-- dump date 20140619_135008 -- class Genbank::misc_feature -- table misc_feature_note -- id note 342108000001 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 342108000002 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 342108000003 trmE is a tRNA modification GTPase; Region: trmE; cd04164 342108000004 G1 box; other site 342108000005 GTP/Mg2+ binding site [chemical binding]; other site 342108000006 Switch I region; other site 342108000007 G2 box; other site 342108000008 Switch II region; other site 342108000009 G3 box; other site 342108000010 G4 box; other site 342108000011 G5 box; other site 342108000012 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 342108000013 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 342108000014 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 342108000015 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 342108000016 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 342108000017 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 342108000018 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 342108000019 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 342108000020 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 342108000021 P-loop; other site 342108000022 Magnesium ion binding site [ion binding]; other site 342108000023 hypothetical protein; Provisional; Region: PRK02250 342108000024 SEC-C motif; Region: SEC-C; pfam02810 342108000025 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 342108000026 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 342108000027 catalytic residues [active] 342108000028 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 342108000029 Uncharacterized conserved protein [Function unknown]; Region: COG2835 342108000030 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 342108000031 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 342108000032 putative deacylase active site [active] 342108000033 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 342108000034 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 342108000035 Nitrogen regulatory protein P-II; Region: P-II; pfam00543 342108000036 Nitrogen regulatory protein P-II; Region: P-II; smart00938 342108000037 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 342108000038 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 342108000039 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 342108000040 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108000041 homodimer interface [polypeptide binding]; other site 342108000042 catalytic residue [active] 342108000043 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 342108000044 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 342108000045 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 342108000046 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 342108000047 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 342108000048 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 342108000049 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 342108000050 putative catalytic site [active] 342108000051 putative phosphate binding site [ion binding]; other site 342108000052 active site 342108000053 metal binding site A [ion binding]; metal-binding site 342108000054 DNA binding site [nucleotide binding] 342108000055 putative AP binding site [nucleotide binding]; other site 342108000056 putative metal binding site B [ion binding]; other site 342108000057 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108000058 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 342108000059 active site 342108000060 phosphorylation site [posttranslational modification] 342108000061 intermolecular recognition site; other site 342108000062 dimerization interface [polypeptide binding]; other site 342108000063 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 342108000064 DNA binding site [nucleotide binding] 342108000065 GTP cyclohydrolase; Provisional; Region: PRK08815 342108000066 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 342108000067 dimerization interface [polypeptide binding]; other site 342108000068 active site 342108000069 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 342108000070 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 342108000071 catalytic residue [active] 342108000072 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 342108000073 thiamine phosphate binding site [chemical binding]; other site 342108000074 active site 342108000075 pyrophosphate binding site [ion binding]; other site 342108000076 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108000077 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 342108000078 binding surface 342108000079 TPR motif; other site 342108000080 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108000081 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 342108000082 TPR motif; other site 342108000083 binding surface 342108000084 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 342108000085 Gram-negative porin; Region: Porin_4; pfam13609 342108000086 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 342108000087 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 342108000088 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 342108000089 HIGH motif; other site 342108000090 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 342108000091 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 342108000092 active site 342108000093 KMSKS motif; other site 342108000094 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 342108000095 tRNA binding surface [nucleotide binding]; other site 342108000096 Lipopolysaccharide-assembly; Region: LptE; cl01125 342108000097 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 342108000098 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 342108000099 GDSL-like Lipase/Acylhydrolase family; Region: Lipase_GDSL_2; pfam13472 342108000100 active site 342108000101 oxyanion hole [active] 342108000102 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 342108000103 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 342108000104 dimer interface [polypeptide binding]; other site 342108000105 active site 342108000106 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 342108000107 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 342108000108 Heparinase II/III-like protein; Region: Hepar_II_III; cl15421 342108000109 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 342108000110 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 342108000111 Substrate binding site; other site 342108000112 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 342108000113 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108000114 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108000115 NAD(P) binding site [chemical binding]; other site 342108000116 active site 342108000117 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 342108000118 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 342108000119 Mg++ binding site [ion binding]; other site 342108000120 putative catalytic motif [active] 342108000121 putative substrate binding site [chemical binding]; other site 342108000122 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 342108000123 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and other MDR family members; Region: 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_; cd08255 342108000124 putative NAD(P) binding site [chemical binding]; other site 342108000125 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 342108000126 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 342108000127 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 342108000128 DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; Region: ERI-1_3'hExo_like; cd06133 342108000129 active site 342108000130 catalytic site [active] 342108000131 substrate binding site [chemical binding]; other site 342108000132 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 342108000133 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 342108000134 active site 342108000135 dimer interface [polypeptide binding]; other site 342108000136 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 342108000137 Ligand Binding Site [chemical binding]; other site 342108000138 Molecular Tunnel; other site 342108000139 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 342108000140 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 342108000141 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 342108000142 putative active site [active] 342108000143 putative metal binding site [ion binding]; other site 342108000144 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 342108000145 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 342108000146 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108000147 catalytic residue [active] 342108000148 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 342108000149 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 342108000150 Radical SAM superfamily; Region: Radical_SAM; pfam04055 342108000151 FeS/SAM binding site; other site 342108000152 Transcriptional regulators [Transcription]; Region: MarR; COG1846 342108000153 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cl17220 342108000154 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 342108000155 transcriptional activator RfaH; Region: RfaH; TIGR01955 342108000156 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 342108000157 heterodimer interface [polypeptide binding]; other site 342108000158 homodimer interface [polypeptide binding]; other site 342108000159 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 342108000160 putative methyltransferase, LIC12133 family; Region: MTase_LIC12133; TIGR04325 342108000161 Putative zinc binding domain; Region: Methyltransf_13; pfam08421 342108000162 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108000163 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 342108000164 S-adenosylmethionine binding site [chemical binding]; other site 342108000165 C-methyltransferase C-terminal domain; Region: Methyltransf_14; pfam08484 342108000166 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 342108000167 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 342108000168 inhibitor-cofactor binding pocket; inhibition site 342108000169 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108000170 catalytic residue [active] 342108000171 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 342108000172 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 342108000173 putative trimer interface [polypeptide binding]; other site 342108000174 putative CoA binding site [chemical binding]; other site 342108000175 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 342108000176 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 342108000177 inhibitor-cofactor binding pocket; inhibition site 342108000178 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108000179 catalytic residue [active] 342108000180 WxcM-like, C-terminal; Region: FdtA; pfam05523 342108000181 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108000182 extended (e) SDRs; Region: SDR_e; cd08946 342108000183 NAD(P) binding site [chemical binding]; other site 342108000184 active site 342108000185 substrate binding site [chemical binding]; other site 342108000186 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 342108000187 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 342108000188 active site 342108000189 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 342108000190 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 342108000191 NAD binding site [chemical binding]; other site 342108000192 substrate binding site [chemical binding]; other site 342108000193 homodimer interface [polypeptide binding]; other site 342108000194 active site 342108000195 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 342108000196 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 342108000197 substrate binding site; other site 342108000198 tetramer interface; other site 342108000199 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 342108000200 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108000201 Walker A/P-loop; other site 342108000202 ATP binding site [chemical binding]; other site 342108000203 Q-loop/lid; other site 342108000204 ABC transporter signature motif; other site 342108000205 Walker B; other site 342108000206 D-loop; other site 342108000207 H-loop/switch region; other site 342108000208 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108000209 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108000210 NAD(P) binding site [chemical binding]; other site 342108000211 active site 342108000212 N-terminal domain of RfaE; Region: RfaE_N; cd02172 342108000213 putative active site [active] 342108000214 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 342108000215 (T/H)XGH motif; other site 342108000216 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 342108000217 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 342108000218 putative ribose interaction site [chemical binding]; other site 342108000219 putative ADP binding site [chemical binding]; other site 342108000220 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108000221 extended (e) SDRs; Region: SDR_e; cd08946 342108000222 NAD(P) binding site [chemical binding]; other site 342108000223 active site 342108000224 substrate binding site [chemical binding]; other site 342108000225 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108000226 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 342108000227 transketolase; Reviewed; Region: PRK05899 342108000228 TPP-binding site [chemical binding]; other site 342108000229 dimer interface [polypeptide binding]; other site 342108000230 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]; Region: COG3958 342108000231 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 342108000232 PYR/PP interface [polypeptide binding]; other site 342108000233 dimer interface [polypeptide binding]; other site 342108000234 TPP binding site [chemical binding]; other site 342108000235 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 342108000236 sporadic carbohydrate cluster 2OG-Fe(II) oxygenase; Region: SpoChoClust_2; TIGR04324 342108000237 sporadic carbohydrate cluster protein, LIC12192 family; Region: SpoChoClust_1; TIGR04323 342108000238 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 342108000239 Radical SAM superfamily; Region: Radical_SAM; pfam04055 342108000240 FeS/SAM binding site; other site 342108000241 Methyltransferase domain; Region: Methyltransf_31; pfam13847 342108000242 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 342108000243 S-adenosylmethionine binding site [chemical binding]; other site 342108000244 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG0535 342108000245 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 342108000246 FeS/SAM binding site; other site 342108000247 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 342108000248 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 342108000249 tetramer interface [polypeptide binding]; other site 342108000250 TPP-binding site [chemical binding]; other site 342108000251 heterodimer interface [polypeptide binding]; other site 342108000252 phosphorylation loop region [posttranslational modification] 342108000253 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 342108000254 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 342108000255 dimer interface [polypeptide binding]; other site 342108000256 PYR/PP interface [polypeptide binding]; other site 342108000257 TPP binding site [chemical binding]; other site 342108000258 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes [Energy production and conversion]; Region: AceF; COG0508 342108000259 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 342108000260 E3 interaction surface; other site 342108000261 lipoyl attachment site [posttranslational modification]; other site 342108000262 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 342108000263 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 342108000264 putative trimer interface [polypeptide binding]; other site 342108000265 putative CoA binding site [chemical binding]; other site 342108000266 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 342108000267 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 342108000268 inhibitor-cofactor binding pocket; inhibition site 342108000269 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108000270 catalytic residue [active] 342108000271 cupin fold metalloprotein, WbuC family; Region: cupin_WbuC; TIGR04366 342108000272 Arna decarboxylase_like, extended (e) SDRs; Region: Arna_like_SDR_e; cd05257 342108000273 NAD dependent epimerase/dehydratase, LLPSF_EDH_00030 family; Region: EDH_00030; TIGR04180 342108000274 NAD binding site [chemical binding]; other site 342108000275 substrate binding site [chemical binding]; other site 342108000276 active site 342108000277 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 342108000278 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 342108000279 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108000280 catalytic residue [active] 342108000281 UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing; Region: NeuC_NnaA; TIGR03568 342108000282 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 342108000283 active site 342108000284 homodimer interface [polypeptide binding]; other site 342108000285 N-acetylneuraminate synthase; Region: NeuB_NnaB; TIGR03569 342108000286 NeuB family; Region: NeuB; pfam03102 342108000287 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 342108000288 NeuB binding interface [polypeptide binding]; other site 342108000289 putative substrate binding site [chemical binding]; other site 342108000290 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108000291 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 342108000292 PHP domain; Region: PHP; pfam02811 342108000293 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 342108000294 active site 342108000295 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 342108000296 ATP-grasp domain; Region: ATP-grasp_4; cl17255 342108000297 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108000298 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108000299 NAD(P) binding site [chemical binding]; other site 342108000300 active site 342108000301 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently...; Region: CBS_pair_NTP_transferase_assoc; cd04607 342108000302 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 342108000303 NTP_trnasferase_like_2 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_2; cd06426 342108000304 Substrate binding site; other site 342108000305 metal-binding site 342108000306 Fe-S oxidoreductase [Energy production and conversion]; Region: COG1032 342108000307 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 342108000308 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 342108000309 FeS/SAM binding site; other site 342108000310 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 342108000311 ligand binding site; other site 342108000312 tetramer interface; other site 342108000313 Radical SAM superfamily; Region: Radical_SAM; pfam04055 342108000314 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 342108000315 FeS/SAM binding site; other site 342108000316 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 342108000317 flagellin modification protein A; Provisional; Region: PRK09186 342108000318 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108000319 NAD(P) binding site [chemical binding]; other site 342108000320 active site 342108000321 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 342108000322 ligand binding site; other site 342108000323 tetramer interface; other site 342108000324 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently...; Region: CBS_pair_NTP_transferase_assoc; cd04607 342108000325 N-acetylneuraminate synthase; Region: NeuB_NnaB; TIGR03569 342108000326 NeuB family; Region: NeuB; pfam03102 342108000327 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 342108000328 NeuB binding interface [polypeptide binding]; other site 342108000329 putative substrate binding site [chemical binding]; other site 342108000330 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 342108000331 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 342108000332 Metal-binding active site; metal-binding site 342108000333 AP (apurinic/apyrimidinic) site pocket; other site 342108000334 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 342108000335 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 342108000336 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 342108000337 active site 342108000338 Bacterial membrane protein YfhO; Region: YfhO; pfam09586 342108000339 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 342108000340 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 342108000341 NAD(P) binding site [chemical binding]; other site 342108000342 homodimer interface [polypeptide binding]; other site 342108000343 substrate binding site [chemical binding]; other site 342108000344 active site 342108000345 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 342108000346 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 342108000347 purine monophosphate binding site [chemical binding]; other site 342108000348 dimer interface [polypeptide binding]; other site 342108000349 putative catalytic residues [active] 342108000350 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 342108000351 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 342108000352 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108000353 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 342108000354 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 342108000355 active site 342108000356 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 342108000357 homodimer interface [polypeptide binding]; other site 342108000358 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 342108000359 dimer interface [polypeptide binding]; other site 342108000360 active site 342108000361 O-antigen ligase like membrane protein; Region: O-antigen_lig; pfam13425 342108000362 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 342108000363 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 342108000364 active site 342108000365 dimer interface [polypeptide binding]; other site 342108000366 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 342108000367 Ligand Binding Site [chemical binding]; other site 342108000368 Molecular Tunnel; other site 342108000369 WcxM-like, Left-handed parallel beta-Helix (LbH) N-terminal domain: This group is composed of Xanthomonas campestris WcxM and proteins with similarity to the WcxM N-terminal domain. WcxM is thought to be bifunctional, catalyzing both the isomerization...; Region: LbH_WxcM_N_like; cd03358 342108000370 putative trimer interface [polypeptide binding]; other site 342108000371 putative active site [active] 342108000372 putative substrate binding site [chemical binding]; other site 342108000373 putative CoA binding site [chemical binding]; other site 342108000374 Flavin Reductases; Region: FlaRed; cl00801 342108000375 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 342108000376 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108000377 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108000378 NAD(P) binding site [chemical binding]; other site 342108000379 active site 342108000380 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 342108000381 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 342108000382 Ligand binding site; other site 342108000383 Putative Catalytic site; other site 342108000384 DXD motif; other site 342108000385 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 342108000386 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 342108000387 inhibitor-cofactor binding pocket; inhibition site 342108000388 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108000389 catalytic residue [active] 342108000390 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 342108000391 trimer interface [polypeptide binding]; other site 342108000392 active site 342108000393 substrate binding site [chemical binding]; other site 342108000394 CoA binding site [chemical binding]; other site 342108000395 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 342108000396 S-adenosylmethionine binding site [chemical binding]; other site 342108000397 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 342108000398 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 342108000399 B12 binding site [chemical binding]; other site 342108000400 Fe-S oxidoreductase [Energy production and conversion]; Region: COG1032 342108000401 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 342108000402 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 342108000403 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 342108000404 FeS/SAM binding site; other site 342108000405 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 342108000406 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 342108000407 active site 342108000408 dimer interface [polypeptide binding]; other site 342108000409 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 342108000410 Ligand Binding Site [chemical binding]; other site 342108000411 Molecular Tunnel; other site 342108000412 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 342108000413 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 342108000414 substrate binding site; other site 342108000415 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 342108000416 extended (e) SDRs; Region: SDR_e; cd08946 342108000417 NAD(P) binding site [chemical binding]; other site 342108000418 active site 342108000419 substrate binding site [chemical binding]; other site 342108000420 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108000421 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108000422 extended (e) SDRs; Region: SDR_e; cd08946 342108000423 NAD(P) binding site [chemical binding]; other site 342108000424 active site 342108000425 substrate binding site [chemical binding]; other site 342108000426 dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfbC; COG1898 342108000427 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 342108000428 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 342108000429 active site 342108000430 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 342108000431 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 342108000432 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 342108000433 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 342108000434 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 342108000435 inhibitor-cofactor binding pocket; inhibition site 342108000436 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108000437 catalytic residue [active] 342108000438 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 342108000439 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 342108000440 putative active site [active] 342108000441 putative metal binding site [ion binding]; other site 342108000442 surface carbohydrate biosynthesis protein, LIC13510 family; Region: O_ant_LIC13510; TIGR04326 342108000443 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 342108000444 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 342108000445 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108000446 homodimer interface [polypeptide binding]; other site 342108000447 catalytic residue [active] 342108000448 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 342108000449 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 342108000450 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 342108000451 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 342108000452 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 342108000453 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 342108000454 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 342108000455 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 342108000456 Ligand binding site; other site 342108000457 oligomer interface; other site 342108000458 short chain dehydrogenase; Provisional; Region: PRK06523 342108000459 classical (c) SDRs; Region: SDR_c; cd05233 342108000460 NAD(P) binding site [chemical binding]; other site 342108000461 active site 342108000462 Dehydroquinate synthase (DHQS)-like. DHQS catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS-like1; cd08196 342108000463 putative active site [active] 342108000464 metal binding site [ion binding]; metal-binding site 342108000465 Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_like_2; cd12172 342108000466 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 342108000467 putative ligand binding site [chemical binding]; other site 342108000468 putative NAD binding site [chemical binding]; other site 342108000469 catalytic site [active] 342108000470 putative transferase, LIC12162 family; Region: o_ant_LIC12162; TIGR04331 342108000471 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 342108000472 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 342108000473 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108000474 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108000475 NAD(P) binding site [chemical binding]; other site 342108000476 active site 342108000477 Putative zinc binding domain; Region: Methyltransf_13; pfam08421 342108000478 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108000479 Methyltransferase domain; Region: Methyltransf_12; pfam08242 342108000480 C-methyltransferase C-terminal domain; Region: Methyltransf_14; pfam08484 342108000481 Cupin domain; Region: Cupin_2; cl17218 342108000482 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 342108000483 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 342108000484 Ligand binding site; other site 342108000485 Putative Catalytic site; other site 342108000486 DXD motif; other site 342108000487 nucleotide sugar dehydrogenase; Region: NDP-sugDHase; TIGR03026 342108000488 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 342108000489 NAD(P) binding site [chemical binding]; other site 342108000490 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 342108000491 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 342108000492 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 342108000493 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 342108000494 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 342108000495 active site 342108000496 motif I; other site 342108000497 motif II; other site 342108000498 16S rRNA methyltransferase B; Provisional; Region: PRK10901 342108000499 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 342108000500 putative RNA binding site [nucleotide binding]; other site 342108000501 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 342108000502 S-adenosylmethionine binding site [chemical binding]; other site 342108000503 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 342108000504 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 342108000505 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108000506 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 342108000507 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 342108000508 putative metal binding site; other site 342108000509 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108000510 This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core; Region: GT1_wlbH_like; cd03798 342108000511 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 342108000512 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 342108000513 NodB motif; other site 342108000514 active site 342108000515 catalytic site [active] 342108000516 metal binding site [ion binding]; metal-binding site 342108000517 Protein of unknown function (DUF2478); Region: DUF2478; pfam10649 342108000518 Uncharacterized conserved protein [Function unknown]; Region: COG2014 342108000519 Domain of unknown function (DUF4213); Region: DUF4213; pfam13938 342108000520 Domain of unknown function (DUF364); Region: DUF364; pfam04016 342108000521 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 342108000522 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 342108000523 FeS/SAM binding site; other site 342108000524 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 342108000525 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 342108000526 GT2_BcbE_like is likely involved in the biosynthesis of the polysaccharide capsule; Region: GT2_BcE_like; cd04183 342108000527 Ligand binding site; other site 342108000528 GT2_BcbE_like is likely involved in the biosynthesis of the polysaccharide capsule; Region: GT2_BcE_like; cd04183 342108000529 Ligand binding site; other site 342108000530 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 342108000531 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 342108000532 motif II; other site 342108000533 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 342108000534 active site 342108000535 catalytic site [active] 342108000536 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 342108000537 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 342108000538 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 342108000539 NADP binding site [chemical binding]; other site 342108000540 active site 342108000541 putative substrate binding site [chemical binding]; other site 342108000542 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 342108000543 ATP-NAD kinase; Region: NAD_kinase; pfam01513 342108000544 Putative ammonia monooxygenase [General function prediction only]; Region: AbrB; COG3180 342108000545 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 342108000546 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 342108000547 cupin fold metalloprotein, WbuC family; Region: cupin_WbuC; TIGR04366 342108000548 Protein of unknown function (DUF992); Region: DUF992; pfam06186 342108000549 UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]; Region: MurC; COG0773 342108000550 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 342108000551 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 342108000552 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 342108000553 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 342108000554 dimer interface [polypeptide binding]; other site 342108000555 catalytic triad [active] 342108000556 anaerobic benzoate catabolism transcriptional regulator; Reviewed; Region: PRK08154 342108000557 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 342108000558 non-specific DNA binding site [nucleotide binding]; other site 342108000559 salt bridge; other site 342108000560 sequence-specific DNA binding site [nucleotide binding]; other site 342108000561 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 342108000562 ADP binding site [chemical binding]; other site 342108000563 magnesium binding site [ion binding]; other site 342108000564 putative shikimate binding site; other site 342108000565 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 342108000566 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 342108000567 SLBB domain; Region: SLBB; pfam10531 342108000568 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 342108000569 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 342108000570 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 342108000571 catalytic loop [active] 342108000572 iron binding site [ion binding]; other site 342108000573 4Fe-4S binding domain; Region: Fer4; pfam00037 342108000574 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 342108000575 [4Fe-4S] binding site [ion binding]; other site 342108000576 molybdopterin cofactor binding site; other site 342108000577 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_CT_Formate-Dh_H; cd02790 342108000578 molybdopterin cofactor binding site; other site 342108000579 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 342108000580 aldehyde dehydrogenase; Provisional; Region: PRK11903 342108000581 N-terminal domain of the monoamine oxidase C dehydratase; Region: ALDH_MaoC-N; cd07128 342108000582 substrate binding site [chemical binding]; other site 342108000583 dimer interface [polypeptide binding]; other site 342108000584 NADP binding site [chemical binding]; other site 342108000585 catalytic residues [active] 342108000586 benzoyl-CoA-dihydrodiol lyase; Provisional; Region: PRK08184 342108000587 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 342108000588 substrate binding site [chemical binding]; other site 342108000589 oxyanion hole (OAH) forming residues; other site 342108000590 trimer interface [polypeptide binding]; other site 342108000591 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 342108000592 substrate binding site [chemical binding]; other site 342108000593 oxyanion hole (OAH) forming residues; other site 342108000594 trimer interface [polypeptide binding]; other site 342108000595 benzoyl-CoA oxygenase, B subunit; Region: benzo_boxB; TIGR03225 342108000596 benzoyl-CoA oxygenase/reductase, BoxA protein; Region: benzo_boxA; TIGR03224 342108000597 4Fe-4S binding domain; Region: Fer4; pfam00037 342108000598 4Fe-4S binding domain; Region: Fer4; pfam00037 342108000599 These ferredoxin reductases are related to the NADPH cytochrome p450 reductases (CYPOR), but lack the FAD-binding region connecting sub-domain. Ferredoxin-NADP+ reductase (FNR) is an FAD-containing enzyme that catalyzes the reversible electron transfer...; Region: CYPOR_like_FNR; cd06208 342108000600 dimerization interface [polypeptide binding]; other site 342108000601 FAD binding pocket [chemical binding]; other site 342108000602 FAD binding motif [chemical binding]; other site 342108000603 catalytic residues [active] 342108000604 NAD binding pocket [chemical binding]; other site 342108000605 phosphate binding motif [ion binding]; other site 342108000606 beta-alpha-beta structure motif; other site 342108000607 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 342108000608 active site 342108000609 enoyl-CoA hydratase; Provisional; Region: PRK08140 342108000610 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 342108000611 substrate binding site [chemical binding]; other site 342108000612 oxyanion hole (OAH) forming residues; other site 342108000613 trimer interface [polypeptide binding]; other site 342108000614 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Energy production and conversion]; Region: COG4231 342108000615 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 342108000616 dimer interface [polypeptide binding]; other site 342108000617 PYR/PP interface [polypeptide binding]; other site 342108000618 TPP binding site [chemical binding]; other site 342108000619 substrate binding site [chemical binding]; other site 342108000620 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 342108000621 TPP-binding site; other site 342108000622 putative indolepyruvate oxidoreductase subunit B; Reviewed; Region: PRK08312 342108000623 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 342108000624 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 342108000625 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108000626 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 342108000627 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 342108000628 Walker A/P-loop; other site 342108000629 ATP binding site [chemical binding]; other site 342108000630 Q-loop/lid; other site 342108000631 ABC transporter signature motif; other site 342108000632 Walker B; other site 342108000633 D-loop; other site 342108000634 H-loop/switch region; other site 342108000635 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 342108000636 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 342108000637 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108000638 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108000639 dimer interface [polypeptide binding]; other site 342108000640 putative CheW interface [polypeptide binding]; other site 342108000641 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 342108000642 PAS fold; Region: PAS_3; pfam08447 342108000643 putative active site [active] 342108000644 heme pocket [chemical binding]; other site 342108000645 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 342108000646 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 342108000647 substrate binding pocket [chemical binding]; other site 342108000648 membrane-bound complex binding site; other site 342108000649 hinge residues; other site 342108000650 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 342108000651 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 342108000652 ATP binding site [chemical binding]; other site 342108000653 Mg2+ binding site [ion binding]; other site 342108000654 G-X-G motif; other site 342108000655 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108000656 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 342108000657 active site 342108000658 phosphorylation site [posttranslational modification] 342108000659 intermolecular recognition site; other site 342108000660 dimerization interface [polypeptide binding]; other site 342108000661 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 342108000662 DNA binding site [nucleotide binding] 342108000663 Predicted membrane protein [Function unknown]; Region: COG3212 342108000664 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 342108000665 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 342108000666 Dihaem cytochrome c; Region: DHC; pfam09626 342108000667 Bacterial SH3 domain; Region: SH3_4; pfam06347 342108000668 Bacterial SH3 domain; Region: SH3_4; pfam06347 342108000669 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 342108000670 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 342108000671 dimerization interface [polypeptide binding]; other site 342108000672 ligand binding site [chemical binding]; other site 342108000673 NADP binding site [chemical binding]; other site 342108000674 catalytic site [active] 342108000675 LTXXQ motif family protein; Region: LTXXQ; pfam07813 342108000676 DsrE/DsrF/DrsH-like family; Region: DrsE_2; cl17453 342108000677 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 342108000678 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 342108000679 ATP binding site [chemical binding]; other site 342108000680 substrate interface [chemical binding]; other site 342108000681 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 342108000682 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 342108000683 dimer interface [polypeptide binding]; other site 342108000684 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108000685 catalytic residue [active] 342108000686 Rrf2 family protein; Region: rrf2_super; TIGR00738 342108000687 Transcriptional regulator; Region: Rrf2; pfam02082 342108000688 