GTP/Mg2+ binding site [chemical binding]; other site 565050010517 Switch I region; other site 565050010518 G2 box; other site 565050010519 Switch II region; other site 565050010520 G3 box; other site 565050010521 G4 box; other site 565050010522 G5 box; other site 565050010523 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 565050010524 Dienelactone hydrolase family; Region: DLH; pfam01738 565050010525 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 565050010526 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 565050010527 NADP binding site [chemical binding]; other site 565050010528 dimer interface [polypeptide binding]; other site 565050010529 transcription termination factor Rho; Provisional; Region: rho; PRK09376 565050010530 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 565050010531 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 565050010532 RNA binding site [nucleotide binding]; other site 565050010533 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 565050010534 multimer interface [polypeptide binding]; other site 565050010535 Walker A motif; other site 565050010536 ATP binding site [chemical binding]; other site 565050010537 Walker B motif; other site 565050010538 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 565050010539 Ferrochelatase; Region: Ferrochelatase; pfam00762 565050010540 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 565050010541 C-terminal domain interface [polypeptide binding]; other site 565050010542 active site 565050010543 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 565050010544 active site 565050010545 N-terminal domain interface [polypeptide binding]; other site 565050010546 methyltransferase, MtaA/CmuA family; Region: mtaA_cmuA; TIGR01463 565050010547 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 565050010548 substrate binding site [chemical binding]; other site 565050010549 active site