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 342108000689 trimer interface [polypeptide binding]; other site 342108000690 active site 342108000691 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 342108000692 Flavoprotein; Region: Flavoprotein; pfam02441 342108000693 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 342108000694 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 342108000695 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 342108000696 ring oligomerisation interface [polypeptide binding]; other site 342108000697 ATP/Mg binding site [chemical binding]; other site 342108000698 stacking interactions; other site 342108000699 hinge regions; other site 342108000700 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; pfam09849 342108000701 Protein of unknown function (DUF1178); Region: DUF1178; cl17833 342108000702 Ni,Fe-hydrogenase III small subunit [Energy production and conversion]; Region: COG3260 342108000703 Ni,Fe-hydrogenase III large subunit [Energy production and conversion]; Region: HycE; COG3261 342108000704 NADH dehydrogenase subunit D; Validated; Region: PRK06075; cl17338 342108000705 hydrogenase 4 subunit F; Validated; Region: PRK06458 342108000706 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 342108000707 Hydrogenase 4 membrane component (E) [Energy production and conversion]; Region: HyfE; cl17899 342108000708 NADH dehydrogenase; Region: NADHdh; cl00469 342108000709 hydrogenase 4 subunit B; Validated; Region: PRK06521 342108000710 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 342108000711 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 342108000712 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 342108000713 generic binding surface II; other site 342108000714 generic binding surface I; other site 342108000715 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 342108000716 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 342108000717 P loop; other site 342108000718 GTP binding site [chemical binding]; other site 342108000719 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 342108000720 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 342108000721 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 342108000722 FeS/SAM binding site; other site 342108000723 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 342108000724 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 342108000725 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 342108000726 potassium/proton antiporter; Reviewed; Region: PRK05326 342108000727 Transporter associated domain; Region: CorC_HlyC; smart01091 342108000728 Polysulfide-sulfurtransferase - Rhodanese Homology Domain. This domain is believed to serve as a polysulfide binding and transferase domain in anaerobic gram-negative bacteria, functioning in oxidative phosphorylation with polysulfide-sulfur as a...; Region: Polysulfide_ST; cd01447 342108000729 active site 342108000730 catalytic residue [active] 342108000731 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 342108000732 beta-galactosidase; Region: BGL; TIGR03356 342108000733 HAMP domain; Region: HAMP; pfam00672 342108000734 dimerization interface [polypeptide binding]; other site 342108000735 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108000736 dimer interface [polypeptide binding]; other site 342108000737 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 342108000738 putative CheW interface [polypeptide binding]; other site 342108000739 Hemerythrin; Region: Hemerythrin; cd12107 342108000740 Fe binding site [ion binding]; other site 342108000741 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 342108000742 ThiC-associated domain; Region: ThiC-associated; pfam13667 342108000743 ThiC family; Region: ThiC; pfam01964 342108000744 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 342108000745 Sel1 repeat; Region: Sel1; cl02723 342108000746 Sporulation related domain; Region: SPOR; pfam05036 342108000747 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 342108000748 LysR family transcriptional regulator; Provisional; Region: PRK14997 342108000749 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 342108000750 putative effector binding pocket; other site 342108000751 dimerization interface [polypeptide binding]; other site 342108000752 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 342108000753 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 342108000754 putative active site [active] 342108000755 metal binding site [ion binding]; metal-binding site 342108000756 Hemerythrin; Region: Hemerythrin; cd12107 342108000757 Fe binding site [ion binding]; other site 342108000758 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 342108000759 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 342108000760 Ligand binding site; other site 342108000761 Putative Catalytic site; other site 342108000762 DXD motif; other site 342108000763 CopC domain; Region: CopC; pfam04234 342108000764 Copper resistance protein D; Region: CopD; cl00563 342108000765 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 342108000766 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 342108000767 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 342108000768 RibD C-terminal domain; Region: RibD_C; cl17279 342108000769 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 342108000770 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108000771 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 342108000772 Protein of unknown function (DUF4237); Region: DUF4237; pfam14021 342108000773 Protein of unknown function (DUF4237); Region: DUF4237; pfam14021 342108000774 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 342108000775 nucleoside/Zn binding site; other site 342108000776 dimer interface [polypeptide binding]; other site 342108000777 catalytic motif [active] 342108000778 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 342108000779 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 342108000780 DNA-binding site [nucleotide binding]; DNA binding site 342108000781 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 342108000782 pyruvate carboxylase; Reviewed; Region: PRK12999 342108000783 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 342108000784 ATP-grasp domain; Region: ATP-grasp_4; cl17255 342108000785 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 342108000786 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 342108000787 active site 342108000788 catalytic residues [active] 342108000789 metal binding site [ion binding]; metal-binding site 342108000790 homodimer binding site [polypeptide binding]; other site 342108000791 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 342108000792 carboxyltransferase (CT) interaction site; other site 342108000793 biotinylation site [posttranslational modification]; other site 342108000794 6-pyruvoyl-tetrahydropterin synthase related domain; membrane protein; Region: PTPS_related; pfam10131 342108000795 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 342108000796 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 342108000797 dimerization interface 3.5A [polypeptide binding]; other site 342108000798 active site 342108000799 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 342108000800 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 342108000801 putative active site [active] 342108000802 substrate binding site [chemical binding]; other site 342108000803 putative cosubstrate binding site; other site 342108000804 catalytic site [active] 342108000805 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 342108000806 substrate binding site [chemical binding]; other site 342108000807 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 342108000808 active site 342108000809 catalytic residues [active] 342108000810 metal binding site [ion binding]; metal-binding site 342108000811 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 342108000812 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 342108000813 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108000814 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108000815 dimer interface [polypeptide binding]; other site 342108000816 putative CheW interface [polypeptide binding]; other site 342108000817 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 342108000818 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 342108000819 FeS/SAM binding site; other site 342108000820 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 342108000821 active site 342108000822 Transcriptional regulator [Transcription]; Region: LysR; COG0583 342108000823 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 342108000824 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 342108000825 putative dimerization interface [polypeptide binding]; other site 342108000826 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2828 342108000827 Amidohydrolase; Region: Amidohydro_2; pfam04909 342108000828 hypothetical protein; Provisional; Region: PRK09262 342108000829 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 342108000830 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; Region: 2-Hacid_dh_C; pfam02826 342108000831 Domain of unknown function (DUF1932); Region: DUF1932; pfam09130 342108000832 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 342108000833 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase hydrolyzes PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM). This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most...; Region: PDC_hydrolase; cd01311 342108000834 active site 342108000835 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 342108000836 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 342108000837 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 342108000838 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 342108000839 active site 342108000840 catalytic tetrad [active] 342108000841 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB); Region: LigA_like_1; cd07925 342108000842 putative dimer interface [polypeptide binding]; other site 342108000843 putative tetramer interface [polypeptide binding]; other site 342108000844 putative active site [active] 342108000845 protocatechuate 4,5-dioxygenase subunit beta; Provisional; Region: PRK13364 342108000846 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 342108000847 active site 342108000848 metal binding site [ion binding]; metal-binding site 342108000849 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 342108000850 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 342108000851 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 342108000852 benzoate transport; Region: 2A0115; TIGR00895 342108000853 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 342108000854 putative substrate translocation pore; other site 342108000855 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 342108000856 PAP2_like proteins, Lipid A 1-phosphatase subfamily. Lipid A 1-phosphatase, or LpxE from Francisella novicida selectively dephosphorylates lipid A at the 1-position. Lipid A is the membrane-anchor component of lipopolysaccharides (LPS), the major...; Region: PAP2_lipid_A_1_phosphatase; cd03389 342108000857 active site 342108000858 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 342108000859 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 342108000860 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 342108000861 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 342108000862 dimerization interface [polypeptide binding]; other site 342108000863 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108000864 dimer interface [polypeptide binding]; other site 342108000865 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 342108000866 putative CheW interface [polypeptide binding]; other site 342108000867 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108000868 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 342108000869 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 342108000870 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 342108000871 putative active site [active] 342108000872 putative metal binding site [ion binding]; other site 342108000873 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 342108000874 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 342108000875 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 342108000876 NADPH bind site [chemical binding]; other site 342108000877 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 342108000878 putative FMN binding site [chemical binding]; other site 342108000879 NADPH bind site [chemical binding]; other site 342108000880 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 342108000881 putative GEF interaction site [polypeptide binding]; other site 342108000882 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 342108000883 Switch I region; other site 342108000884 G2 box; other site 342108000885 G3 box; other site 342108000886 Switch II region; other site 342108000887 GTP/Mg2+ binding site [chemical binding]; other site 342108000888 G4 box; other site 342108000889 G5 box; other site 342108000890 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 342108000891 Sensor N-terminal transmembrane domain; Region: Sensor_TM1; pfam13755 342108000892 Stimulus-sensing domain; Region: Stimulus_sens_1; pfam13756 342108000893 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108000894 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 342108000895 dimer interface [polypeptide binding]; other site 342108000896 phosphorylation site [posttranslational modification] 342108000897 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 342108000898 ATP binding site [chemical binding]; other site 342108000899 Mg2+ binding site [ion binding]; other site 342108000900 G-X-G motif; other site 342108000901 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108000902 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 342108000903 active site 342108000904 phosphorylation site [posttranslational modification] 342108000905 intermolecular recognition site; other site 342108000906 dimerization interface [polypeptide binding]; other site 342108000907 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 342108000908 DNA binding site [nucleotide binding] 342108000909 cobalt transport protein CbiM; Validated; Region: PRK08319 342108000910 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 342108000911 cobalt transport protein CbiN; Provisional; Region: PRK02898 342108000912 Cobalt transport protein; Region: CbiQ; cl00463 342108000913 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 342108000914 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 342108000915 Walker A/P-loop; other site 342108000916 ATP binding site [chemical binding]; other site 342108000917 Q-loop/lid; other site 342108000918 ABC transporter signature motif; other site 342108000919 Walker B; other site 342108000920 D-loop; other site 342108000921 H-loop/switch region; other site 342108000922 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 342108000923 active site residue [active] 342108000924 Uncharacterized conserved protein [Function unknown]; Region: COG3347 342108000925 Class II Aldolase and Adducin N-terminal domain; Region: Aldolase_II; smart01007 342108000926 active site 342108000927 Zn2+ binding site [ion binding]; other site 342108000928 intersubunit interface [polypeptide binding]; other site 342108000929 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108000930 NAD(P) binding site [chemical binding]; other site 342108000931 active site 342108000932 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 342108000933 Peptidase family M23; Region: Peptidase_M23; pfam01551 342108000934 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 342108000935 FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate...; Region: DHOD_e_trans_like; cd06192 342108000936 ferredoxin-NADP(+) reductase subunit alpha; Reviewed; Region: PRK06222 342108000937 FAD binding pocket [chemical binding]; other site 342108000938 FAD binding motif [chemical binding]; other site 342108000939 phosphate binding motif [ion binding]; other site 342108000940 beta-alpha-beta structure motif; other site 342108000941 NAD binding pocket [chemical binding]; other site 342108000942 Iron coordination center [ion binding]; other site 342108000943 Nucleoside recognition; Region: Gate; pfam07670 342108000944 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 342108000945 MutS domain I; Region: MutS_I; pfam01624 342108000946 MutS domain II; Region: MutS_II; pfam05188 342108000947 MutS domain III; Region: MutS_III; pfam05192 342108000948 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 342108000949 Walker A/P-loop; other site 342108000950 ATP binding site [chemical binding]; other site 342108000951 Q-loop/lid; other site 342108000952 ABC transporter signature motif; other site 342108000953 Walker B; other site 342108000954 D-loop; other site 342108000955 H-loop/switch region; other site 342108000956 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 342108000957 Malic enzyme, N-terminal domain; Region: malic; pfam00390 342108000958 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 342108000959 putative NAD(P) binding site [chemical binding]; other site 342108000960 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 342108000961 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 342108000962 dimer interface [polypeptide binding]; other site 342108000963 phosphorylation site [posttranslational modification] 342108000964 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 342108000965 ATP binding site [chemical binding]; other site 342108000966 Mg2+ binding site [ion binding]; other site 342108000967 G-X-G motif; other site 342108000968 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 342108000969 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 342108000970 putative substrate translocation pore; other site 342108000971 cobyric acid synthase; Provisional; Region: PRK00784 342108000972 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 342108000973 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 342108000974 catalytic triad [active] 342108000975 CobD/Cbib protein; Region: CobD_Cbib; pfam03186 342108000976 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]; Region: COG2138 342108000977 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 342108000978 putative active site [active] 342108000979 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_C; cd03414 342108000980 putative active site [active] 342108000981 precorrin-8X methylmutase; Reviewed; Region: cobH; PRK08285 342108000982 Precorrin-8X methylmutase; Region: CbiC; pfam02570 342108000983 Precorrin-6Y methyltransferase, the cobalamin biosynthesis enzyme CbiE; Region: Precorrin-6Y-methylase; cd11644 342108000984 active site 342108000985 putative homodimer interface [polypeptide binding]; other site 342108000986 SAM binding site [chemical binding]; other site 342108000987 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 342108000988 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 342108000989 S-adenosylmethionine binding site [chemical binding]; other site 342108000990 Precorrin-2 C20-methyltransferase, also named CobI or CbiL; Region: Precorrin_2_C20_MT; cd11645 342108000991 active site 342108000992 SAM binding site [chemical binding]; other site 342108000993 homodimer interface [polypeptide binding]; other site 342108000994 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 342108000995 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 342108000996 Cobalamin synthesis G C-terminus; Region: CbiG_C; pfam01890 342108000997 Precorrin-3B C(17)-methyltransferase (CobJ/CbiH); Region: Precorrin_3B_C17_MT; cd11646 342108000998 active site 342108000999 SAM binding site [chemical binding]; other site 342108001000 homodimer interface [polypeptide binding]; other site 342108001001 Peptidase family M48; Region: Peptidase_M48; pfam01435 342108001002 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 342108001003 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cl00107 342108001004 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 342108001005 putative active site [active] 342108001006 Ap4A binding site [chemical binding]; other site 342108001007 nudix motif; other site 342108001008 putative metal binding site [ion binding]; other site 342108001009 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 342108001010 NodB motif; other site 342108001011 putative active site [active] 342108001012 putative catalytic site [active] 342108001013 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 342108001014 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 342108001015 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 342108001016 protein binding site [polypeptide binding]; other site 342108001017 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 342108001018 Catalytic dyad [active] 342108001019 Peptidase family M23; Region: Peptidase_M23; pfam01551 342108001020 phosphoglyceromutase; Provisional; Region: PRK05434 342108001021 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 342108001022 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 342108001023 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 342108001024 active site 342108001025 crotonyl-CoA reductase; Region: crotonyl_coA_red; cd08246 342108001026 crotonyl-CoA reductase; Region: crot-CoA-red; TIGR01751 342108001027 putative NAD(P) binding site [chemical binding]; other site 342108001028 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 342108001029 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 342108001030 B12 binding site [chemical binding]; other site 342108001031 cobalt ligand [ion binding]; other site 342108001032 Mechanosensitive ion channel; Region: MS_channel; pfam00924 342108001033 RecX family; Region: RecX; pfam02631 342108001034 ABC-2 type transporter; Region: ABC2_membrane; cl17235 342108001035 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 342108001036 Helix-turn-helix XRE-family like proteins; Region: HTH_XRE; smart00530 342108001037 Methyltransferase domain; Region: Methyltransf_31; pfam13847 342108001038 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 342108001039 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 342108001040 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 342108001041 inhibitor-cofactor binding pocket; inhibition site 342108001042 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108001043 catalytic residue [active] 342108001044 ornithine carbamoyltransferase; Provisional; Region: PRK00779 342108001045 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 342108001046 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 342108001047 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 342108001048 dimerization interface [polypeptide binding]; other site 342108001049 domain crossover interface; other site 342108001050 redox-dependent activation switch; other site 342108001051 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 342108001052 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 342108001053 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 342108001054 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 342108001055 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 342108001056 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 342108001057 active site 342108001058 phosphorylation site [posttranslational modification] 342108001059 intermolecular recognition site; other site 342108001060 dimerization interface [polypeptide binding]; other site 342108001061 CheB methylesterase; Region: CheB_methylest; pfam01339 342108001062 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 342108001063 Response regulator receiver domain; Region: Response_reg; pfam00072 342108001064 active site 342108001065 phosphorylation site [posttranslational modification] 342108001066 intermolecular recognition site; other site 342108001067 dimerization interface [polypeptide binding]; other site 342108001068 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 342108001069 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 342108001070 putative binding surface; other site 342108001071 active site 342108001072 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 342108001073 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 342108001074 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 342108001075 ATP binding site [chemical binding]; other site 342108001076 Mg2+ binding site [ion binding]; other site 342108001077 G-X-G motif; other site 342108001078 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 342108001079 CheW-like domain; Region: CheW; pfam01584 342108001080 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108001081 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 342108001082 active site 342108001083 phosphorylation site [posttranslational modification] 342108001084 intermolecular recognition site; other site 342108001085 dimerization interface [polypeptide binding]; other site 342108001086 Uncharacterized protein conserved in bacteria (DUF2328); Region: DUF2328; pfam10090 342108001087 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 342108001088 TRAM domain; Region: TRAM; cl01282 342108001089 Protein of unknown function (DUF330); Region: DUF330; cl01135 342108001090 mce related protein; Region: MCE; pfam02470 342108001091 Protein of unknown function (DUF3407); Region: DUF3407; pfam11887 342108001092 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 342108001093 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 342108001094 Walker A/P-loop; other site 342108001095 ATP binding site [chemical binding]; other site 342108001096 Q-loop/lid; other site 342108001097 ABC transporter signature motif; other site 342108001098 Walker B; other site 342108001099 D-loop; other site 342108001100 H-loop/switch region; other site 342108001101 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 342108001102 Permease; Region: Permease; pfam02405 342108001103 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 342108001104 anti sigma factor interaction site; other site 342108001105 regulatory phosphorylation site [posttranslational modification]; other site 342108001106 GAF domain; Region: GAF_2; pfam13185 342108001107 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 342108001108 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 342108001109 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 342108001110 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 342108001111 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 342108001112 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 342108001113 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 342108001114 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 342108001115 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108001116 putative ADP-binding pocket [chemical binding]; other site 342108001117 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 342108001118 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 342108001119 putative active site [active] 342108001120 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 342108001121 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 342108001122 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 342108001123 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 342108001124 active site 342108001125 dimer interface [polypeptide binding]; other site 342108001126 motif 1; other site 342108001127 motif 2; other site 342108001128 motif 3; other site 342108001129 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 342108001130 anticodon binding site; other site 342108001131 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 342108001132 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 342108001133 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 342108001134 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 342108001135 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 342108001136 catalytic residues [active] 342108001137 catalytic nucleophile [active] 342108001138 Presynaptic Site I dimer interface [polypeptide binding]; other site 342108001139 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 342108001140 Synaptic Flat tetramer interface [polypeptide binding]; other site 342108001141 Synaptic Site I dimer interface [polypeptide binding]; other site 342108001142 DNA binding site [nucleotide binding] 342108001143 Recombinase; Region: Recombinase; pfam07508 342108001144 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 342108001145 Protein of unknown function (DUF2924); Region: DUF2924; pfam11149 342108001146 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108001147 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 342108001148 non-specific DNA binding site [nucleotide binding]; other site 342108001149 salt bridge; other site 342108001150 sequence-specific DNA binding site [nucleotide binding]; other site 342108001151 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; cl01049 342108001152 Domain of unknown function (DUF955); Region: DUF955; cl01076 342108001153 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 342108001154 AAA domain; Region: AAA_24; pfam13479 342108001155 phage nucleotide-binding protein; Region: phage_P_loop; TIGR01618 342108001156 Protein of unknown function (DUF669); Region: DUF669; pfam05037 342108001157 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 342108001158 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 342108001159 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 342108001160 ATP binding site [chemical binding]; other site 342108001161 putative Mg++ binding site [ion binding]; other site 342108001162 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 342108001163 nucleotide binding region [chemical binding]; other site 342108001164 ATP-binding site [chemical binding]; other site 342108001165 Uncharacterized protein family UPF0547; Region: UPF0547; pfam10571 342108001166 Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the...; Region: Prim_Pol; cd04859 342108001167 polymerase nucleotide-binding site; other site 342108001168 DNA-binding residues [nucleotide binding]; DNA binding site 342108001169 nucleotide binding site [chemical binding]; other site 342108001170 primase nucleotide-binding site [nucleotide binding]; other site 342108001171 Primase C terminal 2 (PriCT-2); Region: PriCT_2; pfam08707 342108001172 Protein of unknown function (DUF3987); Region: DUF3987; pfam13148 342108001173 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 342108001174 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 342108001175 cofactor binding site; other site 342108001176 DNA binding site [nucleotide binding] 342108001177 substrate interaction site [chemical binding]; other site 342108001178 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 342108001179 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 342108001180 ParB-like nuclease domain; Region: ParBc; pfam02195 342108001181 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 342108001182 DNA methylase; Region: N6_N4_Mtase; pfam01555 342108001183 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 342108001184 IHF - DNA interface [nucleotide binding]; other site 342108001185 IHF dimer interface [polypeptide binding]; other site 342108001186 Protein of unknown function (DUF3489); Region: DUF3489; pfam11994 342108001187 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 342108001188 Phage portal protein, lambda family; Region: Phage_portal_2; pfam05136 342108001189 phage portal protein, lambda family; Region: portal_lambda; TIGR01539 342108001190 Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_36K_type; cd07022 342108001191 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 342108001192 tandem repeat interface [polypeptide binding]; other site 342108001193 oligomer interface [polypeptide binding]; other site 342108001194 active site residues [active] 342108001195 Bacteriophage lambda head decoration protein D; Region: HDPD; pfam02924 342108001196 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 342108001197 Fic family protein [Function unknown]; Region: COG3177 342108001198 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 342108001199 Fic/DOC family; Region: Fic; pfam02661 342108001200 geranyl diphosphate synthase; Region: PLN02890 342108001201 tape measure domain; Region: tape_meas_nterm; TIGR02675 342108001202 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 342108001203 Negative regulator of septation ring formation [Cell division and chromosome partitioning]; Region: EzrA; COG4477 342108001204 Domain of unknown function (DUF1833); Region: DUF1833; pfam08875 342108001205 Bacteriophage lambda tail assembly protein I; Region: Lambda_tail_I; pfam06805 342108001206 Putative phage tail protein; Region: Phage-tail_3; pfam13550 342108001207 virion protein; Provisional; Region: V; PHA02564 342108001208 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 342108001209 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 342108001210 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 342108001211 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 342108001212 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 342108001213 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 342108001214 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 342108001215 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 342108001216 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 342108001217 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 342108001218 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 342108001219 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 342108001220 Transposase; Region: HTH_Tnp_1; pfam01527 342108001221 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108001222 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 342108001223 DDE superfamily endonuclease; Region: DDE_3; pfam13358 342108001224 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 342108001225 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 342108001226 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 342108001227 protein binding site [polypeptide binding]; other site 342108001228 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 342108001229 FOG: Transposase [DNA replication, recombination, and repair]; Region: COG5659 342108001230 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 342108001231 GlcNAc-PI de-N-acetylase; Region: PIG-L; pfam02585 342108001232 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 342108001233 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 342108001234 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 342108001235 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 342108001236 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 342108001237 DctM-like transporters; Region: DctM; pfam06808 342108001238 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 342108001239 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 342108001240 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 342108001241 ligand binding site [chemical binding]; other site 342108001242 hypothetical protein; Provisional; Region: PRK05208 342108001243 Uncharacterized protein family (UPF0160); Region: UPF0160; pfam03690 342108001244 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 342108001245 5-methyltetrahydrofolate--homocysteine methyltransferase; Region: metH; TIGR02082 342108001246 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 342108001247 substrate binding pocket [chemical binding]; other site 342108001248 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 342108001249 B12 binding site [chemical binding]; other site 342108001250 cobalt ligand [ion binding]; other site 342108001251 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 342108001252 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 342108001253 dimerization interface [polypeptide binding]; other site 342108001254 putative DNA binding site [nucleotide binding]; other site 342108001255 putative Zn2+ binding site [ion binding]; other site 342108001256 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108001257 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 342108001258 S-adenosylmethionine binding site [chemical binding]; other site 342108001259 VacJ like lipoprotein; Region: VacJ; cl01073 342108001260 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 342108001261 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 342108001262 substrate binding pocket [chemical binding]; other site 342108001263 membrane-bound complex binding site; other site 342108001264 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 342108001265 dimerization interface [polypeptide binding]; other site 342108001266 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 342108001267 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 342108001268 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 342108001269 anti sigma factor interaction site; other site 342108001270 regulatory phosphorylation site [posttranslational modification]; other site 342108001271 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5381 342108001272 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 342108001273 dimer interface [polypeptide binding]; other site 342108001274 phosphorylation site [posttranslational modification] 342108001275 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 342108001276 ATP binding site [chemical binding]; other site 342108001277 Mg2+ binding site [ion binding]; other site 342108001278 G-X-G motif; other site 342108001279 Response regulator receiver domain; Region: Response_reg; pfam00072 342108001280 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 342108001281 active site 342108001282 phosphorylation site [posttranslational modification] 342108001283 intermolecular recognition site; other site 342108001284 dimerization interface [polypeptide binding]; other site 342108001285 Hpt domain; Region: Hpt; pfam01627 342108001286 putative binding surface; other site 342108001287 active site 342108001288 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108001289 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 342108001290 non-specific DNA binding site [nucleotide binding]; other site 342108001291 salt bridge; other site 342108001292 sequence-specific DNA binding site [nucleotide binding]; other site 342108001293 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 342108001294 sequence-specific DNA binding site [nucleotide binding]; other site 342108001295 salt bridge; other site 342108001296 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 342108001297 Winged helix-turn helix; Region: HTH_29; pfam13551 342108001298 Integrase core domain; Region: rve; pfam00665 342108001299 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 342108001300 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 342108001301 AAA domain; Region: AAA_22; pfam13401 342108001302 Walker A motif; other site 342108001303 ATP binding site [chemical binding]; other site 342108001304 Walker B motif; other site 342108001305 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 342108001306 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 342108001307 DnaA box-binding interface [nucleotide binding]; other site 342108001308 Bacteriophage Mu Gam like protein; Region: Phage_Mu_Gam; pfam07352 342108001309 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 342108001310 RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_I; cd01646 342108001311 putative active site [active] 342108001312 putative NTP binding site [chemical binding]; other site 342108001313 putative nucleic acid binding site [nucleotide binding]; other site 342108001314 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 342108001315 S-adenosylmethionine binding site [chemical binding]; other site 342108001316 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 342108001317 Protein of unknown function (DUF1018); Region: DUF1018; cl01815 342108001318 Uncharacterized protein family UPF0547; Region: UPF0547; pfam10571 342108001319 Homeodomain-like domain; Region: HTH_23; cl17451 342108001320 virion protein; Provisional; Region: V; PHA02564 342108001321 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 342108001322 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 342108001323 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 342108001324 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 342108001325 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 342108001326 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 342108001327 NlpC/P60 family; Region: NLPC_P60; cl17555 342108001328 Putative phage tail protein; Region: Phage-tail_3; pfam13550 342108001329 chitin-binding domain of Chi A1-like proteins; Region: ChiA1_BD; cd12214 342108001330 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 342108001331 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 342108001332 non-specific DNA binding site [nucleotide binding]; other site 342108001333 salt bridge; other site 342108001334 sequence-specific DNA binding site [nucleotide binding]; other site 342108001335 Helix-turn-helix domain; Region: HTH_17; cl17695 342108001336 integrase; Provisional; Region: PRK09692 342108001337 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 342108001338 active site 342108001339 Int/Topo IB signature motif; other site 342108001340 putative protease; Provisional; Region: PRK15447 342108001341 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 342108001342 Peptidase family U32; Region: Peptidase_U32; pfam01136 342108001343 SCP-2 sterol transfer family; Region: SCP2; cl01225 342108001344 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 342108001345 Response regulator receiver domain; Region: Response_reg; pfam00072 342108001346 active site 342108001347 phosphorylation site [posttranslational modification] 342108001348 intermolecular recognition site; other site 342108001349 dimerization interface [polypeptide binding]; other site 342108001350 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108001351 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 342108001352 ligand binding site [chemical binding]; other site 342108001353 flexible hinge region; other site 342108001354 Bacterial SH3 domain; Region: SH3_3; cl17532 342108001355 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 342108001356 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 342108001357 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 342108001358 SRP54-type protein, GTPase domain; Region: SRP54; smart00962 342108001359 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 342108001360 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 342108001361 FHIPEP family; Region: FHIPEP; pfam00771 342108001362 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 342108001363 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 342108001364 active site 342108001365 phosphorylation site [posttranslational modification] 342108001366 intermolecular recognition site; other site 342108001367 dimerization interface [polypeptide binding]; other site 342108001368 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 342108001369 Walker A motif; other site 342108001370 ATP binding site [chemical binding]; other site 342108001371 Walker B motif; other site 342108001372 arginine finger; other site 342108001373 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 342108001374 flagellar motor switch protein; Reviewed; Region: PRK08916 342108001375 flagellar assembly protein H; Validated; Region: fliH; PRK06032 342108001376 Flagellar assembly protein FliH; Region: FliH; pfam02108 342108001377 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 342108001378 FliG C-terminal domain; Region: FliG_C; pfam01706 342108001379 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 342108001380 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 342108001381 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 342108001382 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 342108001383 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 342108001384 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 342108001385 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 342108001386 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 342108001387 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 342108001388 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 342108001389 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 342108001390 putative MPT binding site; other site 342108001391 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 342108001392 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 342108001393 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 342108001394 active site 342108001395 8-oxo-dGMP binding site [chemical binding]; other site 342108001396 nudix motif; other site 342108001397 metal binding site [ion binding]; metal-binding site 342108001398 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 342108001399 heterotetramer interface [polypeptide binding]; other site 342108001400 active site pocket [active] 342108001401 cleavage site 342108001402 PPIC-type PPIASE domain; Region: Rotamase_3; pfam13616 342108001403 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 342108001404 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 342108001405 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 342108001406 Phosphoglycerate kinase; Region: PGK; pfam00162 342108001407 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 342108001408 substrate binding site [chemical binding]; other site 342108001409 hinge regions; other site 342108001410 ADP binding site [chemical binding]; other site 342108001411 catalytic site [active] 342108001412 Precorrin-4 C11-methyltransferase (CbiF/CobM); Region: Precorrin-4_C11-MT; cd11641 342108001413 active site 342108001414 SAM binding site [chemical binding]; other site 342108001415 homodimer interface [polypeptide binding]; other site 342108001416 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 342108001417 active site 342108001418 SAM binding site [chemical binding]; other site 342108001419 homodimer interface [polypeptide binding]; other site 342108001420 Family description; Region: DsbD_2; pfam13386 342108001421 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 342108001422 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 342108001423 Cu(I) binding site [ion binding]; other site 342108001424 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 342108001425 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 342108001426 hypothetical protein; Provisional; Region: PRK05170 342108001427 Hemerythrin family; Region: Hemerythrin-like; cl15774 342108001428 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 342108001429 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 342108001430 active site 342108001431 dimer interface [polypeptide binding]; other site 342108001432 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 342108001433 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 342108001434 active site 342108001435 FMN binding site [chemical binding]; other site 342108001436 substrate binding site [chemical binding]; other site 342108001437 3Fe-4S cluster binding site [ion binding]; other site 342108001438 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 342108001439 domain interface; other site 342108001440 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 342108001441 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 342108001442 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108001443 Bacitracin resistance protein BacA; Region: BacA; pfam02673 342108001444 Transglycosylase; Region: Transgly; pfam00912 342108001445 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 342108001446 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 342108001447 ribbon-helix-helix domain containing protein; Region: PHA00617 342108001448 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 342108001449 FMN binding site [chemical binding]; other site 342108001450 substrate binding site [chemical binding]; other site 342108001451 putative catalytic residue [active] 342108001452 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 342108001453 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 342108001454 putative active site [active] 342108001455 catalytic site [active] 342108001456 putative metal binding site [ion binding]; other site 342108001457 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 342108001458 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 342108001459 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 342108001460 putative active site [active] 342108001461 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 342108001462 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 342108001463 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 342108001464 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 342108001465 [4Fe-4S] binding site [ion binding]; other site 342108001466 molybdopterin cofactor binding site; other site 342108001467 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 342108001468 molybdopterin cofactor binding site; other site 342108001469 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 342108001470 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 342108001471 [2Fe-2S] cluster binding site [ion binding]; other site 342108001472 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 342108001473 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108001474 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 342108001475 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 342108001476 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 342108001477 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 342108001478 NMT1-like family; Region: NMT1_2; pfam13379 342108001479 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 342108001480 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 342108001481 Walker A/P-loop; other site 342108001482 ATP binding site [chemical binding]; other site 342108001483 Q-loop/lid; other site 342108001484 ABC transporter signature motif; other site 342108001485 Walker B; other site 342108001486 D-loop; other site 342108001487 H-loop/switch region; other site 342108001488 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 342108001489 nitrate transport ATP-binding subunits C and D; Region: ntrCD; TIGR01184 342108001490 Walker A/P-loop; other site 342108001491 ATP binding site [chemical binding]; other site 342108001492 Q-loop/lid; other site 342108001493 ABC transporter signature motif; other site 342108001494 Walker B; other site 342108001495 D-loop; other site 342108001496 H-loop/switch region; other site 342108001497 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 342108001498 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 342108001499 dimer interface [polypeptide binding]; other site 342108001500 conserved gate region; other site 342108001501 putative PBP binding loops; other site 342108001502 ABC-ATPase subunit interface; other site 342108001503 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 342108001504 NMT1-like family; Region: NMT1_2; pfam13379 342108001505 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 342108001506 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 342108001507 Histidine phosphatase superfamily (branch 1); Region: His_Phos_1; pfam00300 342108001508 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 342108001509 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 342108001510 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 342108001511 putative dimer interface [polypeptide binding]; other site 342108001512 active site pocket [active] 342108001513 putative cataytic base [active] 342108001514 Membrane fusogenic activity; Region: BMFP; pfam04380 342108001515 Putative bacterial sensory transduction regulator; Region: YbjN; cl15834 342108001516 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 342108001517 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 342108001518 phasin family protein; Region: phasin; TIGR01841 342108001519 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 342108001520 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 342108001521 P-loop; other site 342108001522 Magnesium ion binding site [ion binding]; other site 342108001523 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108001524 HAMP domain; Region: HAMP; pfam00672 342108001525 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 342108001526 dimer interface [polypeptide binding]; other site 342108001527 phosphorylation site [posttranslational modification] 342108001528 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 342108001529 ATP binding site [chemical binding]; other site 342108001530 Mg2+ binding site [ion binding]; other site 342108001531 G-X-G motif; other site 342108001532 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108001533 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 342108001534 active site 342108001535 phosphorylation site [posttranslational modification] 342108001536 intermolecular recognition site; other site 342108001537 dimerization interface [polypeptide binding]; other site 342108001538 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 342108001539 DNA binding site [nucleotide binding] 342108001540 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 342108001541 MarR family; Region: MarR_2; pfam12802 342108001542 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 342108001543 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 342108001544 homodimer interface [polypeptide binding]; other site 342108001545 substrate-cofactor binding pocket; other site 342108001546 catalytic residue [active] 342108001547 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 342108001548 dimerization interface [polypeptide binding]; other site 342108001549 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108001550 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108001551 dimer interface [polypeptide binding]; other site 342108001552 putative CheW interface [polypeptide binding]; other site 342108001553 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 342108001554 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 342108001555 active site 342108001556 phosphorylation site [posttranslational modification] 342108001557 intermolecular recognition site; other site 342108001558 dimerization interface [polypeptide binding]; other site 342108001559 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108001560 Zn2+ binding site [ion binding]; other site 342108001561 Mg2+ binding site [ion binding]; other site 342108001562 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108001563 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 342108001564 dimerization interface [polypeptide binding]; other site 342108001565 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108001566 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108001567 dimer interface [polypeptide binding]; other site 342108001568 putative CheW interface [polypeptide binding]; other site 342108001569 aspartate aminotransferase; Provisional; Region: PRK05764 342108001570 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 342108001571 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108001572 homodimer interface [polypeptide binding]; other site 342108001573 catalytic residue [active] 342108001574 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 342108001575 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 342108001576 Sel1-like repeats; Region: SEL1; smart00671 342108001577 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 342108001578 active site 342108001579 phosphorylation site [posttranslational modification] 342108001580 intermolecular recognition site; other site 342108001581 dimerization interface [polypeptide binding]; other site 342108001582 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 342108001583 aromatic arch; other site 342108001584 DCoH dimer interaction site [polypeptide binding]; other site 342108001585 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 342108001586 DCoH tetramer interaction site [polypeptide binding]; other site 342108001587 substrate binding site [chemical binding]; other site 342108001588 Minimal MMP-like domain found in Acidothermus cellulolyticus hypothetical protein ACEL2062 and similar protein; Region: MMP_ACEL2062; cd12952 342108001589 AAA domain; Region: AAA_32; pfam13654 342108001590 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 342108001591 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 342108001592 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 342108001593 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 342108001594 PAS domain S-box; Region: sensory_box; TIGR00229 342108001595 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 342108001596 putative active site [active] 342108001597 heme pocket [chemical binding]; other site 342108001598 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 342108001599 dimer interface [polypeptide binding]; other site 342108001600 phosphorylation site [posttranslational modification] 342108001601 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 342108001602 ATP binding site [chemical binding]; other site 342108001603 Mg2+ binding site [ion binding]; other site 342108001604 G-X-G motif; other site 342108001605 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 342108001606 Hemerythrin; Region: Hemerythrin; cd12107 342108001607 Fe binding site [ion binding]; other site 342108001608 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 342108001609 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 342108001610 Walker A motif; other site 342108001611 ATP binding site [chemical binding]; other site 342108001612 Walker B motif; other site 342108001613 arginine finger; other site 342108001614 Phasin protein; Region: Phasin_2; pfam09361 342108001615 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 342108001616 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 342108001617 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 342108001618 active site 342108001619 substrate binding site [chemical binding]; other site 342108001620 metal binding site [ion binding]; metal-binding site 342108001621 phosphoglucomutase; Region: PLN02307 342108001622 Phosphoglucomutase 1 (PGM1) catalyzes the bidirectional interconversion of glucose-1-phosphate (G-1-P) and glucose-6-phosphate (G-6-P) via a glucose 1,6-diphosphate intermediate, an important metabolic step in prokaryotes and eukaryotes. In one direction; Region: PGM1; cd03085 342108001623 substrate binding site [chemical binding]; other site 342108001624 dimer interface [polypeptide binding]; other site 342108001625 active site 342108001626 metal binding site [ion binding]; metal-binding site 342108001627 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 342108001628 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 342108001629 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 342108001630 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 342108001631 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 342108001632 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 342108001633 active site 342108001634 tetramer interface; other site 342108001635 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 342108001636 HSP70 interaction site [polypeptide binding]; other site 342108001637 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 342108001638 anti sigma factor interaction site; other site 342108001639 regulatory phosphorylation site [posttranslational modification]; other site 342108001640 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 342108001641 Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS); Region: AACS; cd05943 342108001642 acyl-activating enzyme (AAE) consensus motif; other site 342108001643 putative AMP binding site [chemical binding]; other site 342108001644 putative active site [active] 342108001645 putative CoA binding site [chemical binding]; other site 342108001646 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 342108001647 active site 342108001648 zinc binding site [ion binding]; other site 342108001649 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 342108001650 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 342108001651 PAS fold; Region: PAS_3; pfam08447 342108001652 putative active site [active] 342108001653 heme pocket [chemical binding]; other site 342108001654 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108001655 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108001656 dimer interface [polypeptide binding]; other site 342108001657 putative CheW interface [polypeptide binding]; other site 342108001658 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 342108001659 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 342108001660 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 342108001661 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108001662 Walker A/P-loop; other site 342108001663 ATP binding site [chemical binding]; other site 342108001664 Q-loop/lid; other site 342108001665 ABC transporter signature motif; other site 342108001666 Walker B; other site 342108001667 D-loop; other site 342108001668 H-loop/switch region; other site 342108001669 Transcriptional regulator [Transcription]; Region: LysR; COG0583 342108001670 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 342108001671 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 342108001672 dimerization interface [polypeptide binding]; other site 342108001673 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 342108001674 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 342108001675 active site 342108001676 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 342108001677 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 342108001678 Uncharacterized conserved protein [Function unknown]; Region: COG1565 342108001679 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 342108001680 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 342108001681 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 342108001682 NADP binding site [chemical binding]; other site 342108001683 homopentamer interface [polypeptide binding]; other site 342108001684 substrate binding site [chemical binding]; other site 342108001685 active site 342108001686 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 342108001687 Uncharacterized conserved protein (DUF2048); Region: DUF2048; pfam09752 342108001688 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 342108001689 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 342108001690 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 342108001691 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 342108001692 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 342108001693 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 342108001694 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 342108001695 ligand binding site [chemical binding]; other site 342108001696 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 342108001697 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 342108001698 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 342108001699 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 342108001700 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 342108001701 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 342108001702 isocitrate dehydrogenase; Validated; Region: PRK08299 342108001703 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 342108001704 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 342108001705 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 342108001706 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK06004 342108001707 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 342108001708 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 342108001709 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 342108001710 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 342108001711 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00790 342108001712 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 342108001713 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 342108001714 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 342108001715 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 342108001716 PAS domain; Region: PAS; smart00091 342108001717 putative active site [active] 342108001718 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 342108001719 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 342108001720 putative active site [active] 342108001721 heme pocket [chemical binding]; other site 342108001722 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 342108001723 dimer interface [polypeptide binding]; other site 342108001724 phosphorylation site [posttranslational modification] 342108001725 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 342108001726 ATP binding site [chemical binding]; other site 342108001727 Mg2+ binding site [ion binding]; other site 342108001728 G-X-G motif; other site 342108001729 Response regulator receiver domain; Region: Response_reg; pfam00072 342108001730 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 342108001731 active site 342108001732 phosphorylation site [posttranslational modification] 342108001733 intermolecular recognition site; other site 342108001734 dimerization interface [polypeptide binding]; other site 342108001735 Caspase domain; Region: Peptidase_C14; pfam00656 342108001736 recombinase A; Provisional; Region: recA; PRK09354 342108001737 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 342108001738 hexamer interface [polypeptide binding]; other site 342108001739 Walker A motif; other site 342108001740 ATP binding site [chemical binding]; other site 342108001741 Walker B motif; other site 342108001742 DNA polymerase IV; Provisional; Region: PRK02794 342108001743 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 342108001744 active site 342108001745 DNA binding site [nucleotide binding] 342108001746 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 342108001747 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 342108001748 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 342108001749 PAS fold; Region: PAS_7; pfam12860 342108001750 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108001751 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 342108001752 dimer interface [polypeptide binding]; other site 342108001753 phosphorylation site [posttranslational modification] 342108001754 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 342108001755 ATP binding site [chemical binding]; other site 342108001756 Mg2+ binding site [ion binding]; other site 342108001757 G-X-G motif; other site 342108001758 Predicted membrane protein [Function unknown]; Region: COG1238 342108001759 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 342108001760 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08927 342108001761 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 342108001762 Walker A motif/ATP binding site; other site 342108001763 Walker B motif; other site 342108001764 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108001765 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 342108001766 active site 342108001767 phosphorylation site [posttranslational modification] 342108001768 intermolecular recognition site; other site 342108001769 dimerization interface [polypeptide binding]; other site 342108001770 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 342108001771 DNA binding site [nucleotide binding] 342108001772 ABC1 family; Region: ABC1; cl17513 342108001773 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 342108001774 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 342108001775 S-adenosylmethionine binding site [chemical binding]; other site 342108001776 ubiquinone biosynthesis methyltransferase; Region: PLN02232 342108001777 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 342108001778 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 342108001779 DNA binding site [nucleotide binding] 342108001780 catalytic residue [active] 342108001781 H2TH interface [polypeptide binding]; other site 342108001782 putative catalytic residues [active] 342108001783 turnover-facilitating residue; other site 342108001784 intercalation triad [nucleotide binding]; other site 342108001785 8OG recognition residue [nucleotide binding]; other site 342108001786 putative reading head residues; other site 342108001787 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 342108001788 enoyl-CoA hydratase; Provisional; Region: PRK05862 342108001789 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 342108001790 substrate binding site [chemical binding]; other site 342108001791 oxyanion hole (OAH) forming residues; other site 342108001792 trimer interface [polypeptide binding]; other site 342108001793 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 342108001794 DnaA N-terminal domain; Region: DnaA_N; pfam11638 342108001795 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 342108001796 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 342108001797 Walker A motif; other site 342108001798 ATP binding site [chemical binding]; other site 342108001799 Walker B motif; other site 342108001800 arginine finger; other site 342108001801 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 342108001802 DnaA box-binding interface [nucleotide binding]; other site 342108001803 DNA polymerase III subunit beta; Validated; Region: PRK05643 342108001804 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 342108001805 putative DNA binding surface [nucleotide binding]; other site 342108001806 dimer interface [polypeptide binding]; other site 342108001807 beta-clamp/clamp loader binding surface; other site 342108001808 beta-clamp/translesion DNA polymerase binding surface; other site 342108001809 recombination protein F; Reviewed; Region: recF; PRK00064 342108001810 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108001811 Walker A/P-loop; other site 342108001812 ATP binding site [chemical binding]; other site 342108001813 Q-loop/lid; other site 342108001814 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108001815 ABC transporter signature motif; other site 342108001816 Walker B; other site 342108001817 D-loop; other site 342108001818 H-loop/switch region; other site 342108001819 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 342108001820 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 342108001821 ATP binding site [chemical binding]; other site 342108001822 Mg2+ binding site [ion binding]; other site 342108001823 G-X-G motif; other site 342108001824 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 342108001825 anchoring element; other site 342108001826 dimer interface [polypeptide binding]; other site 342108001827 ATP binding site [chemical binding]; other site 342108001828 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 342108001829 active site 342108001830 putative metal-binding site [ion binding]; other site 342108001831 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 342108001832 Transposase; Region: HTH_Tnp_1; pfam01527 342108001833 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108001834 HTH-like domain; Region: HTH_21; pfam13276 342108001835 Integrase core domain; Region: rve; pfam00665 342108001836 Integrase core domain; Region: rve_3; pfam13683 342108001837 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 342108001838 Transposase; Region: HTH_Tnp_1; pfam01527 342108001839 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 342108001840 Integrase core domain; Region: rve; pfam00665 342108001841 Integrase core domain; Region: rve_3; pfam13683 342108001842 HTH-like domain; Region: HTH_21; pfam13276 342108001843 Integrase core domain; Region: rve; pfam00665 342108001844 Transposase; Region: HTH_Tnp_1; pfam01527 342108001845 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 342108001846 Two component regulator propeller; Region: Reg_prop; pfam07494 342108001847 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 342108001848 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108001849 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 342108001850 dimer interface [polypeptide binding]; other site 342108001851 phosphorylation site [posttranslational modification] 342108001852 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 342108001853 ATP binding site [chemical binding]; other site 342108001854 Mg2+ binding site [ion binding]; other site 342108001855 G-X-G motif; other site 342108001856 Response regulator receiver domain; Region: Response_reg; pfam00072 342108001857 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 342108001858 active site 342108001859 phosphorylation site [posttranslational modification] 342108001860 intermolecular recognition site; other site 342108001861 dimerization interface [polypeptide binding]; other site 342108001862 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 342108001863 putative binding surface; other site 342108001864 active site 342108001865 DNA-binding transcriptional regulator TorR; Provisional; Region: PRK10766 342108001866 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 342108001867 active site 342108001868 phosphorylation site [posttranslational modification] 342108001869 intermolecular recognition site; other site 342108001870 dimerization interface [polypeptide binding]; other site 342108001871 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 342108001872 DNA binding site [nucleotide binding] 342108001873 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 342108001874 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 342108001875 active site 342108001876 phosphorylation site [posttranslational modification] 342108001877 intermolecular recognition site; other site 342108001878 dimerization interface [polypeptide binding]; other site 342108001879 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108001880 Zn2+ binding site [ion binding]; other site 342108001881 Mg2+ binding site [ion binding]; other site 342108001882 integrase; Provisional; Region: PRK09692 342108001883 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 342108001884 active site 342108001885 DNA binding site [nucleotide binding] 342108001886 Int/Topo IB signature motif; other site 342108001887 Helix-turn-helix domain; Region: HTH_17; pfam12728 342108001888 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 342108001889 non-specific DNA binding site [nucleotide binding]; other site 342108001890 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108001891 salt bridge; other site 342108001892 sequence-specific DNA binding site [nucleotide binding]; other site 342108001893 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 342108001894 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 342108001895 non-specific DNA binding site [nucleotide binding]; other site 342108001896 salt bridge; other site 342108001897 sequence-specific DNA binding site [nucleotide binding]; other site 342108001898 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 342108001899 Transcriptional regulator [Transcription]; Region: LysR; COG0583 342108001900 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 342108001901 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 342108001902 putative effector binding pocket; other site 342108001903 dimerization interface [polypeptide binding]; other site 342108001904 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 342108001905 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 342108001906 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108001907 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 342108001908 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 342108001909 dimer interface [polypeptide binding]; other site 342108001910 decamer (pentamer of dimers) interface [polypeptide binding]; other site 342108001911 catalytic triad [active] 342108001912 peroxidatic and resolving cysteines [active] 342108001913 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 342108001914 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 342108001915 putative DNA binding site [nucleotide binding]; other site 342108001916 putative Zn2+ binding site [ion binding]; other site 342108001917 AsnC family; Region: AsnC_trans_reg; pfam01037 342108001918 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 342108001919 PAS fold; Region: PAS_3; pfam08447 342108001920 putative active site [active] 342108001921 heme pocket [chemical binding]; other site 342108001922 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 342108001923 dimer interface [polypeptide binding]; other site 342108001924 phosphorylation site [posttranslational modification] 342108001925 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 342108001926 ATP binding site [chemical binding]; other site 342108001927 Mg2+ binding site [ion binding]; other site 342108001928 G-X-G motif; other site 342108001929 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cl14879 342108001930 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 342108001931 Hemerythrin family; Region: Hemerythrin-like; cl15774 342108001932 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 342108001933 active site 342108001934 catalytic residues [active] 342108001935 metal binding site [ion binding]; metal-binding site 342108001936 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 342108001937 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 342108001938 ATP-grasp domain; Region: ATP-grasp_4; cl17255 342108001939 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 342108001940 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 342108001941 carboxyltransferase (CT) interaction site; other site 342108001942 biotinylation site [posttranslational modification]; other site 342108001943 enoyl-CoA hydratase; Provisional; Region: PRK05995 342108001944 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 342108001945 substrate binding site [chemical binding]; other site 342108001946 oxyanion hole (OAH) forming residues; other site 342108001947 trimer interface [polypeptide binding]; other site 342108001948 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 342108001949 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 342108001950 isovaleryl-CoA dehydrogenase; Region: PLN02519 342108001951 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 342108001952 substrate binding site [chemical binding]; other site 342108001953 FAD binding site [chemical binding]; other site 342108001954 catalytic base [active] 342108001955 Membrane transport protein; Region: Mem_trans; cl09117 342108001956 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108001957 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 342108001958 ligand binding site [chemical binding]; other site 342108001959 flexible hinge region; other site 342108001960 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 342108001961 active site 342108001962 nucleophile elbow; other site 342108001963 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 342108001964 DNA protecting protein DprA; Region: dprA; TIGR00732 342108001965 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 342108001966 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 342108001967 active site 342108001968 interdomain interaction site; other site 342108001969 putative metal-binding site [ion binding]; other site 342108001970 nucleotide binding site [chemical binding]; other site 342108001971 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 342108001972 domain I; other site 342108001973 DNA binding groove [nucleotide binding] 342108001974 phosphate binding site [ion binding]; other site 342108001975 domain II; other site 342108001976 domain III; other site 342108001977 nucleotide binding site [chemical binding]; other site 342108001978 catalytic site [active] 342108001979 domain IV; other site 342108001980 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 342108001981 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 342108001982 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 342108001983 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 342108001984 Flagellin and related hook-associated proteins [Cell motility and secretion]; Region: FlgL; COG1344 342108001985 Protein of unknown function DUF115; Region: MAF_flag10; pfam01973 342108001986 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 342108001987 TPR motif; other site 342108001988 binding surface 342108001989 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 342108001990 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 342108001991 Flagellar protein FlaF; Region: FlaF; pfam07309 342108001992 Flagellar protein FlaF; Region: FlaF; pfam07309 342108001993 TPR repeat; Region: TPR_11; pfam13414 342108001994 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 342108001995 binding surface 342108001996 TPR motif; other site 342108001997 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 342108001998 binding surface 342108001999 TPR motif; other site 342108002000 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 342108002001 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 342108002002 S-adenosylmethionine binding site [chemical binding]; other site 342108002003 hypothetical protein; Provisional; Region: PRK08912 342108002004 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 342108002005 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108002006 homodimer interface [polypeptide binding]; other site 342108002007 catalytic residue [active] 342108002008 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 342108002009 Nitrogen regulatory protein P-II; Region: P-II; smart00938 342108002010 glutamine synthetase; Provisional; Region: glnA; PRK09469 342108002011 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 342108002012 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 342108002013 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 342108002014 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 342108002015 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 342108002016 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 342108002017 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 342108002018 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 342108002019 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 342108002020 DNA binding residues [nucleotide binding] 342108002021 DNA primase, catalytic core; Region: dnaG; TIGR01391 342108002022 CHC2 zinc finger; Region: zf-CHC2; cl17510 342108002023 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 342108002024 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 342108002025 active site 342108002026 metal binding site [ion binding]; metal-binding site 342108002027 interdomain interaction site; other site 342108002028 Yqey-like protein; Region: YqeY; pfam09424 342108002029 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 342108002030 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 342108002031 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 342108002032 catalytic site [active] 342108002033 subunit interface [polypeptide binding]; other site 342108002034 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 342108002035 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 342108002036 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 342108002037 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 342108002038 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 342108002039 ATP-grasp domain; Region: ATP-grasp_4; cl17255 342108002040 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 342108002041 IMP binding site; other site 342108002042 dimer interface [polypeptide binding]; other site 342108002043 partial ornithine binding site; other site 342108002044 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 342108002045 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 342108002046 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 342108002047 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 342108002048 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 342108002049 Cache domain; Region: Cache_1; pfam02743 342108002050 Bacteriophage lysis protein; Region: Phage_lysis; pfam03245 342108002051 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 342108002052 ATP binding site [chemical binding]; other site 342108002053 G-X-G motif; other site 342108002054 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108002055 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 342108002056 TPR motif; other site 342108002057 binding surface 342108002058 TPR repeat; Region: TPR_11; pfam13414 342108002059 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 342108002060 binding surface 342108002061 TPR motif; other site 342108002062 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 342108002063 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 342108002064 binding surface 342108002065 TPR motif; other site 342108002066 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 342108002067 TPR repeat; Region: TPR_11; pfam13414 342108002068 binding surface 342108002069 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 342108002070 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 342108002071 CoA-transferase family III; Region: CoA_transf_3; pfam02515 342108002072 enoyl-CoA hydratase; Provisional; Region: PRK05995 342108002073 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 342108002074 substrate binding site [chemical binding]; other site 342108002075 oxyanion hole (OAH) forming residues; other site 342108002076 trimer interface [polypeptide binding]; other site 342108002077 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 342108002078 elongation factor G; Reviewed; Region: PRK12740 342108002079 G1 box; other site 342108002080 putative GEF interaction site [polypeptide binding]; other site 342108002081 GTP/Mg2+ binding site [chemical binding]; other site 342108002082 Switch I region; other site 342108002083 G2 box; other site 342108002084 G3 box; other site 342108002085 Switch II region; other site 342108002086 G4 box; other site 342108002087 G5 box; other site 342108002088 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 342108002089 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 342108002090 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 342108002091 pseudaminic acid synthase; Region: PseI; TIGR03586 342108002092 NeuB family; Region: NeuB; pfam03102 342108002093 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 342108002094 NeuB binding interface [polypeptide binding]; other site 342108002095 putative substrate binding site [chemical binding]; other site 342108002096 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 342108002097 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 342108002098 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 342108002099 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 342108002100 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 342108002101 NAD(P) binding site [chemical binding]; other site 342108002102 homodimer interface [polypeptide binding]; other site 342108002103 substrate binding site [chemical binding]; other site 342108002104 active site 342108002105 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 342108002106 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 342108002107 inhibitor-cofactor binding pocket; inhibition site 342108002108 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108002109 catalytic residue [active] 342108002110 SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat; Region: GT2_SpsF; cd02518 342108002111 ligand binding site; other site 342108002112 Predicted esterase [General function prediction only]; Region: COG0400 342108002113 malic enzyme; Reviewed; Region: PRK12862 342108002114 Malic enzyme, N-terminal domain; Region: malic; pfam00390 342108002115 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 342108002116 putative NAD(P) binding site [chemical binding]; other site 342108002117 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 342108002118 lipoate-protein ligase B; Provisional; Region: PRK14341 342108002119 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 342108002120 CoA-transferase family III; Region: CoA_transf_3; pfam02515 342108002121 Hemerythrin; Region: Hemerythrin; cd12107 342108002122 Fe binding site [ion binding]; other site 342108002123 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 342108002124 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 342108002125 active site 342108002126 phosphorylation site [posttranslational modification] 342108002127 intermolecular recognition site; other site 342108002128 dimerization interface [polypeptide binding]; other site 342108002129 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 342108002130 Part of AAA domain; Region: AAA_19; pfam13245 342108002131 Family description; Region: UvrD_C_2; pfam13538 342108002132 Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]; Region: PrmA; COG2264 342108002133 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 342108002134 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 342108002135 dimerization interface [polypeptide binding]; other site 342108002136 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108002137 putative CheW interface [polypeptide binding]; other site 342108002138 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 342108002139 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108002140 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108002141 metal binding site [ion binding]; metal-binding site 342108002142 active site 342108002143 I-site; other site 342108002144 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 342108002145 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 342108002146 putative deacylase active site [active] 342108002147 GMP synthase; Reviewed; Region: guaA; PRK00074 342108002148 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 342108002149 AMP/PPi binding site [chemical binding]; other site 342108002150 candidate oxyanion hole; other site 342108002151 catalytic triad [active] 342108002152 potential glutamine specificity residues [chemical binding]; other site 342108002153 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 342108002154 ATP Binding subdomain [chemical binding]; other site 342108002155 Ligand Binding sites [chemical binding]; other site 342108002156 Dimerization subdomain; other site 342108002157 GDSL-like Lipase/Acylhydrolase family; Region: Lipase_GDSL_2; pfam13472 342108002158 Hemerythrin; Region: Hemerythrin; cd12107 342108002159 Fe binding site [ion binding]; other site 342108002160 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 342108002161 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 342108002162 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 342108002163 active site 342108002164 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]; Region: UbiA; cl00337 342108002165 UbiA prenyltransferase family; Region: UbiA; pfam01040 342108002166 Protein of unknown function (DUF420); Region: DUF420; pfam04238 342108002167 Putative anion permease YbiR. Based on sequence similarity, YbiR proteins are predicted to function as anion translocating permeases in eubacteria, archaea and plants. They belong to ArsB/NhaD superfamily of permeases that have been shown to translocate...; Region: YbiR_permease; cd01117 342108002168 transmembrane helices; other site 342108002169 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 342108002170 short chain dehydrogenase; Provisional; Region: PRK07024 342108002171 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108002172 NAD(P) binding site [chemical binding]; other site 342108002173 active site 342108002174 Protein of unknown function DUF86; Region: DUF86; cl01031 342108002175 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 342108002176 active site 342108002177 NTP binding site [chemical binding]; other site 342108002178 metal binding triad [ion binding]; metal-binding site 342108002179 antibiotic binding site [chemical binding]; other site 342108002180 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 342108002181 hypothetical protein; Provisional; Region: PRK11820 342108002182 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 342108002183 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 342108002184 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 342108002185 catalytic site [active] 342108002186 G-X2-G-X-G-K; other site 342108002187 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 342108002188 putative substrate translocation pore; other site 342108002189 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108002190 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 342108002191 Cytochrome C' Region: Cytochrom_C_2; pfam01322 342108002192 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 342108002193 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 342108002194 NAD(P) binding site [chemical binding]; other site 342108002195 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 342108002196 nudix motif; other site 342108002197 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108002198 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 342108002199 binding surface 342108002200 TPR motif; other site 342108002201 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 342108002202 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 342108002203 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108002204 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108002205 metal binding site [ion binding]; metal-binding site 342108002206 active site 342108002207 I-site; other site 342108002208 Response regulator receiver domain; Region: Response_reg; pfam00072 342108002209 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 342108002210 active site 342108002211 phosphorylation site [posttranslational modification] 342108002212 intermolecular recognition site; other site 342108002213 dimerization interface [polypeptide binding]; other site 342108002214 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 342108002215 RNA/DNA hybrid binding site [nucleotide binding]; other site 342108002216 active site 342108002217 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 342108002218 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 342108002219 putative active site [active] 342108002220 putative substrate binding site [chemical binding]; other site 342108002221 ATP binding site [chemical binding]; other site 342108002222 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 342108002223 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 342108002224 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 342108002225 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 342108002226 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 342108002227 lipoyl attachment site [posttranslational modification]; other site 342108002228 glycine dehydrogenase subunit 1; Validated; Region: PRK00451 342108002229 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 342108002230 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108002231 catalytic residue [active] 342108002232 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 342108002233 tetramer interface [polypeptide binding]; other site 342108002234 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108002235 catalytic residue [active] 342108002236 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 342108002237 putative active site [active] 342108002238 heme pocket [chemical binding]; other site 342108002239 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 342108002240 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]; Region: UbiA; cl00337 342108002241 UbiA prenyltransferase family; Region: UbiA; pfam01040 342108002242 Predicted methyltransferase [General function prediction only]; Region: COG3897 342108002243 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 342108002244 S-adenosylmethionine binding site [chemical binding]; other site 342108002245 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 342108002246 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 342108002247 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 342108002248 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108002249 Q-loop/lid; other site 342108002250 ABC transporter signature motif; other site 342108002251 Walker B; other site 342108002252 D-loop; other site 342108002253 H-loop/switch region; other site 342108002254 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; cl00290 342108002255 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 342108002256 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 342108002257 active site 342108002258 metal binding site [ion binding]; metal-binding site 342108002259 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 342108002260 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 342108002261 putative ribose interaction site [chemical binding]; other site 342108002262 putative ADP binding site [chemical binding]; other site 342108002263 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 342108002264 active site 342108002265 nucleotide binding site [chemical binding]; other site 342108002266 HIGH motif; other site 342108002267 KMSKS motif; other site 342108002268 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 342108002269 epoxyqueuosine reductase; Region: TIGR00276 342108002270 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 342108002271 4Fe-4S binding domain; Region: Fer4; pfam00037 342108002272 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108002273 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 342108002274 non-specific DNA binding site [nucleotide binding]; other site 342108002275 salt bridge; other site 342108002276 sequence-specific DNA binding site [nucleotide binding]; other site 342108002277 Pyridoxamine 5'-phosphate oxidase; Region: Pyrid_oxidase_2; pfam13883 342108002278 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_GTP; cd00819 342108002279 active site 342108002280 substrate-binding site [chemical binding]; other site 342108002281 metal-binding site [ion binding] 342108002282 GTP binding site [chemical binding]; other site 342108002283 putative glutathione S-transferase; Provisional; Region: PRK10357 342108002284 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 342108002285 putative C-terminal domain interface [polypeptide binding]; other site 342108002286 putative GSH binding site (G-site) [chemical binding]; other site 342108002287 putative dimer interface [polypeptide binding]; other site 342108002288 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 342108002289 N-terminal domain interface [polypeptide binding]; other site 342108002290 dimer interface [polypeptide binding]; other site 342108002291 Cupin superfamily (DUF985); Region: Cupin_5; pfam06172 342108002292 Cupredoxin-like domain; Region: Cupredoxin_1; cl17234 342108002293 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 342108002294 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 342108002295 motif II; other site 342108002296 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 342108002297 B12 binding site [chemical binding]; other site 342108002298 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 342108002299 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 342108002300 FeS/SAM binding site; other site 342108002301 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvB; COG0028 342108002302 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 342108002303 PYR/PP interface [polypeptide binding]; other site 342108002304 dimer interface [polypeptide binding]; other site 342108002305 TPP binding site [chemical binding]; other site 342108002306 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 342108002307 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; cd00568 342108002308 TPP-binding site [chemical binding]; other site 342108002309 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 342108002310 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 342108002311 inhibitor-cofactor binding pocket; inhibition site 342108002312 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108002313 catalytic residue [active] 342108002314 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 342108002315 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 342108002316 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108002317 homodimer interface [polypeptide binding]; other site 342108002318 catalytic residue [active] 342108002319 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108002320 Methyltransferase domain; Region: Methyltransf_12; pfam08242 342108002321 S-adenosylmethionine binding site [chemical binding]; other site 342108002322 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4627 342108002323 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108002324 extended (e) SDRs; Region: SDR_e; cd08946 342108002325 NAD(P) binding site [chemical binding]; other site 342108002326 active site 342108002327 substrate binding site [chemical binding]; other site 342108002328 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108002329 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 342108002330 WcbM_like is a subfamily of nucleotidyl transferases; Region: NTP_transferase_WcbM_like; cd06915 342108002331 Substrate binding site; other site 342108002332 Mg++ binding site; other site 342108002333 metal-binding site 342108002334 Mg++ binding site; other site 342108002335 metal-binding site 342108002336 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 342108002337 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 342108002338 NADP binding site [chemical binding]; other site 342108002339 active site 342108002340 putative substrate binding site [chemical binding]; other site 342108002341 Transmembrane secretion effector; Region: MFS_3; pfam05977 342108002342 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 342108002343 2-oxo-hepta-3-ene-1,7-dioic acid hydratase; Region: HpaH; TIGR02312 342108002344 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 342108002345 putative substrate binding pocket [chemical binding]; other site 342108002346 trimer interface [polypeptide binding]; other site 342108002347 The Class III extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase, catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate; Region: HPCD; cd07370 342108002348 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 342108002349 putative active site [active] 342108002350 putative metal binding site [ion binding]; other site 342108002351 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase; Region: HpaE; TIGR02299 342108002352 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 342108002353 NAD binding site [chemical binding]; other site 342108002354 catalytic residues [active] 342108002355 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; Region: HpaG-C-term; TIGR02303 342108002356 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 342108002357 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; Region: HpaG-C-term; TIGR02303 342108002358 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 342108002359 DctM-like transporters; Region: DctM; pfam06808 342108002360 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 342108002361 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 342108002362 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 342108002363 MarR family; Region: MarR_2; cl17246 342108002364 Transcriptional regulators [Transcription]; Region: MarR; COG1846 342108002365 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 342108002366 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 342108002367 inhibitor-cofactor binding pocket; inhibition site 342108002368 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108002369 catalytic residue [active] 342108002370 Domain of unknown function (DUF336); Region: DUF336; pfam03928 342108002371 succinic semialdehyde dehydrogenase; Region: PLN02278 342108002372 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 342108002373 tetramerization interface [polypeptide binding]; other site 342108002374 NAD(P) binding site [chemical binding]; other site 342108002375 catalytic residues [active] 342108002376 MarR family; Region: MarR_2; cl17246 342108002377 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 342108002378 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 342108002379 CoA-transferase family III; Region: CoA_transf_3; pfam02515 342108002380 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 342108002381 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 342108002382 Uncharacterized conserved protein [Function unknown]; Region: COG2308 342108002383 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 342108002384 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 342108002385 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 342108002386 Putative amidoligase enzyme (DUF2126); Region: DUF2126; pfam09899 342108002387 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4196 342108002388 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 342108002389 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 342108002390 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 342108002391 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 342108002392 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 342108002393 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 342108002394 Cache domain; Region: Cache_1; pfam02743 342108002395 PAS domain S-box; Region: sensory_box; TIGR00229 342108002396 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 342108002397 putative active site [active] 342108002398 heme pocket [chemical binding]; other site 342108002399 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108002400 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 342108002401 dimer interface [polypeptide binding]; other site 342108002402 phosphorylation site [posttranslational modification] 342108002403 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 342108002404 ATP binding site [chemical binding]; other site 342108002405 Mg2+ binding site [ion binding]; other site 342108002406 G-X-G motif; other site 342108002407 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 342108002408 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 342108002409 heme binding site [chemical binding]; other site 342108002410 ferroxidase pore; other site 342108002411 ferroxidase diiron center [ion binding]; other site 342108002412 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 342108002413 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 342108002414 heme binding site [chemical binding]; other site 342108002415 ferroxidase pore; other site 342108002416 ferroxidase diiron center [ion binding]; other site 342108002417 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 342108002418 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 342108002419 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 342108002420 dimerization interface [polypeptide binding]; other site 342108002421 substrate binding pocket [chemical binding]; other site 342108002422 EamA-like transporter family; Region: EamA; pfam00892 342108002423 EamA-like transporter family; Region: EamA; pfam00892 342108002424 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 342108002425 active site 342108002426 (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 342108002427 dimer interaction site [polypeptide binding]; other site 342108002428 substrate-binding tunnel; other site 342108002429 active site 342108002430 catalytic site [active] 342108002431 substrate binding site [chemical binding]; other site 342108002432 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 342108002433 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 342108002434 active site 342108002435 Riboflavin kinase; Region: Flavokinase; smart00904 342108002436 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 342108002437 active site 342108002438 HIGH motif; other site 342108002439 nucleotide binding site [chemical binding]; other site 342108002440 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 342108002441 active site 342108002442 KMSKS motif; other site 342108002443 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 342108002444 tRNA binding surface [nucleotide binding]; other site 342108002445 anticodon binding site; other site 342108002446 Anticodon-binding domain of tRNA; Region: Anticodon_1; pfam08264 342108002447 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 342108002448 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 342108002449 lipoprotein signal peptidase; Provisional; Region: PRK14787 342108002450 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 342108002451 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 342108002452 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 342108002453 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 342108002454 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 342108002455 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 342108002456 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 342108002457 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 342108002458 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 342108002459 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 342108002460 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 342108002461 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 342108002462 putative acyltransferase; Provisional; Region: PRK05790 342108002463 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 342108002464 dimer interface [polypeptide binding]; other site 342108002465 active site 342108002466 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 342108002467 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 342108002468 NAD(P) binding site [chemical binding]; other site 342108002469 homotetramer interface [polypeptide binding]; other site 342108002470 homodimer interface [polypeptide binding]; other site 342108002471 active site 342108002472 Response regulator receiver domain; Region: Response_reg; pfam00072 342108002473 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 342108002474 active site 342108002475 phosphorylation site [posttranslational modification] 342108002476 intermolecular recognition site; other site 342108002477 dimerization interface [polypeptide binding]; other site 342108002478 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 342108002479 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108002480 Zn2+ binding site [ion binding]; other site 342108002481 Mg2+ binding site [ion binding]; other site 342108002482 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 342108002483 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 342108002484 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 342108002485 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108002486 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 342108002487 putative active site [active] 342108002488 heme pocket [chemical binding]; other site 342108002489 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 342108002490 dimer interface [polypeptide binding]; other site 342108002491 phosphorylation site [posttranslational modification] 342108002492 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 342108002493 ATP binding site [chemical binding]; other site 342108002494 Mg2+ binding site [ion binding]; other site 342108002495 G-X-G motif; other site 342108002496 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108002497 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 342108002498 active site 342108002499 phosphorylation site [posttranslational modification] 342108002500 intermolecular recognition site; other site 342108002501 dimerization interface [polypeptide binding]; other site 342108002502 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 342108002503 DNA binding site [nucleotide binding] 342108002504 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 342108002505 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 342108002506 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 342108002507 selenium-dependent molybdenum hydroxylase system protein, YqeB family; Region: matur_yqeB; TIGR03309 342108002508 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 342108002509 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 342108002510 CoenzymeA binding site [chemical binding]; other site 342108002511 subunit interaction site [polypeptide binding]; other site 342108002512 PHB binding site; other site 342108002513 enoyl-CoA hydratase; Validated; Region: PRK08139 342108002514 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 342108002515 substrate binding site [chemical binding]; other site 342108002516 oxyanion hole (OAH) forming residues; other site 342108002517 trimer interface [polypeptide binding]; other site 342108002518 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 342108002519 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 342108002520 anti sigma factor interaction site; other site 342108002521 regulatory phosphorylation site [posttranslational modification]; other site 342108002522 Nitrate and nitrite sensing; Region: NIT; pfam08376 342108002523 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 342108002524 HAMP domain; Region: HAMP; pfam00672 342108002525 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108002526 dimer interface [polypeptide binding]; other site 342108002527 putative CheW interface [polypeptide binding]; other site 342108002528 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 342108002529 sulfur oxidation protein SoxY; Provisional; Region: PRK07474 342108002530 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 342108002531 Predicted transporter component [General function prediction only]; Region: COG2391 342108002532 Sulphur transport; Region: Sulf_transp; pfam04143 342108002533 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 342108002534 CPxP motif; other site 342108002535 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 342108002536 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 342108002537 amidase catalytic site [active] 342108002538 Zn binding residues [ion binding]; other site 342108002539 substrate binding site [chemical binding]; other site 342108002540 EamA-like transporter family; Region: EamA; pfam00892 342108002541 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 342108002542 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 342108002543 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 342108002544 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; cl00391 342108002545 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 342108002546 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 342108002547 potassium uptake protein; Region: kup; TIGR00794 342108002548 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 342108002549 NAD-dependent deacetylase; Provisional; Region: PRK00481 342108002550 NAD+ binding site [chemical binding]; other site 342108002551 substrate binding site [chemical binding]; other site 342108002552 Zn binding site [ion binding]; other site 342108002553 Aspartyl/Asparaginyl beta-hydroxylase; Region: Asp_Arg_Hydrox; cl17820 342108002554 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 342108002555 Low molecular weight phosphatase family; Region: LMWPc; cd00115 342108002556 active site 342108002557 Hemerythrin; Region: Hemerythrin; cd12107 342108002558 Fe binding site [ion binding]; other site 342108002559 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 342108002560 FOG: CBS domain [General function prediction only]; Region: COG0517 342108002561 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 342108002562 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 342108002563 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 342108002564 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 342108002565 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 342108002566 ABC transporter; Region: ABC_tran_2; pfam12848 342108002567 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 342108002568 ribonuclease R; Region: RNase_R; TIGR02063 342108002569 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 342108002570 RNB domain; Region: RNB; pfam00773 342108002571 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 342108002572 RNA binding site [nucleotide binding]; other site 342108002573 phosphonate metabolim protein, transferase hexapeptide repeat family; Region: phn_thr-fam; TIGR03308 342108002574 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 342108002575 trimer interface [polypeptide binding]; other site 342108002576 active site 342108002577 substrate binding site [chemical binding]; other site 342108002578 CoA binding site [chemical binding]; other site 342108002579 Uncharacterized conserved protein [Function unknown]; Region: COG3777 342108002580 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 342108002581 active site 2 [active] 342108002582 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 342108002583 active site 2 [active] 342108002584 active site 1 [active] 342108002585 short chain dehydrogenase; Provisional; Region: PRK06500 342108002586 classical (c) SDRs; Region: SDR_c; cd05233 342108002587 NAD(P) binding site [chemical binding]; other site 342108002588 active site 342108002589 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 342108002590 Ethylbenzene dehydrogenase; Region: EB_dh; smart00887 342108002591 Domon-like ligand-binding domains; Region: DOMON_like; cd00241 342108002592 Cytochrome c; Region: Cytochrom_C; pfam00034 342108002593 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 342108002594 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 342108002595 Cation efflux family; Region: Cation_efflux; cl00316 342108002596 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 342108002597 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 342108002598 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 342108002599 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 342108002600 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 342108002601 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 342108002602 HSP70 interaction site [polypeptide binding]; other site 342108002603 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 342108002604 substrate binding site [polypeptide binding]; other site 342108002605 dimer interface [polypeptide binding]; other site 342108002606 Protein of unknown function, DUF399; Region: DUF399; pfam04187 342108002607 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 342108002608 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 342108002609 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 342108002610 DctM-like transporters; Region: DctM; pfam06808 342108002611 Domain of unknown function (DUF1850); Region: DUF1850; pfam08905 342108002612 DctM-like transporters; Region: DctM; pfam06808 342108002613 TRAP transporter, DctM subunit; Region: dctM; TIGR00786 342108002614 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 342108002615 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 342108002616 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 342108002617 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 342108002618 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 342108002619 putative active site [active] 342108002620 heme pocket [chemical binding]; other site 342108002621 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 342108002622 dimer interface [polypeptide binding]; other site 342108002623 phosphorylation site [posttranslational modification] 342108002624 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 342108002625 ATP binding site [chemical binding]; other site 342108002626 Mg2+ binding site [ion binding]; other site 342108002627 G-X-G motif; other site 342108002628 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 342108002629 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 342108002630 active site 342108002631 phosphorylation site [posttranslational modification] 342108002632 intermolecular recognition site; other site 342108002633 dimerization interface [polypeptide binding]; other site 342108002634 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 342108002635 DNA binding residues [nucleotide binding] 342108002636 dimerization interface [polypeptide binding]; other site 342108002637 response regulator FixJ; Provisional; Region: fixJ; PRK09390 342108002638 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 342108002639 active site 342108002640 phosphorylation site [posttranslational modification] 342108002641 intermolecular recognition site; other site 342108002642 dimerization interface [polypeptide binding]; other site 342108002643 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 342108002644 DNA binding residues [nucleotide binding] 342108002645 dimerization interface [polypeptide binding]; other site 342108002646 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 342108002647 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 342108002648 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that...; Region: proteasome_beta_bacterial; cd03765 342108002649 putative peptidase; Provisional; Region: PRK11649 342108002650 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cl00107 342108002651 Peptidase family M23; Region: Peptidase_M23; pfam01551 342108002652 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 342108002653 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 342108002654 active site 342108002655 DNA binding site [nucleotide binding] 342108002656 Int/Topo IB signature motif; other site 342108002657 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 342108002658 ATP binding site [chemical binding]; other site 342108002659 putative Mg++ binding site [ion binding]; other site 342108002660 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 342108002661 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 342108002662 nucleotide binding region [chemical binding]; other site 342108002663 ATP-binding site [chemical binding]; other site 342108002664 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 342108002665 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 342108002666 metal ion-dependent adhesion site (MIDAS); other site 342108002667 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 342108002668 ATP binding site [chemical binding]; other site 342108002669 Mg2+ binding site [ion binding]; other site 342108002670 G-X-G motif; other site 342108002671 Transposase, Mutator family; Region: Transposase_mut; pfam00872 342108002672 Transposase; Region: HTH_Tnp_1; pfam01527 342108002673 Transposase; Region: HTH_Tnp_1; pfam01527 342108002674 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 342108002675 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 342108002676 Response regulator receiver domain; Region: Response_reg; pfam00072 342108002677 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 342108002678 active site 342108002679 phosphorylation site [posttranslational modification] 342108002680 intermolecular recognition site; other site 342108002681 dimerization interface [polypeptide binding]; other site 342108002682 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 342108002683 ATP cone domain; Region: ATP-cone; pfam03477 342108002684 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 342108002685 IHF - DNA interface [nucleotide binding]; other site 342108002686 IHF dimer interface [polypeptide binding]; other site 342108002687 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 342108002688 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 342108002689 Integrase core domain; Region: rve; pfam00665 342108002690 Integrase core domain; Region: rve_3; pfam13683 342108002691 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 342108002692 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 342108002693 Int/Topo IB signature motif; other site 342108002694 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 342108002695 Putative transposase; Region: Y2_Tnp; pfam04986 342108002696 rod shape-determining protein MreC; Provisional; Region: PRK13922 342108002697 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 342108002698 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 342108002699 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 342108002700 Hemerythrin; Region: Hemerythrin; cd12107 342108002701 Fe binding site [ion binding]; other site 342108002702 High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism]; Region: FTR1; COG0672 342108002703 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 342108002704 4Fe-4S binding domain; Region: Fer4_5; pfam12801 342108002705 Fe2+ transport protein; Region: Iron_transport; pfam10634 342108002706 Fe2+ transport protein; Region: Iron_transport; pfam10634 342108002707 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 342108002708 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 342108002709 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108002710 TPR repeat; Region: TPR_11; pfam13414 342108002711 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 342108002712 Response regulator receiver domain; Region: Response_reg; pfam00072 342108002713 active site 342108002714 phosphorylation site [posttranslational modification] 342108002715 intermolecular recognition site; other site 342108002716 dimerization interface [polypeptide binding]; other site 342108002717 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 342108002718 Transposase; Region: DEDD_Tnp_IS110; pfam01548 342108002719 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 342108002720 HemY protein N-terminus; Region: HemY_N; pfam07219 342108002721 Protein of unknown function (DUF445); Region: DUF445; pfam04286 342108002722 Primosomal protein DnaI N-terminus; Region: DnaI_N; pfam07319 342108002723 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108002724 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 342108002725 putative substrate translocation pore; other site 342108002726 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 342108002727 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 342108002728 protein binding site [polypeptide binding]; other site 342108002729 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 342108002730 protein binding site [polypeptide binding]; other site 342108002731 Actin-like ATPase involved in cell morphogenesis [Cell division and chromosome partitioning]; Region: MreB; COG1077 342108002732 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 342108002733 nucleotide binding site [chemical binding]; other site 342108002734 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 342108002735 Cation efflux family; Region: Cation_efflux; pfam01545 342108002736 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 342108002737 Permease P (pink-eyed dilution). Mutations in the human melanosomal P gene were responsible for classic phenotype of oculocutaneous albinism type 2 (OCA2). Although the precise function of the P protein is unknown, it was predicted to regulate the...; Region: P_permease; cd01116 342108002738 transmembrane helices; other site 342108002739 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 342108002740 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 342108002741 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 342108002742 protein binding site [polypeptide binding]; other site 342108002743 TPR repeat; Region: TPR_11; pfam13414 342108002744 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 342108002745 TPR motif; other site 342108002746 binding surface 342108002747 TPR repeat; Region: TPR_11; pfam13414 342108002748 LemA family; Region: LemA; cl00742 342108002749 Helix-turn-helix domain; Region: HTH_17; pfam12728 342108002750 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 342108002751 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 342108002752 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 342108002753 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 342108002754 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 342108002755 Cation efflux family; Region: Cation_efflux; pfam01545 342108002756 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 342108002757 salt bridge; other site 342108002758 non-specific DNA binding site [nucleotide binding]; other site 342108002759 sequence-specific DNA binding site [nucleotide binding]; other site 342108002760 Hemerythrin; Region: Hemerythrin; cd12107 342108002761 Fe binding site [ion binding]; other site 342108002762 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 342108002763 IHF - DNA interface [nucleotide binding]; other site 342108002764 IHF dimer interface [polypeptide binding]; other site 342108002765 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 342108002766 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108002767 dimer interface [polypeptide binding]; other site 342108002768 putative CheW interface [polypeptide binding]; other site 342108002769 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 342108002770 PAS domain; Region: PAS_9; pfam13426 342108002771 putative active site [active] 342108002772 heme pocket [chemical binding]; other site 342108002773 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 342108002774 phosphorylation site [posttranslational modification] 342108002775 intermolecular recognition site; other site 342108002776 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 342108002777 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 342108002778 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 342108002779 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 342108002780 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 342108002781 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 342108002782 protein binding site [polypeptide binding]; other site 342108002783 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 342108002784 LemA family; Region: LemA; cl00742 342108002785 Helix-turn-helix domain; Region: HTH_17; pfam12728 342108002786 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 342108002787 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 342108002788 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 342108002789 metal binding site 2 [ion binding]; metal-binding site 342108002790 putative DNA binding helix; other site 342108002791 metal binding site 1 [ion binding]; metal-binding site 342108002792 dimer interface [polypeptide binding]; other site 342108002793 structural Zn2+ binding site [ion binding]; other site 342108002794 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 342108002795 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 342108002796 Soluble P-type ATPase [General function prediction only]; Region: COG4087 342108002797 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 342108002798 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 342108002799 Uncharacterized conserved protein [Function unknown]; Region: COG1742 342108002800 cell division protein FtsZ; Validated; Region: PRK09330 342108002801 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 342108002802 nucleotide binding site [chemical binding]; other site 342108002803 SulA interaction site; other site 342108002804 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108002805 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 342108002806 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108002807 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 342108002808 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 342108002809 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 342108002810 active site 342108002811 ATP binding site [chemical binding]; other site 342108002812 substrate binding site [chemical binding]; other site 342108002813 activation loop (A-loop); other site 342108002814 Carbohydrate-selective porin, OprB family; Region: OprB; cl17816 342108002815 FeoA domain; Region: FeoA; pfam04023 342108002816 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 342108002817 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 342108002818 G1 box; other site 342108002819 GTP/Mg2+ binding site [chemical binding]; other site 342108002820 Switch I region; other site 342108002821 G2 box; other site 342108002822 G3 box; other site 342108002823 Switch II region; other site 342108002824 G4 box; other site 342108002825 G5 box; other site 342108002826 Nucleoside recognition; Region: Gate; pfam07670 342108002827 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 342108002828 Nucleoside recognition; Region: Gate; pfam07670 342108002829 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 342108002830 active site 342108002831 ATP binding site [chemical binding]; other site 342108002832 substrate binding site [chemical binding]; other site 342108002833 activation loop (A-loop); other site 342108002834 Short C-terminal domain; Region: SHOCT; pfam09851 342108002835 HEAT repeats; Region: HEAT_2; pfam13646 342108002836 HEAT repeats; Region: HEAT_2; pfam13646 342108002837 HTH-like domain; Region: HTH_21; pfam13276 342108002838 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 342108002839 Integrase core domain; Region: rve; pfam00665 342108002840 Integrase core domain; Region: rve_3; pfam13683 342108002841 rod shape-determining protein MreC; Provisional; Region: PRK13922 342108002842 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 342108002843 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 342108002844 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 342108002845 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 342108002846 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 342108002847 Walker A motif; other site 342108002848 ATP binding site [chemical binding]; other site 342108002849 Walker B motif; other site 342108002850 arginine finger; other site 342108002851 Peptidase family M41; Region: Peptidase_M41; pfam01434 342108002852 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 342108002853 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108002854 Transposase; Region: HTH_Tnp_1; pfam01527 342108002855 insertion element IS2 transposase InsD; Provisional; Region: PRK14702 342108002856 HTH-like domain; Region: HTH_21; pfam13276 342108002857 Integrase core domain; Region: rve; pfam00665 342108002858 Integrase core domain; Region: rve_3; pfam13683 342108002859 Response regulator receiver domain; Region: Response_reg; pfam00072 342108002860 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 342108002861 active site 342108002862 phosphorylation site [posttranslational modification] 342108002863 intermolecular recognition site; other site 342108002864 dimerization interface [polypeptide binding]; other site 342108002865 DNA-binding HTH domain-containing proteins [Transcription]; Region: CsgD; COG2771 342108002866 CHASE domain; Region: CHASE; pfam03924 342108002867 PAS fold; Region: PAS_3; pfam08447 342108002868 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 342108002869 ATP binding site [chemical binding]; other site 342108002870 Mg2+ binding site [ion binding]; other site 342108002871 G-X-G motif; other site 342108002872 Response regulator receiver domain; Region: Response_reg; pfam00072 342108002873 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 342108002874 active site 342108002875 phosphorylation site [posttranslational modification] 342108002876 intermolecular recognition site; other site 342108002877 dimerization interface [polypeptide binding]; other site 342108002878 HDOD domain; Region: HDOD; pfam08668 342108002879 HTH-like domain; Region: HTH_21; pfam13276 342108002880 Integrase core domain; Region: rve; pfam00665 342108002881 Integrase core domain; Region: rve_3; pfam13683 342108002882 Transposase; Region: HTH_Tnp_1; pfam01527 342108002883 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108002884 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 342108002885 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 342108002886 active site 342108002887 phosphorylation site [posttranslational modification] 342108002888 intermolecular recognition site; other site 342108002889 dimerization interface [polypeptide binding]; other site 342108002890 HD domain; Region: HD_5; pfam13487 342108002891 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 342108002892 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 342108002893 dimerization interface [polypeptide binding]; other site 342108002894 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 342108002895 PAS domain; Region: PAS_9; pfam13426 342108002896 putative active site [active] 342108002897 heme pocket [chemical binding]; other site 342108002898 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 342108002899 ATP binding site [chemical binding]; other site 342108002900 Mg2+ binding site [ion binding]; other site 342108002901 G-X-G motif; other site 342108002902 Helix-turn-helix domain; Region: HTH_36; pfam13730 342108002903 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 342108002904 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 342108002905 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108002906 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream. The vitamin B6 complex comprises pyridoxine, pyridoxal, and pyridoxamine, as well...; Region: CBS_pair_PALP_assoc2; cd04609 342108002907 FOG: CBS domain [General function prediction only]; Region: COG0517 342108002908 Rrf2 family protein; Region: rrf2_super; TIGR00738 342108002909 Transcriptional regulator; Region: Rrf2; pfam02082 342108002910 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 342108002911 putative oxidoreductase; Provisional; Region: PRK08275 342108002912 L-aspartate oxidase; Provisional; Region: PRK06175 342108002913 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 342108002914 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 342108002915 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 342108002916 putative oxidoreductase/HEAT repeat-containing protein; Provisional; Region: PRK13800 342108002917 4Fe-4S binding domain; Region: Fer4_5; pfam12801 342108002918 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 342108002919 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 342108002920 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 342108002921 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 342108002922 Walker A/P-loop; other site 342108002923 ATP binding site [chemical binding]; other site 342108002924 Q-loop/lid; other site 342108002925 ABC transporter signature motif; other site 342108002926 Walker B; other site 342108002927 D-loop; other site 342108002928 H-loop/switch region; other site 342108002929 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 342108002930 putative carbohydrate binding site [chemical binding]; other site 342108002931 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 342108002932 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 342108002933 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 342108002934 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 342108002935 dimer interface [polypeptide binding]; other site 342108002936 ADP-ribose binding site [chemical binding]; other site 342108002937 active site 342108002938 nudix motif; other site 342108002939 metal binding site [ion binding]; metal-binding site 342108002940 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 342108002941 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 342108002942 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 342108002943 Glycosyltransferase 4 (GT4) includes both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases. They catalyze the transfer of a D-N-acetylhexosamine 1-phosphate to a membrane-bound...; Region: GT_MraY-like; cl10571 342108002944 putative catalytic motif [active] 342108002945 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108002946 Arna decarboxylase_like, extended (e) SDRs; Region: Arna_like_SDR_e; cd05257 342108002947 NAD binding site [chemical binding]; other site 342108002948 substrate binding site [chemical binding]; other site 342108002949 active site 342108002950 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 342108002951 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108002952 Walker A/P-loop; other site 342108002953 ATP binding site [chemical binding]; other site 342108002954 Q-loop/lid; other site 342108002955 ABC transporter signature motif; other site 342108002956 Walker B; other site 342108002957 D-loop; other site 342108002958 H-loop/switch region; other site 342108002959 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 342108002960 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 342108002961 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 342108002962 inhibitor-cofactor binding pocket; inhibition site 342108002963 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108002964 catalytic residue [active] 342108002965 Predicted kinase related to galactokinase and mevalonate kinase [General function prediction only]; Region: COG2605 342108002966 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 342108002967 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 342108002968 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 342108002969 Probable Catalytic site; other site 342108002970 metal-binding site 342108002971 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 342108002972 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 342108002973 NADP-binding site; other site 342108002974 homotetramer interface [polypeptide binding]; other site 342108002975 substrate binding site [chemical binding]; other site 342108002976 homodimer interface [polypeptide binding]; other site 342108002977 active site 342108002978 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 342108002979 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 342108002980 NADP-binding site; other site 342108002981 homotetramer interface [polypeptide binding]; other site 342108002982 substrate binding site [chemical binding]; other site 342108002983 homodimer interface [polypeptide binding]; other site 342108002984 active site 342108002985 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 342108002986 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 342108002987 metal-binding site 342108002988 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108002989 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 342108002990 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 342108002991 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 342108002992 active site 342108002993 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 342108002994 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108002995 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 342108002996 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 342108002997 metal-binding site 342108002998 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 342108002999 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 342108003000 Putative Catalytic site; other site 342108003001 DXD motif; other site 342108003002 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 342108003003 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108003004 Autotransporter beta-domain; Region: Autotransporter; pfam03797 342108003005 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 342108003006 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 342108003007 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 342108003008 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 342108003009 ABC transporter; Region: ABC_tran_2; pfam12848 342108003010 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 342108003011 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 342108003012 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 342108003013 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 342108003014 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 342108003015 Cl binding site [ion binding]; other site 342108003016 oligomer interface [polypeptide binding]; other site 342108003017 Phasin protein; Region: Phasin_2; cl11491 342108003018 Uncharacterized ACR, YagE family COG1723; Region: DUF155; cl00751 342108003019 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 342108003020 Agmatinase-like family includes proclavaminic acid amidinohydrolase; Region: Agmatinase_PAH; cd11592 342108003021 agmatinase; Region: agmatinase; TIGR01230 342108003022 oligomer interface [polypeptide binding]; other site 342108003023 putative active site [active] 342108003024 Mn binding site [ion binding]; other site 342108003025 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 342108003026 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 342108003027 dimer interface [polypeptide binding]; other site 342108003028 active site 342108003029 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 342108003030 catalytic residues [active] 342108003031 substrate binding site [chemical binding]; other site 342108003032 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 342108003033 Low molecular weight phosphatase family; Region: LMWPc; cl00105 342108003034 active site 342108003035 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108003036 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108003037 metal binding site [ion binding]; metal-binding site 342108003038 active site 342108003039 I-site; other site 342108003040 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 342108003041 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 342108003042 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 342108003043 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 342108003044 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108003045 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108003046 metal binding site [ion binding]; metal-binding site 342108003047 active site 342108003048 I-site; other site 342108003049 phosphate transporter ATP-binding protein; Provisional; Region: PRK14235 342108003050 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 342108003051 Walker A/P-loop; other site 342108003052 ATP binding site [chemical binding]; other site 342108003053 Q-loop/lid; other site 342108003054 ABC transporter signature motif; other site 342108003055 Walker B; other site 342108003056 D-loop; other site 342108003057 H-loop/switch region; other site 342108003058 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 342108003059 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 342108003060 ornithine decarboxylase; Provisional; Region: PRK13578 342108003061 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 342108003062 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108003063 catalytic residue [active] 342108003064 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 342108003065 PAS domain S-box; Region: sensory_box; TIGR00229 342108003066 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 342108003067 putative active site [active] 342108003068 heme pocket [chemical binding]; other site 342108003069 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 342108003070 PAS fold; Region: PAS_3; pfam08447 342108003071 putative active site [active] 342108003072 heme pocket [chemical binding]; other site 342108003073 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 342108003074 dimer interface [polypeptide binding]; other site 342108003075 phosphorylation site [posttranslational modification] 342108003076 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 342108003077 ATP binding site [chemical binding]; other site 342108003078 Mg2+ binding site [ion binding]; other site 342108003079 G-X-G motif; other site 342108003080 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108003081 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 342108003082 active site 342108003083 phosphorylation site [posttranslational modification] 342108003084 intermolecular recognition site; other site 342108003085 dimerization interface [polypeptide binding]; other site 342108003086 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 342108003087 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 342108003088 PAS fold; Region: PAS_3; pfam08447 342108003089 putative active site [active] 342108003090 heme pocket [chemical binding]; other site 342108003091 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108003092 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 342108003093 dimer interface [polypeptide binding]; other site 342108003094 phosphorylation site [posttranslational modification] 342108003095 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 342108003096 ATP binding site [chemical binding]; other site 342108003097 Mg2+ binding site [ion binding]; other site 342108003098 G-X-G motif; other site 342108003099 Response regulator receiver domain; Region: Response_reg; pfam00072 342108003100 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 342108003101 active site 342108003102 phosphorylation site [posttranslational modification] 342108003103 intermolecular recognition site; other site 342108003104 dimerization interface [polypeptide binding]; other site 342108003105 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 342108003106 dimerization interface [polypeptide binding]; other site 342108003107 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108003108 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 342108003109 ATP binding site [chemical binding]; other site 342108003110 Mg2+ binding site [ion binding]; other site 342108003111 G-X-G motif; other site 342108003112 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108003113 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 342108003114 putative active site [active] 342108003115 heme pocket [chemical binding]; other site 342108003116 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 342108003117 dimer interface [polypeptide binding]; other site 342108003118 phosphorylation site [posttranslational modification] 342108003119 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 342108003120 ATP binding site [chemical binding]; other site 342108003121 Mg2+ binding site [ion binding]; other site 342108003122 G-X-G motif; other site 342108003123 Response regulator receiver domain; Region: Response_reg; pfam00072 342108003124 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 342108003125 active site 342108003126 phosphorylation site [posttranslational modification] 342108003127 intermolecular recognition site; other site 342108003128 dimerization interface [polypeptide binding]; other site 342108003129 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108003130 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 342108003131 active site 342108003132 phosphorylation site [posttranslational modification] 342108003133 intermolecular recognition site; other site 342108003134 dimerization interface [polypeptide binding]; other site 342108003135 Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing...; Region: H2MP; cl00477 342108003136 nickel binding site [ion binding]; other site 342108003137 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 342108003138 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 342108003139 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 342108003140 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 342108003141 active site 342108003142 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 342108003143 phosphorylation site [posttranslational modification] 342108003144 intermolecular recognition site; other site 342108003145 dimerization interface [polypeptide binding]; other site 342108003146 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 342108003147 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 342108003148 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 342108003149 anti sigma factor interaction site; other site 342108003150 regulatory phosphorylation site [posttranslational modification]; other site 342108003151 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 342108003152 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 342108003153 Sporulation related domain; Region: SPOR; pfam05036 342108003154 Phasin protein; Region: Phasin_2; pfam09361 342108003155 Uncharacterized conserved protein [Function unknown]; Region: COG2127 342108003156 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 342108003157 Clp amino terminal domain; Region: Clp_N; pfam02861 342108003158 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 342108003159 Walker A motif; other site 342108003160 ATP binding site [chemical binding]; other site 342108003161 Walker B motif; other site 342108003162 5-bromo-4-chloroindolyl phosphate hydrolysis protein; Region: Halogen_Hydrol; cl02059 342108003163 arginine finger; other site 342108003164 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 342108003165 Walker A motif; other site 342108003166 ATP binding site [chemical binding]; other site 342108003167 Walker B motif; other site 342108003168 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 342108003169 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 342108003170 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 342108003171 FeS/SAM binding site; other site 342108003172 argininosuccinate synthase; Provisional; Region: PRK13820 342108003173 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 342108003174 ANP binding site [chemical binding]; other site 342108003175 Substrate Binding Site II [chemical binding]; other site 342108003176 Substrate Binding Site I [chemical binding]; other site 342108003177 PAS fold; Region: PAS_3; pfam08447 342108003178 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 342108003179 putative active site [active] 342108003180 heme pocket [chemical binding]; other site 342108003181 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 342108003182 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 342108003183 dimer interface [polypeptide binding]; other site 342108003184 phosphorylation site [posttranslational modification] 342108003185 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 342108003186 ATP binding site [chemical binding]; other site 342108003187 Mg2+ binding site [ion binding]; other site 342108003188 G-X-G motif; other site 342108003189 HerA helicase [Replication, recombination, and repair]; Region: COG0433 342108003190 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 342108003191 Walker A motif; other site 342108003192 ATP binding site [chemical binding]; other site 342108003193 Walker B motif; other site 342108003194 Helix-turn-helix domain; Region: HTH_36; pfam13730 342108003195 Abi-like protein; Region: Abi_2; pfam07751 342108003196 Protein of unknown function (DUF3732); Region: DUF3732; pfam12532 342108003197 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 342108003198 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 342108003199 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 342108003200 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 342108003201 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 342108003202 Domain of unknown function (DUF4347); Region: DUF4347; pfam14252 342108003203 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108003204 Putative Ig domain; Region: He_PIG; pfam05345 342108003205 Cadherin repeat-like domain; Region: CA_like; cl15786 342108003206 Ca2+ binding site [ion binding]; other site 342108003207 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108003208 Outer membrane efflux protein; Region: OEP; pfam02321 342108003209 Outer membrane efflux protein; Region: OEP; pfam02321 342108003210 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 342108003211 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108003212 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 342108003213 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108003214 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 342108003215 Peptidase family M50; Region: Peptidase_M50; pfam02163 342108003216 active site 342108003217 putative substrate binding region [chemical binding]; other site 342108003218 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 342108003219 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108003220 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 342108003221 AAA domain; Region: AAA_24; pfam13479 342108003222 Walker A motif; other site 342108003223 ATP binding site [chemical binding]; other site 342108003224 Toprim domain; Region: Toprim_3; pfam13362 342108003225 Predicted P-loop ATPase and inactivated derivatives [General function prediction only]; Region: COG5545 342108003226 Virulence-associated protein E; Region: VirE; pfam05272 342108003227 MTH538 TIR-like domain (DUF1863); Region: DUF1863; pfam08937 342108003228 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cl17280 342108003229 active site 342108003230 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 342108003231 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 342108003232 cofactor binding site; other site 342108003233 DNA binding site [nucleotide binding] 342108003234 substrate interaction site [chemical binding]; other site 342108003235 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 342108003236 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 342108003237 Active Sites [active] 342108003238 ParB-like nuclease domain; Region: ParBc; pfam02195 342108003239 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 342108003240 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 342108003241 DNA methylase; Region: N6_N4_Mtase; pfam01555 342108003242 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 342108003243 IHF - DNA interface [nucleotide binding]; other site 342108003244 IHF dimer interface [polypeptide binding]; other site 342108003245 Protein of unknown function (DUF3489); Region: DUF3489; pfam11994 342108003246 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 342108003247 Phage portal protein, lambda family; Region: Phage_portal_2; pfam05136 342108003248 phage portal protein, lambda family; Region: portal_lambda; TIGR01539 342108003249 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 342108003250 Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_36K_type; cd07022 342108003251 tandem repeat interface [polypeptide binding]; other site 342108003252 oligomer interface [polypeptide binding]; other site 342108003253 active site residues [active] 342108003254 Bacteriophage lambda head decoration protein D; Region: HDPD; pfam02924 342108003255 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 342108003256 geranyl diphosphate synthase; Region: PLN02890 342108003257 Radical SAM superfamily; Region: Radical_SAM; pfam04055 342108003258 tape measure domain; Region: tape_meas_nterm; TIGR02675 342108003259 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 342108003260 Negative regulator of septation ring formation [Cell division and chromosome partitioning]; Region: EzrA; COG4477 342108003261 Domain of unknown function (DUF1833); Region: DUF1833; pfam08875 342108003262 NlpC/P60 family; Region: NLPC_P60; cl17555 342108003263 Bacteriophage lambda tail assembly protein I; Region: Lambda_tail_I; pfam06805 342108003264 Putative phage tail protein; Region: Phage-tail_3; pfam13550 342108003265 virion protein; Provisional; Region: V; PHA02564 342108003266 ParB-like nuclease domain; Region: ParBc; cl02129 342108003267 RepB plasmid partitioning protein; Region: RepB; pfam07506 342108003268 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 342108003269 ParB-like nuclease domain; Region: ParB; smart00470 342108003270 RepB plasmid partitioning protein; Region: RepB; pfam07506 342108003271 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 342108003272 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 342108003273 catalytic residues [active] 342108003274 catalytic nucleophile [active] 342108003275 Recombinase; Region: Recombinase; pfam07508 342108003276 Protein of unknown function (DUF2924); Region: DUF2924; pfam11149 342108003277 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 342108003278 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 342108003279 catalytic residues [active] 342108003280 catalytic nucleophile [active] 342108003281 Presynaptic Site I dimer interface [polypeptide binding]; other site 342108003282 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 342108003283 Synaptic Flat tetramer interface [polypeptide binding]; other site 342108003284 Synaptic Site I dimer interface [polypeptide binding]; other site 342108003285 DNA binding site [nucleotide binding] 342108003286 Recombinase; Region: Recombinase; pfam07508 342108003287 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 342108003288 tetrahydromethanopterin S-methyltransferase subunit A; Provisional; Region: PRK00964 342108003289 Tetrahydromethanopterin S-methyltransferase, subunit A; Region: MtrA; cl04449 342108003290 Domain of unknown function (DUF4346); Region: DUF4346; pfam14251 342108003291 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 342108003292 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108003293 putative substrate translocation pore; other site 342108003294 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 342108003295 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 342108003296 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 342108003297 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 342108003298 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 342108003299 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108003300 Zn2+ binding site [ion binding]; other site 342108003301 Mg2+ binding site [ion binding]; other site 342108003302 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 342108003303 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108003304 putative substrate translocation pore; other site 342108003305 FOG: CBS domain [General function prediction only]; Region: COG0517 342108003306 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 342108003307 FOG: CBS domain [General function prediction only]; Region: COG0517 342108003308 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 342108003309 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 342108003310 PAS domain; Region: PAS_9; pfam13426 342108003311 putative active site [active] 342108003312 heme pocket [chemical binding]; other site 342108003313 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108003314 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108003315 metal binding site [ion binding]; metal-binding site 342108003316 active site 342108003317 I-site; other site 342108003318 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 342108003319 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 342108003320 putative binding surface; other site 342108003321 active site 342108003322 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 342108003323 active site 342108003324 phosphorylation site [posttranslational modification] 342108003325 intermolecular recognition site; other site 342108003326 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 342108003327 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 342108003328 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108003329 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 342108003330 dimerization interface [polypeptide binding]; other site 342108003331 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108003332 dimer interface [polypeptide binding]; other site 342108003333 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108003334 putative CheW interface [polypeptide binding]; other site 342108003335 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 342108003336 putative active site [active] 342108003337 putative catalytic site [active] 342108003338 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 342108003339 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 342108003340 S-adenosylmethionine binding site [chemical binding]; other site 342108003341 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108003342 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 342108003343 ligand binding site [chemical binding]; other site 342108003344 flexible hinge region; other site 342108003345 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 342108003346 putative switch regulator; other site 342108003347 non-specific DNA interactions [nucleotide binding]; other site 342108003348 DNA binding site [nucleotide binding] 342108003349 sequence specific DNA binding site [nucleotide binding]; other site 342108003350 putative cAMP binding site [chemical binding]; other site 342108003351 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 342108003352 Protein of unknown function (DUF4242); Region: DUF4242; pfam14026 342108003353 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 342108003354 dimer interface [polypeptide binding]; other site 342108003355 phosphorylation site [posttranslational modification] 342108003356 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 342108003357 ATP binding site [chemical binding]; other site 342108003358 Mg2+ binding site [ion binding]; other site 342108003359 G-X-G motif; other site 342108003360 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 342108003361 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 342108003362 Cache domain; Region: Cache_1; pfam02743 342108003363 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 342108003364 cyclase homology domain; Region: CHD; cd07302 342108003365 nucleotidyl binding site; other site 342108003366 metal binding site [ion binding]; metal-binding site 342108003367 dimer interface [polypeptide binding]; other site 342108003368 Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(P)...; Region: BluB; cd02145 342108003369 putative FMN binding site [chemical binding]; other site 342108003370 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; cl15777 342108003371 Protein of unknown function (DUF3095); Region: DUF3095; pfam11294 342108003372 NAD synthetase; Provisional; Region: PRK13981 342108003373 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 342108003374 multimer interface [polypeptide binding]; other site 342108003375 active site 342108003376 catalytic triad [active] 342108003377 protein interface 1 [polypeptide binding]; other site 342108003378 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 342108003379 homodimer interface [polypeptide binding]; other site 342108003380 NAD binding pocket [chemical binding]; other site 342108003381 ATP binding pocket [chemical binding]; other site 342108003382 Mg binding site [ion binding]; other site 342108003383 active-site loop [active] 342108003384 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 342108003385 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 342108003386 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 342108003387 active site 342108003388 HIGH motif; other site 342108003389 nucleotide binding site [chemical binding]; other site 342108003390 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 342108003391 active site 342108003392 KMSKS motif; other site 342108003393 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 342108003394 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 342108003395 active site 342108003396 HIGH motif; other site 342108003397 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 342108003398 KMSKS motif; other site 342108003399 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 342108003400 tRNA binding surface [nucleotide binding]; other site 342108003401 anticodon binding site; other site 342108003402 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 342108003403 CoA binding domain; Region: CoA_binding_2; pfam13380 342108003404 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 342108003405 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 342108003406 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 342108003407 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 342108003408 Predicted thioesterase [General function prediction only]; Region: COG5496 342108003409 The MopB_Phenylacetyl-CoA-OR CD contains the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), and other related proteins. The phenylacetyl-CoA:acceptor oxidoreductase has been characterized as a membrane-bound molybdenum-iron-sulfur...; Region: MopB_Phenylacetyl-CoA-OR; cd02760 342108003410 anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 342108003411 putative molybdopterin cofactor binding site; other site 342108003412 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 342108003413 molybdopterin cofactor binding site; other site 342108003414 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 342108003415 4Fe-4S binding domain; Region: Fer4; pfam00037 342108003416 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl17519 342108003417 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 342108003418 CoA binding domain; Region: CoA_binding_2; pfam13380 342108003419 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 342108003420 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 342108003421 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 342108003422 acyl-activating enzyme (AAE) consensus motif; other site 342108003423 AMP binding site [chemical binding]; other site 342108003424 active site 342108003425 CoA binding site [chemical binding]; other site 342108003426 Protein of unknown function, DUF; Region: DUF411; cl01142 342108003427 Cytochrome c; Region: Cytochrom_C; pfam00034 342108003428 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 342108003429 Protein export membrane protein; Region: SecD_SecF; cl14618 342108003430 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 342108003431 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 342108003432 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108003433 putative active site [active] 342108003434 heme pocket [chemical binding]; other site 342108003435 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 342108003436 dimer interface [polypeptide binding]; other site 342108003437 phosphorylation site [posttranslational modification] 342108003438 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 342108003439 ATP binding site [chemical binding]; other site 342108003440 Mg2+ binding site [ion binding]; other site 342108003441 G-X-G motif; other site 342108003442 Predicted permeases [General function prediction only]; Region: RarD; COG2962 342108003443 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 342108003444 diiron binding motif [ion binding]; other site 342108003445 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 342108003446 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 342108003447 active site 342108003448 phosphorylation site [posttranslational modification] 342108003449 intermolecular recognition site; other site 342108003450 dimerization interface [polypeptide binding]; other site 342108003451 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 342108003452 DNA binding residues [nucleotide binding] 342108003453 dimerization interface [polypeptide binding]; other site 342108003454 CHAP domain; Region: CHAP; cl17642 342108003455 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 342108003456 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 342108003457 Cytochrome c; Region: Cytochrom_C; cl11414 342108003458 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 342108003459 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 342108003460 ATP binding site [chemical binding]; other site 342108003461 putative Mg++ binding site [ion binding]; other site 342108003462 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 342108003463 nucleotide binding region [chemical binding]; other site 342108003464 Helicase associated domain (HA2); Region: HA2; pfam04408 342108003465 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 342108003466 EF hand; Region: EF_hand_3; pfam13202 342108003467 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 342108003468 Cache domain; Region: Cache_1; pfam02743 342108003469 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 342108003470 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108003471 putative active site [active] 342108003472 heme pocket [chemical binding]; other site 342108003473 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 342108003474 dimer interface [polypeptide binding]; other site 342108003475 phosphorylation site [posttranslational modification] 342108003476 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 342108003477 ATP binding site [chemical binding]; other site 342108003478 Mg2+ binding site [ion binding]; other site 342108003479 G-X-G motif; other site 342108003480 dihydroorotase; Validated; Region: PRK09060 342108003481 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 342108003482 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 342108003483 active site 342108003484 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 342108003485 active site 342108003486 asparagine synthase (glutamine-hydrolyzing); Region: asn_synth_AEB; TIGR01536 342108003487 dimer interface [polypeptide binding]; other site 342108003488 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 342108003489 Ligand Binding Site [chemical binding]; other site 342108003490 Molecular Tunnel; other site 342108003491 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 342108003492 putative ADP-binding pocket [chemical binding]; other site 342108003493 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108003494 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003495 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003496 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003497 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003498 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003499 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003500 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003501 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003502 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003503 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003504 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003505 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003506 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003507 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003508 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003509 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003510 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003511 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003512 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003513 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003514 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003515 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003516 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003517 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003518 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003519 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003520 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003521 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003522 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003523 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003524 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003525 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003526 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003527 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003528 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003529 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003530 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003531 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003532 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003533 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003534 Siphovirus protein of unknown function (DUF859); Region: DUF859; pfam05895 342108003535 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003536 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003537 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003538 Intracellular septation protein A; Region: IspA; pfam04279 342108003539 Transcriptional regulator [Transcription]; Region: LysR; COG0583 342108003540 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 342108003541 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_2; cd08471 342108003542 putative effector binding pocket; other site 342108003543 putative dimerization interface [polypeptide binding]; other site 342108003544 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 342108003545 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 342108003546 C-terminal, alpha helical domain of an unknown subfamily 7 of Glutathione S-transferases; Region: GST_C_7; cd03206 342108003547 putative N-terminal domain interface [polypeptide binding]; other site 342108003548 putative dimer interface [polypeptide binding]; other site 342108003549 putative substrate binding pocket (H-site) [chemical binding]; other site 342108003550 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 342108003551 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 342108003552 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003553 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003554 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003555 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003556 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003557 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003558 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003559 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003560 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003561 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003562 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003563 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003564 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003565 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003566 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003567 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003568 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003569 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003570 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003571 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003572 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003573 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003574 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003575 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003576 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003577 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003578 Siphovirus protein of unknown function (DUF859); Region: DUF859; pfam05895 342108003579 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003580 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003581 Domain of unknown function (DUF4114); Region: DUF4114; pfam13448 342108003582 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003583 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108003584 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 342108003585 Catalytic domain of Protein Kinases; Region: PKc; cd00180 342108003586 active site 342108003587 substrate binding site [chemical binding]; other site 342108003588 ATP binding site [chemical binding]; other site 342108003589 activation loop (A-loop); other site 342108003590 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 342108003591 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 342108003592 glutaminase active site [active] 342108003593 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 342108003594 dimer interface [polypeptide binding]; other site 342108003595 active site 342108003596 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 342108003597 dimer interface [polypeptide binding]; other site 342108003598 active site 342108003599 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14353 342108003600 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 342108003601 Substrate binding site; other site 342108003602 Mg++ binding site; other site 342108003603 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 342108003604 active site 342108003605 substrate binding site [chemical binding]; other site 342108003606 CoA binding site [chemical binding]; other site 342108003607 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 342108003608 PAS domain; Region: PAS_9; pfam13426 342108003609 putative active site [active] 342108003610 heme pocket [chemical binding]; other site 342108003611 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108003612 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108003613 metal binding site [ion binding]; metal-binding site 342108003614 active site 342108003615 I-site; other site 342108003616 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 342108003617 Response regulator receiver domain; Region: Response_reg; pfam00072 342108003618 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 342108003619 active site 342108003620 phosphorylation site [posttranslational modification] 342108003621 intermolecular recognition site; other site 342108003622 dimerization interface [polypeptide binding]; other site 342108003623 Transcriptional regulator; Region: Rrf2; cl17282 342108003624 Rrf2 family protein; Region: rrf2_super; TIGR00738 342108003625 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 342108003626 motif 1; other site 342108003627 dimer interface [polypeptide binding]; other site 342108003628 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 342108003629 active site 342108003630 motif 2; other site 342108003631 motif 3; other site 342108003632 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 342108003633 Radical SAM superfamily; Region: Radical_SAM; pfam04055 342108003634 FeS/SAM binding site; other site 342108003635 Lysine-2,3-aminomutase; Region: LAM_C; pfam12544 342108003636 translation elongation factor P; Region: efp; TIGR00038 342108003637 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 342108003638 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 342108003639 RNA binding site [nucleotide binding]; other site 342108003640 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 342108003641 RNA binding site [nucleotide binding]; other site 342108003642 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 342108003643 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 342108003644 active site 342108003645 dimerization interface [polypeptide binding]; other site 342108003646 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 342108003647 ligand binding site [chemical binding]; other site 342108003648 hypothetical protein; Validated; Region: PRK09039 342108003649 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 342108003650 ligand binding site [chemical binding]; other site 342108003651 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 342108003652 High-affinity nickel-transport protein; Region: NicO; cl00964 342108003653 Protein of unknown function (DUF1007); Region: DUF1007; pfam06226 342108003654 cystathionine beta-lyase; Provisional; Region: PRK09028 342108003655 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 342108003656 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108003657 catalytic residue [active] 342108003658 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 342108003659 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108003660 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 342108003661 dimerization interface [polypeptide binding]; other site 342108003662 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 342108003663 PAS domain; Region: PAS_9; pfam13426 342108003664 putative active site [active] 342108003665 heme pocket [chemical binding]; other site 342108003666 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108003667 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108003668 metal binding site [ion binding]; metal-binding site 342108003669 active site 342108003670 I-site; other site 342108003671 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 342108003672 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 342108003673 active site residue [active] 342108003674 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 342108003675 active site residue [active] 342108003676 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 342108003677 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 342108003678 dimer interface [polypeptide binding]; other site 342108003679 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108003680 Membrane bound FAD containing D-sorbitol dehydrogenase; Region: FAD-SLDH; pfam12318 342108003681 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 342108003682 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 342108003683 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 342108003684 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 342108003685 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 342108003686 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 342108003687 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 342108003688 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 342108003689 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 342108003690 P-loop; other site 342108003691 Magnesium ion binding site [ion binding]; other site 342108003692 Predicted integral membrane protein [Function unknown]; Region: COG5615 342108003693 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 342108003694 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 342108003695 dimer interface [polypeptide binding]; other site 342108003696 ADP-ribose binding site [chemical binding]; other site 342108003697 active site 342108003698 nudix motif; other site 342108003699 metal binding site [ion binding]; metal-binding site 342108003700 Integral membrane protein TerC family; Region: TerC; cl10468 342108003701 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 342108003702 Uncharacterized membrane protein [Function unknown]; Region: SpmB; cl17667 342108003703 LrgB-like family; Region: LrgB; pfam04172 342108003704 LrgA family; Region: LrgA; pfam03788 342108003705 Uncharacterized conserved protein [Function unknown]; Region: COG4095 342108003706 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 342108003707 active site 342108003708 enoyl-CoA hydratase; Provisional; Region: PRK06127 342108003709 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 342108003710 substrate binding site [chemical binding]; other site 342108003711 oxyanion hole (OAH) forming residues; other site 342108003712 trimer interface [polypeptide binding]; other site 342108003713 Adenine-specific DNA methylase containing a Zn-ribbon [DNA replication, recombination, and repair]; Region: COG1743 342108003714 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 342108003715 dimer interface [polypeptide binding]; other site 342108003716 phosphorylation site [posttranslational modification] 342108003717 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 342108003718 ATP binding site [chemical binding]; other site 342108003719 Mg2+ binding site [ion binding]; other site 342108003720 G-X-G motif; other site 342108003721 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108003722 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 342108003723 active site 342108003724 phosphorylation site [posttranslational modification] 342108003725 intermolecular recognition site; other site 342108003726 dimerization interface [polypeptide binding]; other site 342108003727 Transcriptional regulator; Region: Rrf2; cl17282 342108003728 Rrf2 family protein; Region: rrf2_super; TIGR00738 342108003729 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108003730 succinic semialdehyde dehydrogenase; Region: PLN02278 342108003731 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 342108003732 tetramerization interface [polypeptide binding]; other site 342108003733 NAD(P) binding site [chemical binding]; other site 342108003734 catalytic residues [active] 342108003735 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 342108003736 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108003737 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 342108003738 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 342108003739 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 342108003740 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 342108003741 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 342108003742 Walker A/P-loop; other site 342108003743 ATP binding site [chemical binding]; other site 342108003744 Q-loop/lid; other site 342108003745 ABC transporter signature motif; other site 342108003746 Walker B; other site 342108003747 D-loop; other site 342108003748 H-loop/switch region; other site 342108003749 ABC nitrate/sulfonate/bicarbonate family transporter, ATPase subunit; Region: ABC_transp; pfam09821 342108003750 ABC-type anion transport system, duplicated permease component [Inorganic ion transport and metabolism]; Region: COG4986 342108003751 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 342108003752 dimer interface [polypeptide binding]; other site 342108003753 conserved gate region; other site 342108003754 putative PBP binding loops; other site 342108003755 ABC-ATPase subunit interface; other site 342108003756 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 342108003757 dimer interface [polypeptide binding]; other site 342108003758 conserved gate region; other site 342108003759 putative PBP binding loops; other site 342108003760 ABC-ATPase subunit interface; other site 342108003761 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 342108003762 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 342108003763 folate binding site [chemical binding]; other site 342108003764 NADP+ binding site [chemical binding]; other site 342108003765 thymidylate synthase; Reviewed; Region: thyA; PRK01827 342108003766 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 342108003767 dimerization interface [polypeptide binding]; other site 342108003768 active site 342108003769 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108003770 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108003771 metal binding site [ion binding]; metal-binding site 342108003772 active site 342108003773 I-site; other site 342108003774 Stringent starvation protein B; Region: SspB; pfam04386 342108003775 fumarate hydratase; Provisional; Region: PRK15389 342108003776 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 342108003777 Fumarase C-terminus; Region: Fumerase_C; pfam05683 342108003778 TfoX N-terminal domain; Region: TfoX_N; pfam04993 342108003779 Protein of unknown function (DUF983); Region: DUF983; pfam06170 342108003780 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108003781 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 342108003782 DNA binding site [nucleotide binding] 342108003783 Response regulator receiver domain; Region: Response_reg; pfam00072 342108003784 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 342108003785 active site 342108003786 phosphorylation site [posttranslational modification] 342108003787 intermolecular recognition site; other site 342108003788 dimerization interface [polypeptide binding]; other site 342108003789 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 342108003790 dimer interface [polypeptide binding]; other site 342108003791 phosphorylation site [posttranslational modification] 342108003792 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 342108003793 ATP binding site [chemical binding]; other site 342108003794 Mg2+ binding site [ion binding]; other site 342108003795 G-X-G motif; other site 342108003796 Protein of unknown function (DUF2794); Region: DUF2794; pfam10984 342108003797 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 342108003798 putative catalytic residue [active] 342108003799 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4649 342108003800 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 342108003801 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 342108003802 active site 342108003803 PQQ-like domain; Region: PQQ_2; pfam13360 342108003804 Trp docking motif [polypeptide binding]; other site 342108003805 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 342108003806 GTP-binding protein Der; Reviewed; Region: PRK00093 342108003807 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 342108003808 G1 box; other site 342108003809 GTP/Mg2+ binding site [chemical binding]; other site 342108003810 Switch I region; other site 342108003811 G2 box; other site 342108003812 Switch II region; other site 342108003813 G3 box; other site 342108003814 G4 box; other site 342108003815 G5 box; other site 342108003816 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 342108003817 G1 box; other site 342108003818 GTP/Mg2+ binding site [chemical binding]; other site 342108003819 Switch I region; other site 342108003820 G2 box; other site 342108003821 G3 box; other site 342108003822 Switch II region; other site 342108003823 G4 box; other site 342108003824 G5 box; other site 342108003825 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108003826 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108003827 metal binding site [ion binding]; metal-binding site 342108003828 active site 342108003829 I-site; other site 342108003830 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 342108003831 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 342108003832 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 342108003833 active site 342108003834 phosphorylation site [posttranslational modification] 342108003835 intermolecular recognition site; other site 342108003836 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 342108003837 DNA binding residues [nucleotide binding] 342108003838 dimerization interface [polypeptide binding]; other site 342108003839 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3224 342108003840 Protein of unknown function (DUF3572); Region: DUF3572; pfam12096 342108003841 Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_uncharacterized_transporter; cd06325 342108003842 zinc binding site [ion binding]; other site 342108003843 putative ligand binding site [chemical binding]; other site 342108003844 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 342108003845 dimerization interface [polypeptide binding]; other site 342108003846 PAS domain S-box; Region: sensory_box; TIGR00229 342108003847 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 342108003848 putative active site [active] 342108003849 heme pocket [chemical binding]; other site 342108003850 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108003851 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108003852 metal binding site [ion binding]; metal-binding site 342108003853 active site 342108003854 I-site; other site 342108003855 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 342108003856 Protein of unknown function (DUF2934); Region: DUF2934; pfam11154 342108003857 Ribbon-helix-helix domain; Region: RHH_4; pfam13467 342108003858 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 342108003859 AMP binding site [chemical binding]; other site 342108003860 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 342108003861 non-ribosomal peptide synthetase terminal domain of unknown function; Region: NRPS_term_dom; TIGR02353 342108003862 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 342108003863 putative trimer interface [polypeptide binding]; other site 342108003864 putative CoA binding site [chemical binding]; other site 342108003865 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 342108003866 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 342108003867 acyl-activating enzyme (AAE) consensus motif; other site 342108003868 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 342108003869 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 342108003870 Sel1-like repeats; Region: SEL1; smart00671 342108003871 Sel1-like repeats; Region: SEL1; smart00671 342108003872 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 342108003873 Sel1-like repeats; Region: SEL1; smart00671 342108003874 Sel1-like repeats; Region: SEL1; smart00671 342108003875 Sel1-like repeats; Region: SEL1; smart00671 342108003876 Sel1-like repeats; Region: SEL1; smart00671 342108003877 hopanoid-associated sugar epimerase; Region: HpnA; TIGR03466 342108003878 uncharacterized subgroup of aldehyde reductase and flavonoid reductase related proteins, extended (e) SDRs; Region: AR_FR_like_1_SDR_e; cd05228 342108003879 putative NADP binding site [chemical binding]; other site 342108003880 putative substrate binding site [chemical binding]; other site 342108003881 active site 342108003882 hopene-associated glycosyltransferase HpnB; Region: HpnB; TIGR03469 342108003883 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 342108003884 active site 342108003885 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 342108003886 active site lid residues [active] 342108003887 substrate binding pocket [chemical binding]; other site 342108003888 catalytic residues [active] 342108003889 substrate-Mg2+ binding site; other site 342108003890 aspartate-rich region 1; other site 342108003891 aspartate-rich region 2; other site 342108003892 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 342108003893 Prenyltransferase-like; Region: Prenyltrans_2; pfam13249 342108003894 hopanoid-associated phosphorylase; Region: HpnG; TIGR03468 342108003895 hopanoid biosynthesis associated radical SAM protein HpnH; Region: HpnH; TIGR03470 342108003896 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 342108003897 FeS/SAM binding site; other site 342108003898 Domain of unknown function (DUF3463); Region: DUF3463; pfam11946 342108003899 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 342108003900 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 342108003901 active site 342108003902 phosphorylation site [posttranslational modification] 342108003903 intermolecular recognition site; other site 342108003904 dimerization interface [polypeptide binding]; other site 342108003905 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 342108003906 DNA binding site [nucleotide binding] 342108003907 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 342108003908 PhoU domain; Region: PhoU; pfam01895 342108003909 PhoU domain; Region: PhoU; pfam01895 342108003910 phosphate transporter ATP-binding protein; Provisional; Region: PRK14235 342108003911 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 342108003912 Walker A/P-loop; other site 342108003913 ATP binding site [chemical binding]; other site 342108003914 Q-loop/lid; other site 342108003915 ABC transporter signature motif; other site 342108003916 Walker B; other site 342108003917 D-loop; other site 342108003918 H-loop/switch region; other site 342108003919 Domain of unknown function (DUF3333); Region: DUF3333; pfam11812 342108003920 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 342108003921 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 342108003922 dimer interface [polypeptide binding]; other site 342108003923 conserved gate region; other site 342108003924 putative PBP binding loops; other site 342108003925 ABC-type sugar transport systems, permease components [Carbohydrate transport and metabolism]; Region: UgpA; COG1175 342108003926 ABC-ATPase subunit interface; other site 342108003927 Phosphate ATP-binding cassette transporter; Region: DUF3708; pfam12501 342108003928 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 342108003929 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 342108003930 dimer interface [polypeptide binding]; other site 342108003931 conserved gate region; other site 342108003932 putative PBP binding loops; other site 342108003933 ABC-ATPase subunit interface; other site 342108003934 PBP superfamily domain; Region: PBP_like_2; pfam12849 342108003935 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 342108003936 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 342108003937 DNA-binding site [nucleotide binding]; DNA binding site 342108003938 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 342108003939 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108003940 homodimer interface [polypeptide binding]; other site 342108003941 catalytic residue [active] 342108003942 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_ox_2; pfam12900 342108003943 Hemerythrin; Region: Hemerythrin; cd12107 342108003944 Fe binding site [ion binding]; other site 342108003945 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 342108003946 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 342108003947 substrate binding site [chemical binding]; other site 342108003948 hexamer interface [polypeptide binding]; other site 342108003949 metal binding site [ion binding]; metal-binding site 342108003950 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 342108003951 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 342108003952 intersubunit interface [polypeptide binding]; other site 342108003953 active site 342108003954 zinc binding site [ion binding]; other site 342108003955 Na+ binding site [ion binding]; other site 342108003956 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 342108003957 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 342108003958 TPP-binding site [chemical binding]; other site 342108003959 dimer interface [polypeptide binding]; other site 342108003960 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 342108003961 PYR/PP interface [polypeptide binding]; other site 342108003962 dimer interface [polypeptide binding]; other site 342108003963 TPP binding site [chemical binding]; other site 342108003964 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 342108003965 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 342108003966 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 342108003967 putative active site [active] 342108003968 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 342108003969 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 342108003970 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 342108003971 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 342108003972 AsnC family; Region: AsnC_trans_reg; pfam01037 342108003973 helicase 45; Provisional; Region: PTZ00424 342108003974 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 342108003975 ATP binding site [chemical binding]; other site 342108003976 Mg++ binding site [ion binding]; other site 342108003977 motif III; other site 342108003978 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 342108003979 nucleotide binding region [chemical binding]; other site 342108003980 ATP-binding site [chemical binding]; other site 342108003981 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 342108003982 Isochorismatase family; Region: Isochorismatase; pfam00857 342108003983 catalytic triad [active] 342108003984 dimer interface [polypeptide binding]; other site 342108003985 conserved cis-peptide bond; other site 342108003986 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 342108003987 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 342108003988 dimer interface [polypeptide binding]; other site 342108003989 active site 342108003990 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 342108003991 catalytic residues [active] 342108003992 substrate binding site [chemical binding]; other site 342108003993 flagellar hook protein FlgE; Validated; Region: flgE; PRK05841 342108003994 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 342108003995 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 342108003996 aspartate aminotransferase; Provisional; Region: PRK05764 342108003997 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 342108003998 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108003999 homodimer interface [polypeptide binding]; other site 342108004000 catalytic residue [active] 342108004001 Peptidase family M48; Region: Peptidase_M48; cl12018 342108004002 TPR repeat; Region: TPR_11; pfam13414 342108004003 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 342108004004 binding surface 342108004005 TPR motif; other site 342108004006 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 342108004007 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 342108004008 catalytic residues [active] 342108004009 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 342108004010 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 342108004011 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 342108004012 transcriptional activator FtrB; Provisional; Region: ftrB; PRK09392 342108004013 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 342108004014 ligand binding site [chemical binding]; other site 342108004015 flexible hinge region; other site 342108004016 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108004017 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 342108004018 ligand binding site [chemical binding]; other site 342108004019 flexible hinge region; other site 342108004020 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 342108004021 putative switch regulator; other site 342108004022 non-specific DNA interactions [nucleotide binding]; other site 342108004023 DNA binding site [nucleotide binding] 342108004024 sequence specific DNA binding site [nucleotide binding]; other site 342108004025 putative cAMP binding site [chemical binding]; other site 342108004026 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 342108004027 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 342108004028 Ethylbenzene dehydrogenase; Region: EB_dh; smart00887 342108004029 Ethylbenzene dehydrogenase; Region: EB_dh; pfam09459 342108004030 putative ligand binding site [chemical binding]; other site 342108004031 Plastocyanin [Energy production and conversion]; Region: PetE; COG3794 342108004032 Cupredoxin-like domain; Region: Cupredoxin_1; cl17234 342108004033 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 342108004034 active site 342108004035 SAM binding site [chemical binding]; other site 342108004036 homodimer interface [polypeptide binding]; other site 342108004037 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 342108004038 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 342108004039 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 342108004040 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 342108004041 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 342108004042 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 342108004043 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 342108004044 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 342108004045 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 342108004046 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 342108004047 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 342108004048 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 342108004049 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 342108004050 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108004051 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108004052 PAS domain; Region: PAS; smart00091 342108004053 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108004054 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 342108004055 dimer interface [polypeptide binding]; other site 342108004056 phosphorylation site [posttranslational modification] 342108004057 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 342108004058 ATP binding site [chemical binding]; other site 342108004059 Mg2+ binding site [ion binding]; other site 342108004060 G-X-G motif; other site 342108004061 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 342108004062 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 342108004063 dimer interface [polypeptide binding]; other site 342108004064 phosphorylation site [posttranslational modification] 342108004065 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 342108004066 ATP binding site [chemical binding]; other site 342108004067 Mg2+ binding site [ion binding]; other site 342108004068 G-X-G motif; other site 342108004069 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 342108004070 membrane-bound complex binding site; other site 342108004071 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 342108004072 Salmonella typhimurium Zn2+ transporter ZntB-like subgroup; Region: ZntB-like_1; cd12833 342108004073 Cl binding site [ion binding]; other site 342108004074 oligomer interface [polypeptide binding]; other site 342108004075 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 342108004076 PAS domain; Region: PAS_9; pfam13426 342108004077 putative active site [active] 342108004078 heme pocket [chemical binding]; other site 342108004079 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 342108004080 Hemerythrin; Region: Hemerythrin; cd12107 342108004081 Fe binding site [ion binding]; other site 342108004082 Hemerythrin family; Region: Hemerythrin-like; cl15774 342108004083 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 342108004084 Part of AAA domain; Region: AAA_19; pfam13245 342108004085 Family description; Region: UvrD_C_2; pfam13538 342108004086 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 342108004087 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 342108004088 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 342108004089 nucleotide binding site/active site [active] 342108004090 HIT family signature motif; other site 342108004091 catalytic residue [active] 342108004092 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cd00229 342108004093 active site 342108004094 catalytic triad [active] 342108004095 oxyanion hole [active] 342108004096 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 342108004097 AMP-binding enzyme; Region: AMP-binding; pfam00501 342108004098 acyl-activating enzyme (AAE) consensus motif; other site 342108004099 AMP binding site [chemical binding]; other site 342108004100 active site 342108004101 CoA binding site [chemical binding]; other site 342108004102 ATP-grasp domain; Region: ATP-grasp_4; cl17255 342108004103 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 342108004104 transmembrane helices; other site 342108004105 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 342108004106 TrkA-C domain; Region: TrkA_C; pfam02080 342108004107 TrkA-C domain; Region: TrkA_C; pfam02080 342108004108 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 342108004109 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 342108004110 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 342108004111 ATP binding site [chemical binding]; other site 342108004112 Mg++ binding site [ion binding]; other site 342108004113 motif III; other site 342108004114 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 342108004115 nucleotide binding region [chemical binding]; other site 342108004116 ATP-binding site [chemical binding]; other site 342108004117 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 342108004118 nudix motif; other site 342108004119 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 342108004120 PAS fold; Region: PAS_3; pfam08447 342108004121 putative active site [active] 342108004122 heme pocket [chemical binding]; other site 342108004123 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 342108004124 dimer interface [polypeptide binding]; other site 342108004125 phosphorylation site [posttranslational modification] 342108004126 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 342108004127 ATP binding site [chemical binding]; other site 342108004128 Mg2+ binding site [ion binding]; other site 342108004129 G-X-G motif; other site 342108004130 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 342108004131 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 342108004132 active site 342108004133 phosphorylation site [posttranslational modification] 342108004134 intermolecular recognition site; other site 342108004135 dimerization interface [polypeptide binding]; other site 342108004136 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108004137 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 342108004138 active site 342108004139 phosphorylation site [posttranslational modification] 342108004140 intermolecular recognition site; other site 342108004141 dimerization interface [polypeptide binding]; other site 342108004142 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 342108004143 dimer interface [polypeptide binding]; other site 342108004144 phosphorylation site [posttranslational modification] 342108004145 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 342108004146 ATP binding site [chemical binding]; other site 342108004147 Mg2+ binding site [ion binding]; other site 342108004148 G-X-G motif; other site 342108004149 Response regulator receiver domain; Region: Response_reg; pfam00072 342108004150 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 342108004151 active site 342108004152 phosphorylation site [posttranslational modification] 342108004153 intermolecular recognition site; other site 342108004154 dimerization interface [polypeptide binding]; other site 342108004155 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 342108004156 PAS domain; Region: PAS_9; pfam13426 342108004157 putative active site [active] 342108004158 heme pocket [chemical binding]; other site 342108004159 PAS fold; Region: PAS_4; pfam08448 342108004160 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108004161 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 342108004162 dimer interface [polypeptide binding]; other site 342108004163 phosphorylation site [posttranslational modification] 342108004164 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 342108004165 ATP binding site [chemical binding]; other site 342108004166 Mg2+ binding site [ion binding]; other site 342108004167 G-X-G motif; other site 342108004168 VacJ like lipoprotein; Region: VacJ; cl01073 342108004169 Methyltransferase domain; Region: Methyltransf_24; pfam13578 342108004170 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108004171 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108004172 NAD(P) binding site [chemical binding]; other site 342108004173 active site 342108004174 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108004175 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 342108004176 Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]; Region: WecG; COG1922 342108004177 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 342108004178 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108004179 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 342108004180 Putative catalytic NodB homology domain of gellan lyase and similar proteins; Region: CE4_GLA_like_6s; cd10967 342108004181 putative active site [active] 342108004182 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 342108004183 putative metal binding site [ion binding]; other site 342108004184 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 342108004185 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 342108004186 active site 342108004187 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108004188 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 342108004189 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 342108004190 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108004191 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 342108004192 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 342108004193 Bacterial sugar transferase; Region: Bac_transf; pfam02397 342108004194 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; pfam10082 342108004195 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 342108004196 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 342108004197 active site 342108004198 metal binding site [ion binding]; metal-binding site 342108004199 exopolysaccharide transport protein family; Region: eps_transp_fam; TIGR01005 342108004200 Chain length determinant protein; Region: Wzz; pfam02706 342108004201 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 342108004202 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 342108004203 O-Antigen ligase; Region: Wzy_C; pfam04932 342108004204 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 342108004205 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 342108004206 active site 342108004207 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 342108004208 sulfotransferase; Region: PLN02164 342108004209 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 342108004210 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 342108004211 Coenzyme A binding pocket [chemical binding]; other site 342108004212 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 342108004213 Phage Tail Collar Domain; Region: Collar; pfam07484 342108004214 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 342108004215 Phage Tail Collar Domain; Region: Collar; pfam07484 342108004216 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 342108004217 Phage Tail Collar Domain; Region: Collar; pfam07484 342108004218 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 342108004219 Glutamine amidotransferase domain; Region: GATase_6; pfam13522 342108004220 active site 342108004221 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 342108004222 Ligand Binding Site [chemical binding]; other site 342108004223 Molecular Tunnel; other site 342108004224 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 342108004225 Methyltransferase domain; Region: Methyltransf_11; pfam08241 342108004226 Transglutaminase-like superfamily; Region: Transglut_core3; pfam13471 342108004227 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 342108004228 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108004229 Walker A/P-loop; other site 342108004230 ATP binding site [chemical binding]; other site 342108004231 Q-loop/lid; other site 342108004232 ABC transporter signature motif; other site 342108004233 Walker B; other site 342108004234 D-loop; other site 342108004235 H-loop/switch region; other site 342108004236 Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair]; Region: SPS1; COG0515 342108004237 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 342108004238 substrate binding site [chemical binding]; other site 342108004239 activation loop (A-loop); other site 342108004240 AAA ATPase domain; Region: AAA_16; pfam13191 342108004241 Predicted ATPase [General function prediction only]; Region: COG3899 342108004242 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 342108004243 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 342108004244 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 342108004245 PAS domain; Region: PAS_9; pfam13426 342108004246 putative active site [active] 342108004247 heme pocket [chemical binding]; other site 342108004248 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 342108004249 ATP binding site [chemical binding]; other site 342108004250 Mg2+ binding site [ion binding]; other site 342108004251 G-X-G motif; other site 342108004252 HAMP domain; Region: HAMP; pfam00672 342108004253 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108004254 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108004255 metal binding site [ion binding]; metal-binding site 342108004256 active site 342108004257 I-site; other site 342108004258 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 342108004259 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 342108004260 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 342108004261 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 342108004262 NADP binding site [chemical binding]; other site 342108004263 active site 342108004264 putative substrate binding site [chemical binding]; other site 342108004265 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 342108004266 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 342108004267 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 342108004268 Walker A/P-loop; other site 342108004269 ATP binding site [chemical binding]; other site 342108004270 Q-loop/lid; other site 342108004271 ABC transporter signature motif; other site 342108004272 Walker B; other site 342108004273 D-loop; other site 342108004274 H-loop/switch region; other site 342108004275 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 342108004276 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 342108004277 Walker A/P-loop; other site 342108004278 ATP binding site [chemical binding]; other site 342108004279 Q-loop/lid; other site 342108004280 ABC transporter signature motif; other site 342108004281 Walker B; other site 342108004282 D-loop; other site 342108004283 H-loop/switch region; other site 342108004284 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 342108004285 TM-ABC transporter signature motif; other site 342108004286 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 342108004287 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 342108004288 TM-ABC transporter signature motif; other site 342108004289 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 342108004290 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_Arsenic_SBP_like; cd06330 342108004291 putative ligand binding site [chemical binding]; other site 342108004292 Amino acid synthesis; Region: AA_synth; pfam06684 342108004293 Amino acid synthesis; Region: AA_synth; pfam06684 342108004294 hypothetical protein; Provisional; Region: PRK04334 342108004295 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 342108004296 selenium-dependent molybdenum hydroxylase 1; Region: Se_dep_Molyb_1; TIGR03311 342108004297 catalytic loop [active] 342108004298 iron binding site [ion binding]; other site 342108004299 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 342108004300 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 342108004301 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 342108004302 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 342108004303 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 342108004304 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 342108004305 MarR family; Region: MarR_2; pfam12802 342108004306 Amidohydrolase; Region: Amidohydro_5; pfam13594 342108004307 Amidohydrolase; Region: Amidohydro_4; pfam13147 342108004308 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; cd01292 342108004309 active site 342108004310 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 342108004311 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 342108004312 CoA-transferase family III; Region: CoA_transf_3; pfam02515 342108004313 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 342108004314 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; smart00790 342108004315 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 342108004316 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 342108004317 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 342108004318 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 342108004319 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 342108004320 active site 342108004321 DNA binding site [nucleotide binding] 342108004322 Int/Topo IB signature motif; other site 342108004323 Helix-turn-helix domain; Region: HTH_17; pfam12728 342108004324 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 342108004325 RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_I; cd01646 342108004326 putative active site [active] 342108004327 putative NTP binding site [chemical binding]; other site 342108004328 putative nucleic acid binding site [nucleotide binding]; other site 342108004329 Fibrobacter succinogenes major domain (Fib_succ_major); Region: Fib_succ_major; cl09821 342108004330 DNA polymerase III gamma and tau subunits C terminal; Region: DUF3646; pfam12362 342108004331 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 342108004332 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 342108004333 dimer interface [polypeptide binding]; other site 342108004334 ssDNA binding site [nucleotide binding]; other site 342108004335 tetramer (dimer of dimers) interface [polypeptide binding]; other site 342108004336 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 342108004337 DNA binding residues [nucleotide binding] 342108004338 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 342108004339 ParB-like nuclease domain; Region: ParB; smart00470 342108004340 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 342108004341 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 342108004342 non-specific DNA binding site [nucleotide binding]; other site 342108004343 salt bridge; other site 342108004344 sequence-specific DNA binding site [nucleotide binding]; other site 342108004345 DNA primase, catalytic core; Region: dnaG; TIGR01391 342108004346 CHC2 zinc finger; Region: zf-CHC2; pfam01807 342108004347 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 342108004348 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 342108004349 active site 342108004350 metal binding site [ion binding]; metal-binding site 342108004351 interdomain interaction site; other site 342108004352 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 342108004353 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 342108004354 Putative phage tail protein; Region: Phage-tail_3; pfam13550 342108004355 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 342108004356 catalytic residues [active] 342108004357 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 342108004358 trimer interface [polypeptide binding]; other site 342108004359 active site 342108004360 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 342108004361 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; COG3281 342108004362 Predicted kinase [General function prediction only]; Region: COG0645 342108004363 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 342108004364 active site 342108004365 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 342108004366 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 342108004367 Ligand Binding Site [chemical binding]; other site 342108004368 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 342108004369 ADP-ribose binding site [chemical binding]; other site 342108004370 dimer interface [polypeptide binding]; other site 342108004371 active site 342108004372 nudix motif; other site 342108004373 metal binding site [ion binding]; metal-binding site 342108004374 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 342108004375 catalytic core [active] 342108004376 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 342108004377 diiron binding motif [ion binding]; other site 342108004378 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 342108004379 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 342108004380 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 342108004381 PAS domain; Region: PAS_9; pfam13426 342108004382 putative active site [active] 342108004383 heme pocket [chemical binding]; other site 342108004384 PAS domain S-box; Region: sensory_box; TIGR00229 342108004385 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 342108004386 putative active site [active] 342108004387 heme pocket [chemical binding]; other site 342108004388 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108004389 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108004390 metal binding site [ion binding]; metal-binding site 342108004391 active site 342108004392 I-site; other site 342108004393 Domain of unknown function (DUF1476); Region: DUF1476; pfam07345 342108004394 NRDE protein; Region: NRDE; cl01315 342108004395 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108004396 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 342108004397 dimer interface [polypeptide binding]; other site 342108004398 putative CheW interface [polypeptide binding]; other site 342108004399 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 342108004400 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 342108004401 ATP binding site [chemical binding]; other site 342108004402 active site 342108004403 substrate binding site [chemical binding]; other site 342108004404 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; pfam02700 342108004405 PAS domain; Region: PAS; smart00091 342108004406 putative active site [active] 342108004407 heme pocket [chemical binding]; other site 342108004408 exonuclease, DNA polymerase III, epsilon subunit family; Region: dnaq; TIGR00573 342108004409 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 342108004410 active site 342108004411 catalytic site [active] 342108004412 substrate binding site [chemical binding]; other site 342108004413 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 342108004414 FOG: CBS domain [General function prediction only]; Region: COG0517 342108004415 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 342108004416 metal binding triad; other site 342108004417 Putative nucleotidyltransferase substrate binding domain; Region: DUF294_C; pfam10335 342108004418 Protein of unknown function, DUF485; Region: DUF485; pfam04341 342108004419 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 342108004420 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 342108004421 Na binding site [ion binding]; other site 342108004422 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 342108004423 Hemerythrin; Region: Hemerythrin; cd12107 342108004424 Fe binding site [ion binding]; other site 342108004425 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 342108004426 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 342108004427 putative NAD(P) binding site [chemical binding]; other site 342108004428 benzoate-CoA ligase family; Region: benz_CoA_lig; TIGR02262 342108004429 Benzoate CoA ligase (BCL) and similar adenylate forming enzymes; Region: BCL_like; cd05919 342108004430 dimer interface [polypeptide binding]; other site 342108004431 acyl-activating enzyme (AAE) consensus motif; other site 342108004432 putative active site [active] 342108004433 putative AMP binding site [chemical binding]; other site 342108004434 putative CoA binding site [chemical binding]; other site 342108004435 chemical substrate binding site [chemical binding]; other site 342108004436 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 342108004437 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 342108004438 putative ligand binding site [chemical binding]; other site 342108004439 Transcriptional regulators [Transcription]; Region: FadR; COG2186 342108004440 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 342108004441 DNA-binding site [nucleotide binding]; DNA binding site 342108004442 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 342108004443 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 342108004444 domain interfaces; other site 342108004445 active site 342108004446 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108004447 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108004448 dimer interface [polypeptide binding]; other site 342108004449 putative CheW interface [polypeptide binding]; other site 342108004450 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 342108004451 global nitrogen regulator NtcA, cyanobacterial; Region: NtcA_cyano; TIGR03697 342108004452 ligand binding site [chemical binding]; other site 342108004453 flexible hinge region; other site 342108004454 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 342108004455 non-specific DNA interactions [nucleotide binding]; other site 342108004456 DNA binding site [nucleotide binding] 342108004457 sequence specific DNA binding site [nucleotide binding]; other site 342108004458 putative cAMP binding site [chemical binding]; other site 342108004459 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 342108004460 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 342108004461 Walker A motif; other site 342108004462 ATP binding site [chemical binding]; other site 342108004463 Walker B motif; other site 342108004464 arginine finger; other site 342108004465 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 342108004466 Walker A motif; other site 342108004467 ATP binding site [chemical binding]; other site 342108004468 Walker B motif; other site 342108004469 arginine finger; other site 342108004470 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 342108004471 Nitrogen fixation protein NifW; Region: NifW; pfam03206 342108004472 homocitrate synthase NifV; Region: nifV_homocitr; TIGR02660 342108004473 Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain; Region: DRE_TIM_NifV; cd07939 342108004474 active site 342108004475 catalytic residues [active] 342108004476 metal binding site [ion binding]; metal-binding site 342108004477 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 342108004478 NifQ; Region: NifQ; pfam04891 342108004479 ferredoxin III, nif-specific; Region: fdxN_nitrog; TIGR02936 342108004480 probable nitrogen fixation protein; Region: TIGR02935 342108004481 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 342108004482 Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the...; Region: Nitrogenase_NifN_1; cd01966 342108004483 Nitrogenase component 1 type Oxidoreductase; Region: Oxidored_nitro; pfam00148 342108004484 nitrogenase molybdenum-cofactor biosynthesis protein NifE; Provisional; Region: PRK14478 342108004485 nitrogenase molybdenum-iron cofactor biosynthesis protein NifE; Region: nifE; TIGR01283 342108004486 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 342108004487 Coenzyme A binding pocket [chemical binding]; other site 342108004488 nitrogenase molybdenum-iron protein beta chain; Region: nifK; TIGR01286 342108004489 Domain of unknown function (DUF3364); Region: DUF3364; pfam11844 342108004490 Nitrogenase_MoFe_beta: Nitrogenase MoFe protein, beta subunit. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Molybdenum (Mo-) nitrogenase is the most widespread and best characterized of these systems; Region: Nitrogenase_MoFe_beta; cd01974 342108004491 MoFe protein beta/alpha subunit interactions; other site 342108004492 Beta subunit P cluster binding residues; other site 342108004493 MoFe protein beta subunit/Fe protein contacts; other site 342108004494 MoFe protein dimer/ dimer interactions; other site 342108004495 Nitrogenase molybdenum-iron protein, alpha and beta chains [Energy production and conversion]; Region: NifD; COG2710 342108004496 Nitrogenase_MoFe_alpha_II: Nitrogenase MoFe protein, beta subunit. A group of proteins similar to the alpha subunit of the MoFe protein of the molybdenum (Mo-) nitrogenase. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to...; Region: Nitrogenase_MoFe_alpha; cd01976 342108004497 MoFe protein alpha/beta subunit interactions; other site 342108004498 Alpha subunit P cluster binding residues; other site 342108004499 FeMoco binding residues [chemical binding]; other site 342108004500 MoFe protein alpha subunit/Fe protein contacts; other site 342108004501 MoFe protein dimer/ dimer interactions; other site 342108004502 nitrogenase reductase; Reviewed; Region: nifH; PRK13234 342108004503 NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the...; Region: NifH; cd02040 342108004504 Nucleotide-binding sites [chemical binding]; other site 342108004505 Walker A motif; other site 342108004506 Switch I region of nucleotide binding site; other site 342108004507 Fe4S4 binding sites [ion binding]; other site 342108004508 Switch II region of nucleotide binding site; other site 342108004509 Dinitrogenase reductase ADP-ribosyltransferase (DRAT); Region: DRAT; pfam07357 342108004510 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 342108004511 Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also...; Region: ArsC_15kD; cd03033 342108004512 putative catalytic residues [active] 342108004513 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 342108004514 dimerization interface [polypeptide binding]; other site 342108004515 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108004516 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108004517 dimer interface [polypeptide binding]; other site 342108004518 putative CheW interface [polypeptide binding]; other site 342108004519 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 342108004520 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 342108004521 catalytic loop [active] 342108004522 iron binding site [ion binding]; other site 342108004523 SIR2-like domain; Region: SIR2_2; pfam13289 342108004524 NifT/FixU protein; Region: NifT; pfam06988 342108004525 NifZ domain; Region: NifZ; pfam04319 342108004526 nitrogenase cofactor biosynthesis protein NifB; Region: nifB; TIGR01290 342108004527 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 342108004528 FeS/SAM binding site; other site 342108004529 NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of...; Region: NifB; cd00852 342108004530 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 342108004531 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 342108004532 GatB domain; Region: GatB_Yqey; smart00845 342108004533 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 342108004534 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 342108004535 LytTr DNA-binding domain; Region: LytTR; smart00850 342108004536 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 342108004537 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 342108004538 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 342108004539 Tetramer interface [polypeptide binding]; other site 342108004540 active site 342108004541 FMN-binding site [chemical binding]; other site 342108004542 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08159 342108004543 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 342108004544 NAD binding site [chemical binding]; other site 342108004545 homotetramer interface [polypeptide binding]; other site 342108004546 homodimer interface [polypeptide binding]; other site 342108004547 substrate binding site [chemical binding]; other site 342108004548 active site 342108004549 FOG: CBS domain [General function prediction only]; Region: COG0517 342108004550 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 342108004551 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 342108004552 DNA-binding site [nucleotide binding]; DNA binding site 342108004553 RNA-binding motif; other site 342108004554 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 342108004555 active site residue [active] 342108004556 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 342108004557 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 342108004558 DNA binding residues [nucleotide binding] 342108004559 signal peptide peptidase SppA, 67K type; Region: SppA_67K; TIGR00705 342108004560 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 342108004561 tandem repeat interface [polypeptide binding]; other site 342108004562 oligomer interface [polypeptide binding]; other site 342108004563 active site residues [active] 342108004564 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 342108004565 tandem repeat interface [polypeptide binding]; other site 342108004566 oligomer interface [polypeptide binding]; other site 342108004567 active site residues [active] 342108004568 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 342108004569 classical (c) SDRs; Region: SDR_c; cd05233 342108004570 NAD(P) binding site [chemical binding]; other site 342108004571 active site 342108004572 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 342108004573 active site 342108004574 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 342108004575 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 342108004576 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 342108004577 S-adenosylmethionine binding site [chemical binding]; other site 342108004578 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 342108004579 GSH binding site [chemical binding]; other site 342108004580 catalytic residues [active] 342108004581 nitrilase; Region: PLN02798 342108004582 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 342108004583 putative active site [active] 342108004584 catalytic triad [active] 342108004585 dimer interface [polypeptide binding]; other site 342108004586 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108004587 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 342108004588 S-adenosylmethionine binding site [chemical binding]; other site 342108004589 Protein of unknown function (DUF1178); Region: DUF1178; pfam06676 342108004590 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 342108004591 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 342108004592 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 342108004593 aspartate kinase; Reviewed; Region: PRK06635 342108004594 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 342108004595 putative nucleotide binding site [chemical binding]; other site 342108004596 putative catalytic residues [active] 342108004597 putative Mg ion binding site [ion binding]; other site 342108004598 putative aspartate binding site [chemical binding]; other site 342108004599 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 342108004600 putative allosteric regulatory site; other site 342108004601 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 342108004602 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 342108004603 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 342108004604 FMN binding site [chemical binding]; other site 342108004605 substrate binding site [chemical binding]; other site 342108004606 putative catalytic residue [active] 342108004607 Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; Region: PtsP; COG3605 342108004608 GAF domain; Region: GAF; pfam01590 342108004609 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 342108004610 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 342108004611 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 342108004612 Helix-turn-helix domain; Region: HTH_25; pfam13413 342108004613 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 342108004614 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 342108004615 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 342108004616 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 342108004617 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 342108004618 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 342108004619 dimer interface [polypeptide binding]; other site 342108004620 motif 1; other site 342108004621 active site 342108004622 motif 2; other site 342108004623 motif 3; other site 342108004624 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 342108004625 anticodon binding site; other site 342108004626 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 342108004627 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 342108004628 tRNA; other site 342108004629 putative tRNA binding site [nucleotide binding]; other site 342108004630 putative NADP binding site [chemical binding]; other site 342108004631 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 342108004632 peptide chain release factor 1; Validated; Region: prfA; PRK00591 342108004633 This domain is found in peptide chain release factors; Region: PCRF; smart00937 342108004634 RF-1 domain; Region: RF-1; pfam00472 342108004635 protein-(glutamine-N5) methyltransferase, release factor-specific; Region: RF_mod_PrmC; TIGR03534 342108004636 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 342108004637 Hemerythrin family; Region: Hemerythrin-like; cl15774 342108004638 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 342108004639 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 342108004640 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 342108004641 Predicted transcriptional regulator [Transcription]; Region: COG2378 342108004642 WYL domain; Region: WYL; pfam13280 342108004643 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 342108004644 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cd00397 342108004645 active site 342108004646 DNA binding site [nucleotide binding] 342108004647 Int/Topo IB signature motif; other site 342108004648 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 342108004649 endonuclease subunit; Provisional; Region: 46; PHA02562 342108004650 Meiotically up-regulated gene 113; Region: MUG113; pfam13455 342108004651 HypX protein, N-terminal hydrolase domain; Region: FMT_core_HypX_N; cd08650 342108004652 putative active site [active] 342108004653 putative substrate binding site [chemical binding]; other site 342108004654 putative cosubstrate binding site; other site 342108004655 catalytic site [active] 342108004656 C-terminal subdomain of the Formyltransferase-like domain found in HypX-like proteins; Region: FMT_C_HypX; cd08701 342108004657 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 342108004658 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 342108004659 substrate binding site [chemical binding]; other site 342108004660 oxyanion hole (OAH) forming residues; other site 342108004661 trimer interface [polypeptide binding]; other site 342108004662 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 342108004663 dimerization interface [polypeptide binding]; other site 342108004664 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 342108004665 ATP binding site [chemical binding]; other site 342108004666 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 342108004667 Domain of unknown function (DUF4160); Region: DUF4160; pfam13711 342108004668 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 342108004669 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 342108004670 HupF/HypC family; Region: HupF_HypC; pfam01455 342108004671 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 342108004672 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 342108004673 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 342108004674 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 342108004675 Hydrogenase expression/synthesis hypA family; Region: HypA; cl17671 342108004676 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 342108004677 HupF/HypC family; Region: HupF_HypC; pfam01455 342108004678 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 342108004679 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 342108004680 putative substrate-binding site; other site 342108004681 nickel binding site [ion binding]; other site 342108004682 hydrogenase 2 large subunit; Provisional; Region: PRK10467 342108004683 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 342108004684 putative hydrogenase 2 b cytochrome subunit; Provisional; Region: PRK10881 342108004685 hydrogenase 2 protein HybA; Provisional; Region: PRK10882 342108004686 4Fe-4S binding domain; Region: Fer4_6; pfam12837 342108004687 Tat (twin-arginine translocation) pathway signal sequence; Region: TAT_signal_seq; TIGR01409 342108004688 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 342108004689 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 342108004690 CoA-transferase family III; Region: CoA_transf_3; pfam02515 342108004691 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 342108004692 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 342108004693 putative substrate translocation pore; other site 342108004694 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 342108004695 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 342108004696 active site 342108004697 phosphorylation site [posttranslational modification] 342108004698 intermolecular recognition site; other site 342108004699 dimerization interface [polypeptide binding]; other site 342108004700 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 342108004701 Walker A motif; other site 342108004702 ATP binding site [chemical binding]; other site 342108004703 Walker B motif; other site 342108004704 arginine finger; other site 342108004705 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 342108004706 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 342108004707 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 342108004708 dimer interface [polypeptide binding]; other site 342108004709 phosphorylation site [posttranslational modification] 342108004710 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 342108004711 ATP binding site [chemical binding]; other site 342108004712 G-X-G motif; other site 342108004713 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 342108004714 Septum formation initiator; Region: DivIC; pfam04977 342108004715 Inward rectifier potassium channel; Region: IRK; pfam01007 342108004716 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 342108004717 SBF-like CPA transporter family (DUF4137); Region: DUF4137; pfam13593 342108004718 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 342108004719 metal binding site 2 [ion binding]; metal-binding site 342108004720 putative DNA binding helix; other site 342108004721 metal binding site 1 [ion binding]; metal-binding site 342108004722 dimer interface [polypeptide binding]; other site 342108004723 structural Zn2+ binding site [ion binding]; other site 342108004724 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 342108004725 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 342108004726 heme binding site [chemical binding]; other site 342108004727 ferroxidase pore; other site 342108004728 ferroxidase diiron center [ion binding]; other site 342108004729 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 342108004730 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 342108004731 heme binding site [chemical binding]; other site 342108004732 ferroxidase pore; other site 342108004733 ferroxidase diiron center [ion binding]; other site 342108004734 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 342108004735 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108004736 putative substrate translocation pore; other site 342108004737 glutathione reductase; Validated; Region: PRK06116 342108004738 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 342108004739 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108004740 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 342108004741 Radical SAM superfamily; Region: Radical_SAM; pfam04055 342108004742 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 342108004743 FeS/SAM binding site; other site 342108004744 amidase; Provisional; Region: PRK08310 342108004745 indole-3-acetamide amidohydrolase; Region: PLN02722 342108004746 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 342108004747 putative active site [active] 342108004748 heme pocket [chemical binding]; other site 342108004749 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 342108004750 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 342108004751 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 342108004752 putative ligand binding site [chemical binding]; other site 342108004753 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 342108004754 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 342108004755 TM-ABC transporter signature motif; other site 342108004756 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 342108004757 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 342108004758 TM-ABC transporter signature motif; other site 342108004759 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 342108004760 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 342108004761 Walker A/P-loop; other site 342108004762 ATP binding site [chemical binding]; other site 342108004763 Q-loop/lid; other site 342108004764 ABC transporter signature motif; other site 342108004765 Walker B; other site 342108004766 D-loop; other site 342108004767 H-loop/switch region; other site 342108004768 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 342108004769 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 342108004770 Walker A/P-loop; other site 342108004771 ATP binding site [chemical binding]; other site 342108004772 Q-loop/lid; other site 342108004773 ABC transporter signature motif; other site 342108004774 Walker B; other site 342108004775 D-loop; other site 342108004776 H-loop/switch region; other site 342108004777 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 342108004778 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 342108004779 Ferredoxin [Energy production and conversion]; Region: COG1146 342108004780 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 342108004781 pyruvate ferredoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK08367 342108004782 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 342108004783 dimer interface [polypeptide binding]; other site 342108004784 PYR/PP interface [polypeptide binding]; other site 342108004785 TPP binding site [chemical binding]; other site 342108004786 substrate binding site [chemical binding]; other site 342108004787 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 342108004788 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 342108004789 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108004790 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 342108004791 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 342108004792 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 342108004793 2-ketoisovalerate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11864 342108004794 Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea...; Region: TPP_PFOR_porB_like; cd03376 342108004795 TPP-binding site [chemical binding]; other site 342108004796 putative dimer interface [polypeptide binding]; other site 342108004797 Iron permease FTR1 family; Region: FTR1; cl00475 342108004798 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 342108004799 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108004800 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 342108004801 ligand binding site [chemical binding]; other site 342108004802 flexible hinge region; other site 342108004803 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108004804 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 342108004805 ligand binding site [chemical binding]; other site 342108004806 Hemerythrin; Region: Hemerythrin; cd12107 342108004807 Fe binding site [ion binding]; other site 342108004808 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 342108004809 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 342108004810 substrate-cofactor binding pocket; other site 342108004811 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108004812 catalytic residue [active] 342108004813 aminotransferase; Provisional; Region: PRK06105 342108004814 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 342108004815 inhibitor-cofactor binding pocket; inhibition site 342108004816 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108004817 catalytic residue [active] 342108004818 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 342108004819 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 342108004820 Walker A motif; other site 342108004821 ATP binding site [chemical binding]; other site 342108004822 Walker B motif; other site 342108004823 arginine finger; other site 342108004824 Peptidase family M41; Region: Peptidase_M41; pfam01434 342108004825 Helix-turn-helix domain; Region: HTH_17; pfam12728 342108004826 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 342108004827 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 342108004828 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 342108004829 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 342108004830 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 342108004831 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 342108004832 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 342108004833 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 342108004834 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 342108004835 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 342108004836 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 342108004837 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 342108004838 PQQ-like domain; Region: PQQ_2; pfam13360 342108004839 Trp docking motif [polypeptide binding]; other site 342108004840 active site 342108004841 FOG: WD40-like repeat [Function unknown]; Region: COG1520 342108004842 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 342108004843 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108004844 Zn2+ binding site [ion binding]; other site 342108004845 Mg2+ binding site [ion binding]; other site 342108004846 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 342108004847 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 342108004848 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 342108004849 FliG C-terminal domain; Region: FliG_C; pfam01706 342108004850 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 342108004851 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 342108004852 FliG C-terminal domain; Region: FliG_C; pfam01706 342108004853 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 342108004854 Bacterial SH3 domain; Region: SH3_3; pfam08239 342108004855 PIN domain of the VapC-like Sll0205 protein and homologs; Region: PIN_Sll0205; cd09872 342108004856 putative active site [active] 342108004857 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 342108004858 TPR repeat; Region: TPR_11; pfam13414 342108004859 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 342108004860 binding surface 342108004861 TPR motif; other site 342108004862 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 342108004863 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 342108004864 Uncharacterized conserved protein [Function unknown]; Region: COG1262 342108004865 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 342108004866 Uncharacterized conserved protein [Function unknown]; Region: COG1262 342108004867 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 342108004868 Domain of unknown function (DUF4384); Region: DUF4384; pfam14326 342108004869 Putative bacterial lipoprotein (DUF799); Region: DUF799; cl01813 342108004870 Uncharacterized conserved protein [Function unknown]; Region: COG1262 342108004871 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 342108004872 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 342108004873 Sel1-like repeats; Region: SEL1; smart00671 342108004874 Caspase domain; Region: Peptidase_C14; pfam00656 342108004875 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 342108004876 active site 342108004877 DNA binding site [nucleotide binding] 342108004878 Int/Topo IB signature motif; other site 342108004879 Transposase; Region: HTH_Tnp_1; pfam01527 342108004880 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108004881 HTH-like domain; Region: HTH_21; pfam13276 342108004882 Integrase core domain; Region: rve; pfam00665 342108004883 Integrase core domain; Region: rve_3; pfam13683 342108004884 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108004885 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 342108004886 non-specific DNA binding site [nucleotide binding]; other site 342108004887 salt bridge; other site 342108004888 sequence-specific DNA binding site [nucleotide binding]; other site 342108004889 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 342108004890 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 342108004891 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 342108004892 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 342108004893 sequence-specific DNA binding site [nucleotide binding]; other site 342108004894 salt bridge; other site 342108004895 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 342108004896 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; pfam10124 342108004897 Prophage tail length tape measure protein; Region: TMP_2; pfam06791 342108004898 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108004899 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 342108004900 sequence-specific DNA binding site [nucleotide binding]; other site 342108004901 salt bridge; other site 342108004902 ParB-like nuclease domain; Region: ParB; smart00470 342108004903 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 342108004904 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 342108004905 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 342108004906 DNA binding site [nucleotide binding] 342108004907 substrate interaction site [chemical binding]; other site 342108004908 Protein of unknown function (DUF1018); Region: DUF1018; pfam06252 342108004909 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 342108004910 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 342108004911 N-acetyl-D-glucosamine binding site [chemical binding]; other site 342108004912 catalytic residue [active] 342108004913 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 342108004914 Protein of unknown function (DUF3486); Region: DUF3486; pfam11985 342108004915 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 342108004916 Protein of unknown function (DUF935); Region: DUF935; pfam06074 342108004917 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 342108004918 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 342108004919 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 342108004920 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; pfam10124 342108004921 Protein of unknown function (DUF1320); Region: DUF1320; pfam07030 342108004922 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 342108004923 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 342108004924 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; pfam09343 342108004925 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 342108004926 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 342108004927 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 342108004928 NlpC/P60 family; Region: NLPC_P60; cl17555 342108004929 Putative phage tail protein; Region: Phage-tail_3; pfam13550 342108004930 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 342108004931 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 342108004932 DNA binding site [nucleotide binding] 342108004933 active site 342108004934 Int/Topo IB signature motif; other site 342108004935 catalytic residues [active] 342108004936 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 342108004937 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 342108004938 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108004939 catalytic residue [active] 342108004940 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 342108004941 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 342108004942 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 342108004943 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 342108004944 trimer interface [polypeptide binding]; other site 342108004945 putative metal binding site [ion binding]; other site 342108004946 Probable N-acetyl-gamma-glutamyl-phosphate reductase; Region: PLN02968 342108004947 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 342108004948 modified peptide precursor CbpA; Region: cobo_pep; TIGR04164 342108004949 peptide-modifying radical SAM enzyme CbpB; Region: rSAM_cobopep; TIGR04163 342108004950 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 342108004951 FeS/SAM binding site; other site 342108004952 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 342108004953 Domain of unknown function (DUF4189); Region: DUF4189; pfam13827 342108004954 Protein of unknown function (DUF3897); Region: DUF3897; cl17494 342108004955 Putative periplasmic lipoprotein; Region: DUF1425; cl12345 342108004956 putative dimer interface [polypeptide binding]; other site 342108004957 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 342108004958 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 342108004959 Response regulator receiver domain; Region: Response_reg; pfam00072 342108004960 active site 342108004961 phosphorylation site [posttranslational modification] 342108004962 intermolecular recognition site; other site 342108004963 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108004964 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108004965 metal binding site [ion binding]; metal-binding site 342108004966 active site 342108004967 I-site; other site 342108004968 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 342108004969 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 342108004970 Walker A/P-loop; other site 342108004971 ATP binding site [chemical binding]; other site 342108004972 Q-loop/lid; other site 342108004973 ABC transporter signature motif; other site 342108004974 Walker B; other site 342108004975 D-loop; other site 342108004976 H-loop/switch region; other site 342108004977 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 342108004978 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 342108004979 Walker A/P-loop; other site 342108004980 ATP binding site [chemical binding]; other site 342108004981 Q-loop/lid; other site 342108004982 ABC transporter signature motif; other site 342108004983 Walker B; other site 342108004984 D-loop; other site 342108004985 H-loop/switch region; other site 342108004986 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 342108004987 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 342108004988 TM-ABC transporter signature motif; other site 342108004989 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 342108004990 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 342108004991 TM-ABC transporter signature motif; other site 342108004992 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 342108004993 HAMP domain; Region: HAMP; pfam00672 342108004994 dimerization interface [polypeptide binding]; other site 342108004995 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108004996 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108004997 dimer interface [polypeptide binding]; other site 342108004998 putative CheW interface [polypeptide binding]; other site 342108004999 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 342108005000 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 342108005001 metal-binding site [ion binding] 342108005002 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 342108005003 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 342108005004 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 342108005005 DNA binding residues [nucleotide binding] 342108005006 dimer interface [polypeptide binding]; other site 342108005007 copper binding site [ion binding]; other site 342108005008 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 342108005009 NodB motif; other site 342108005010 putative active site [active] 342108005011 putative catalytic site [active] 342108005012 Zn binding site [ion binding]; other site 342108005013 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 342108005014 metal-binding site [ion binding] 342108005015 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 342108005016 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 342108005017 anthranilate synthase component I; Provisional; Region: PRK13573 342108005018 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 342108005019 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 342108005020 periplasmic folding chaperone; Provisional; Region: PRK10788 342108005021 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 342108005022 DsrE/DsrF/DrsH-like family; Region: DrsE_2; cl17453 342108005023 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 342108005024 CPxP motif; other site 342108005025 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 342108005026 triosephosphate isomerase; Provisional; Region: PRK14567 342108005027 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 342108005028 substrate binding site [chemical binding]; other site 342108005029 dimer interface [polypeptide binding]; other site 342108005030 catalytic triad [active] 342108005031 Preprotein translocase SecG subunit; Region: SecG; cl09123 342108005032 CTP synthetase; Validated; Region: pyrG; PRK05380 342108005033 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 342108005034 Catalytic site [active] 342108005035 active site 342108005036 UTP binding site [chemical binding]; other site 342108005037 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 342108005038 active site 342108005039 putative oxyanion hole; other site 342108005040 catalytic triad [active] 342108005041 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 342108005042 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 342108005043 enolase; Provisional; Region: eno; PRK00077 342108005044 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 342108005045 dimer interface [polypeptide binding]; other site 342108005046 metal binding site [ion binding]; metal-binding site 342108005047 substrate binding pocket [chemical binding]; other site 342108005048 Methyltransferase domain; Region: Methyltransf_11; pfam08241 342108005049 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 342108005050 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 342108005051 substrate binding pocket [chemical binding]; other site 342108005052 membrane-bound complex binding site; other site 342108005053 hinge residues; other site 342108005054 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 342108005055 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 342108005056 dimer interface [polypeptide binding]; other site 342108005057 phosphorylation site [posttranslational modification] 342108005058 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 342108005059 ATP binding site [chemical binding]; other site 342108005060 Mg2+ binding site [ion binding]; other site 342108005061 G-X-G motif; other site 342108005062 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 342108005063 dimerization interface [polypeptide binding]; other site 342108005064 putative DNA binding site [nucleotide binding]; other site 342108005065 putative Zn2+ binding site [ion binding]; other site 342108005066 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 342108005067 Low molecular weight phosphatase family; Region: LMWPc; cd00115 342108005068 active site 342108005069 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 342108005070 Low molecular weight phosphatase family; Region: LMWPc; cd00115 342108005071 active site 342108005072 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 342108005073 Sodium Bile acid symporter family; Region: SBF; cl17470 342108005074 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 342108005075 ArsC family; Region: ArsC; pfam03960 342108005076 catalytic residues [active] 342108005077 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 342108005078 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 342108005079 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 342108005080 P loop; other site 342108005081 Nucleotide binding site [chemical binding]; other site 342108005082 DTAP/Switch II; other site 342108005083 Switch I; other site 342108005084 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 342108005085 DTAP/Switch II; other site 342108005086 Switch I; other site 342108005087 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 342108005088 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 342108005089 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 342108005090 DNA binding residues [nucleotide binding] 342108005091 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 342108005092 Rubrerythrin [Energy production and conversion]; Region: COG1592 342108005093 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 342108005094 binuclear metal center [ion binding]; other site 342108005095 Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either...; Region: rubredoxin_like; cl00202 342108005096 iron binding site [ion binding]; other site 342108005097 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 342108005098 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 342108005099 active site 342108005100 phosphorylation site [posttranslational modification] 342108005101 intermolecular recognition site; other site 342108005102 dimerization interface [polypeptide binding]; other site 342108005103 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108005104 Zn2+ binding site [ion binding]; other site 342108005105 Mg2+ binding site [ion binding]; other site 342108005106 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 342108005107 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 342108005108 active site 342108005109 phosphorylation site [posttranslational modification] 342108005110 intermolecular recognition site; other site 342108005111 dimerization interface [polypeptide binding]; other site 342108005112 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108005113 Zn2+ binding site [ion binding]; other site 342108005114 Mg2+ binding site [ion binding]; other site 342108005115 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 342108005116 PAS domain; Region: PAS_9; pfam13426 342108005117 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 342108005118 putative active site [active] 342108005119 heme pocket [chemical binding]; other site 342108005120 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 342108005121 PAS domain; Region: PAS_9; pfam13426 342108005122 putative active site [active] 342108005123 heme pocket [chemical binding]; other site 342108005124 PAS domain S-box; Region: sensory_box; TIGR00229 342108005125 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 342108005126 dimer interface [polypeptide binding]; other site 342108005127 phosphorylation site [posttranslational modification] 342108005128 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 342108005129 ATP binding site [chemical binding]; other site 342108005130 Mg2+ binding site [ion binding]; other site 342108005131 G-X-G motif; other site 342108005132 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108005133 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 342108005134 active site 342108005135 phosphorylation site [posttranslational modification] 342108005136 intermolecular recognition site; other site 342108005137 dimerization interface [polypeptide binding]; other site 342108005138 Response regulator receiver domain; Region: Response_reg; pfam00072 342108005139 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 342108005140 active site 342108005141 phosphorylation site [posttranslational modification] 342108005142 intermolecular recognition site; other site 342108005143 dimerization interface [polypeptide binding]; other site 342108005144 Hpt domain; Region: Hpt; pfam01627 342108005145 putative binding surface; other site 342108005146 active site 342108005147 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 342108005148 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 342108005149 Inner membrane protein CreD; Region: CreD; pfam06123 342108005150 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 342108005151 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108005152 active site 342108005153 phosphorylation site [posttranslational modification] 342108005154 intermolecular recognition site; other site 342108005155 dimerization interface [polypeptide binding]; other site 342108005156 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 342108005157 DNA binding site [nucleotide binding] 342108005158 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 342108005159 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 342108005160 dimer interface [polypeptide binding]; other site 342108005161 phosphorylation site [posttranslational modification] 342108005162 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 342108005163 ATP binding site [chemical binding]; other site 342108005164 Mg2+ binding site [ion binding]; other site 342108005165 G-X-G motif; other site 342108005166 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 342108005167 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 342108005168 dimer interface [polypeptide binding]; other site 342108005169 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108005170 catalytic residue [active] 342108005171 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream. The vitamin B6 complex comprises pyridoxine, pyridoxal, and pyridoxamine, as well...; Region: CBS_pair_PALP_assoc2; cd04609 342108005172 FOG: CBS domain [General function prediction only]; Region: COG0517 342108005173 Rrf2 family protein; Region: rrf2_super; TIGR00738 342108005174 Transcriptional regulator; Region: Rrf2; pfam02082 342108005175 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 342108005176 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 342108005177 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108005178 catalytic residue [active] 342108005179 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; pfam10087 342108005180 Serine acetyltransferase, N-terminal; Region: SATase_N; smart00971 342108005181 Serine acetyltransferase [Amino acid transport and metabolism]; Region: CysE; COG1045 342108005182 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 342108005183 trimer interface [polypeptide binding]; other site 342108005184 active site 342108005185 substrate binding site [chemical binding]; other site 342108005186 CoA binding site [chemical binding]; other site 342108005187 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 342108005188 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 342108005189 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 342108005190 substrate binding pocket [chemical binding]; other site 342108005191 membrane-bound complex binding site; other site 342108005192 hinge residues; other site 342108005193 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 342108005194 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 342108005195 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 342108005196 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108005197 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 342108005198 ligand binding site [chemical binding]; other site 342108005199 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 342108005200 non-specific DNA interactions [nucleotide binding]; other site 342108005201 DNA binding site [nucleotide binding] 342108005202 sequence specific DNA binding site [nucleotide binding]; other site 342108005203 putative cAMP binding site [chemical binding]; other site 342108005204 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 342108005205 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 342108005206 Walker A/P-loop; other site 342108005207 ATP binding site [chemical binding]; other site 342108005208 Q-loop/lid; other site 342108005209 ABC transporter signature motif; other site 342108005210 Walker B; other site 342108005211 D-loop; other site 342108005212 H-loop/switch region; other site 342108005213 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 342108005214 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 342108005215 dimer interface [polypeptide binding]; other site 342108005216 conserved gate region; other site 342108005217 putative PBP binding loops; other site 342108005218 ABC-ATPase subunit interface; other site 342108005219 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 342108005220 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 342108005221 substrate binding pocket [chemical binding]; other site 342108005222 membrane-bound complex binding site; other site 342108005223 hinge residues; other site 342108005224 NosL; Region: NosL; cl01769 342108005225 Arylsulfotransferase (ASST); Region: Arylsulfotran_2; pfam14269 342108005226 NMT1-like family; Region: NMT1_2; pfam13379 342108005227 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 342108005228 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 342108005229 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 342108005230 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 342108005231 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 342108005232 Walker A/P-loop; other site 342108005233 ATP binding site [chemical binding]; other site 342108005234 Q-loop/lid; other site 342108005235 ABC transporter signature motif; other site 342108005236 Walker B; other site 342108005237 D-loop; other site 342108005238 H-loop/switch region; other site 342108005239 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 342108005240 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 342108005241 conserved cys residue [active] 342108005242 HAMP domain; Region: HAMP; pfam00672 342108005243 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108005244 dimer interface [polypeptide binding]; other site 342108005245 putative CheW interface [polypeptide binding]; other site 342108005246 Response regulator receiver domain; Region: Response_reg; pfam00072 342108005247 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 342108005248 active site 342108005249 phosphorylation site [posttranslational modification] 342108005250 intermolecular recognition site; other site 342108005251 dimerization interface [polypeptide binding]; other site 342108005252 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 342108005253 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 342108005254 active site 342108005255 phosphorylation site [posttranslational modification] 342108005256 intermolecular recognition site; other site 342108005257 dimerization interface [polypeptide binding]; other site 342108005258 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 342108005259 DNA binding residues [nucleotide binding] 342108005260 dimerization interface [polypeptide binding]; other site 342108005261 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 342108005262 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 342108005263 putative active site [active] 342108005264 heme pocket [chemical binding]; other site 342108005265 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 342108005266 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 342108005267 putative active site [active] 342108005268 heme pocket [chemical binding]; other site 342108005269 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 342108005270 dimer interface [polypeptide binding]; other site 342108005271 phosphorylation site [posttranslational modification] 342108005272 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 342108005273 ATP binding site [chemical binding]; other site 342108005274 Mg2+ binding site [ion binding]; other site 342108005275 G-X-G motif; other site 342108005276 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108005277 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 342108005278 active site 342108005279 phosphorylation site [posttranslational modification] 342108005280 intermolecular recognition site; other site 342108005281 dimerization interface [polypeptide binding]; other site 342108005282 PAS domain S-box; Region: sensory_box; TIGR00229 342108005283 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 342108005284 GAF domain; Region: GAF_3; pfam13492 342108005285 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108005286 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 342108005287 dimer interface [polypeptide binding]; other site 342108005288 phosphorylation site [posttranslational modification] 342108005289 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 342108005290 ATP binding site [chemical binding]; other site 342108005291 Mg2+ binding site [ion binding]; other site 342108005292 G-X-G motif; other site 342108005293 Response regulator receiver domain; Region: Response_reg; pfam00072 342108005294 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 342108005295 active site 342108005296 phosphorylation site [posttranslational modification] 342108005297 intermolecular recognition site; other site 342108005298 dimerization interface [polypeptide binding]; other site 342108005299 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 342108005300 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 342108005301 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 342108005302 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 342108005303 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 342108005304 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108005305 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 342108005306 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 342108005307 Protein of unknown function (DUF4255); Region: DUF4255; pfam14065 342108005308 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 342108005309 tail sheath protein; Provisional; Region: 18; PHA02539 342108005310 Phage tail sheath protein FI [General function prediction only]; Region: COG3497 342108005311 T4-like virus tail tube protein gp19; Region: Phage_T4_gp19; pfam06841 342108005312 T4-like virus tail tube protein gp19; Region: Phage_T4_gp19; pfam06841 342108005313 Phage protein D [General function prediction only]; Region: COG3500 342108005314 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 342108005315 Domain of unknown function (DUF4150); Region: DUF4150; pfam13665 342108005316 Gene 25-like lysozyme; Region: GPW_gp25; pfam04965 342108005317 conserved hypothetical protein, phage tail-like region; Region: TIGR02243 342108005318 conserved hypothetical protein, phage tail-like region; Region: TIGR02243 342108005319 conserved hypothetical protein, phage tail-like region; Region: TIGR02243 342108005320 phage tail protein domain; Region: tail_TIGR02242 342108005321 Aspartyl/Asparaginyl beta-hydroxylase; Region: Asp_Arg_Hydrox; cl17820 342108005322 ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]; Region: SpoVK; COG0464 342108005323 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 342108005324 Walker A motif; other site 342108005325 ATP binding site [chemical binding]; other site 342108005326 Walker B motif; other site 342108005327 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 342108005328 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 342108005329 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 342108005330 Soluble P-type ATPase [General function prediction only]; Region: COG4087 342108005331 potassium-transporting ATPase subunit C; Reviewed; Region: PRK00315 342108005332 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 342108005333 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 342108005334 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 342108005335 Ligand Binding Site [chemical binding]; other site 342108005336 GAF domain; Region: GAF_3; pfam13492 342108005337 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 342108005338 dimer interface [polypeptide binding]; other site 342108005339 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 342108005340 ATP binding site [chemical binding]; other site 342108005341 Mg2+ binding site [ion binding]; other site 342108005342 G-X-G motif; other site 342108005343 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108005344 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 342108005345 active site 342108005346 phosphorylation site [posttranslational modification] 342108005347 intermolecular recognition site; other site 342108005348 dimerization interface [polypeptide binding]; other site 342108005349 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 342108005350 DNA binding site [nucleotide binding] 342108005351 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 342108005352 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 342108005353 active site 342108005354 phosphorylation site [posttranslational modification] 342108005355 intermolecular recognition site; other site 342108005356 dimerization interface [polypeptide binding]; other site 342108005357 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 342108005358 Walker A motif; other site 342108005359 ATP binding site [chemical binding]; other site 342108005360 Walker B motif; other site 342108005361 arginine finger; other site 342108005362 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 342108005363 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108005364 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 342108005365 ATP binding site [chemical binding]; other site 342108005366 G-X-G motif; other site 342108005367 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 342108005368 putative NAD(P) binding site [chemical binding]; other site 342108005369 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 342108005370 active site 342108005371 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 342108005372 dimerization interface [polypeptide binding]; other site 342108005373 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 342108005374 PAS domain; Region: PAS_9; pfam13426 342108005375 putative active site [active] 342108005376 heme pocket [chemical binding]; other site 342108005377 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108005378 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108005379 metal binding site [ion binding]; metal-binding site 342108005380 active site 342108005381 I-site; other site 342108005382 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 342108005383 Flagellin N-methylase; Region: FliB; cl00497 342108005384 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3012 342108005385 SEC-C motif; Region: SEC-C; pfam02810 342108005386 SEC-C motif; Region: SEC-C; pfam02810 342108005387 Cytochrome b(N-terminal)/b6/petB; Region: Cytochrom_B_N; pfam00033 342108005388 Transposase; Region: HTH_Tnp_1; pfam01527 342108005389 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108005390 HTH-like domain; Region: HTH_21; pfam13276 342108005391 Integrase core domain; Region: rve; pfam00665 342108005392 Integrase core domain; Region: rve_3; pfam13683 342108005393 Bacteriophage lambda integrase, N-terminal domain; Region: Phage_integ_N; pfam09003 342108005394 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 342108005395 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 342108005396 Conserved hypothetical phage protein (DUF2376); Region: DUF2376; cl09774 342108005397 Protein of unknown function (DUF3356); Region: DUF3356; pfam11836 342108005398 Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the...; Region: Prim_Pol; cd04859 342108005399 polymerase nucleotide-binding site; other site 342108005400 DNA-binding residues [nucleotide binding]; DNA binding site 342108005401 nucleotide binding site [chemical binding]; other site 342108005402 primase nucleotide-binding site [nucleotide binding]; other site 342108005403 Primase C terminal 1 (PriCT-1); Region: PriCT_1; cl07362 342108005404 AAA domain; Region: AAA_25; pfam13481 342108005405 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 342108005406 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 342108005407 DNA binding site [nucleotide binding] 342108005408 active site 342108005409 catalytic site [active] 342108005410 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 342108005411 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 342108005412 Predicted transcriptional regulator [Transcription]; Region: COG2932 342108005413 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 342108005414 Catalytic site [active] 342108005415 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108005416 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 342108005417 non-specific DNA binding site [nucleotide binding]; other site 342108005418 salt bridge; other site 342108005419 sequence-specific DNA binding site [nucleotide binding]; other site 342108005420 Endodeoxyribonuclease RusA; Region: RusA; pfam05866 342108005421 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 342108005422 Protein of unknown function (DUF2800); Region: DUF2800; pfam10926 342108005423 Protein of unknown function (DUF2815); Region: DUF2815; pfam10991 342108005424 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; cl11480 342108005425 Bacteriophage lambda integrase, N-terminal domain; Region: Phage_integ_N; pfam09003 342108005426 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 342108005427 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 342108005428 active site 342108005429 DNA binding site [nucleotide binding] 342108005430 Int/Topo IB signature motif; other site 342108005431 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 342108005432 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 342108005433 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 342108005434 Predicted membrane protein [Function unknown]; Region: COG2860 342108005435 UPF0126 domain; Region: UPF0126; pfam03458 342108005436 UPF0126 domain; Region: UPF0126; pfam03458 342108005437 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108005438 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108005439 metal binding site [ion binding]; metal-binding site 342108005440 active site 342108005441 I-site; other site 342108005442 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 342108005443 Response regulator receiver domain; Region: Response_reg; pfam00072 342108005444 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 342108005445 active site 342108005446 phosphorylation site [posttranslational modification] 342108005447 intermolecular recognition site; other site 342108005448 dimerization interface [polypeptide binding]; other site 342108005449 Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair]; Region: SPS1; COG0515 342108005450 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 342108005451 substrate binding site [chemical binding]; other site 342108005452 activation loop (A-loop); other site 342108005453 Predicted ATPase [General function prediction only]; Region: COG3899 342108005454 AAA ATPase domain; Region: AAA_16; pfam13191 342108005455 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 342108005456 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 342108005457 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 342108005458 ATP binding site [chemical binding]; other site 342108005459 Mg2+ binding site [ion binding]; other site 342108005460 G-X-G motif; other site 342108005461 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 342108005462 Beta-ketoacyl synthase; Region: PKS_KS; smart00825 342108005463 active site 342108005464 Acyl transferase domain in polyketide synthase (PKS) enzymes; Region: PKS_AT; smart00827 342108005465 Dehydratase domain in polyketide synthase (PKS) enzymes; Region: PKS_DH; smart00826 342108005466 beta-ketoacyl reductase (KR) domain of fatty acid synthase (FAS), subgroup 2, complex (x); Region: KR_2_FAS_SDR_x; cd08955 342108005467 putative NADP binding site [chemical binding]; other site 342108005468 This enzymatic domain is part of bacterial polyketide synthases; Region: PKS_KR; smart00822 342108005469 active site 342108005470 Phosphopantetheine attachment site; Region: PKS_PP; smart00823 342108005471 Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: GrsT; COG3208 342108005472 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 342108005473 Patatin-like phospholipase; Region: Patatin; pfam01734 342108005474 active site 342108005475 nucleophile elbow; other site 342108005476 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 342108005477 Hemerythrin family; Region: Hemerythrin-like; cl15774 342108005478 methionine sulfoxide reductase A; Provisional; Region: PRK00058 342108005479 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 342108005480 PAS fold; Region: PAS_7; pfam12860 342108005481 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 342108005482 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 342108005483 dimer interface [polypeptide binding]; other site 342108005484 phosphorylation site [posttranslational modification] 342108005485 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 342108005486 ATP binding site [chemical binding]; other site 342108005487 Mg2+ binding site [ion binding]; other site 342108005488 G-X-G motif; other site 342108005489 Response regulator receiver domain; Region: Response_reg; pfam00072 342108005490 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 342108005491 active site 342108005492 phosphorylation site [posttranslational modification] 342108005493 intermolecular recognition site; other site 342108005494 dimerization interface [polypeptide binding]; other site 342108005495 Patatin-like phospholipase; Region: Patatin; pfam01734 342108005496 HAMP domain; Region: HAMP; pfam00672 342108005497 dimerization interface [polypeptide binding]; other site 342108005498 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108005499 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108005500 dimer interface [polypeptide binding]; other site 342108005501 putative CheW interface [polypeptide binding]; other site 342108005502 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108005503 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 342108005504 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 342108005505 P-loop; other site 342108005506 Magnesium ion binding site [ion binding]; other site 342108005507 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 342108005508 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 342108005509 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 342108005510 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 342108005511 TPR motif; other site 342108005512 binding surface 342108005513 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 342108005514 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 342108005515 HAMP domain; Region: HAMP; pfam00672 342108005516 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108005517 dimer interface [polypeptide binding]; other site 342108005518 putative CheW interface [polypeptide binding]; other site 342108005519 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 342108005520 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 342108005521 active site 342108005522 phosphorylation site [posttranslational modification] 342108005523 intermolecular recognition site; other site 342108005524 dimerization interface [polypeptide binding]; other site 342108005525 CheB methylesterase; Region: CheB_methylest; pfam01339 342108005526 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108005527 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 342108005528 active site 342108005529 phosphorylation site [posttranslational modification] 342108005530 intermolecular recognition site; other site 342108005531 dimerization interface [polypeptide binding]; other site 342108005532 Response regulator receiver domain; Region: Response_reg; pfam00072 342108005533 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 342108005534 active site 342108005535 phosphorylation site [posttranslational modification] 342108005536 intermolecular recognition site; other site 342108005537 dimerization interface [polypeptide binding]; other site 342108005538 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 342108005539 dimer interface [polypeptide binding]; other site 342108005540 phosphorylation site [posttranslational modification] 342108005541 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 342108005542 ATP binding site [chemical binding]; other site 342108005543 Mg2+ binding site [ion binding]; other site 342108005544 G-X-G motif; other site 342108005545 Response regulator receiver domain; Region: Response_reg; pfam00072 342108005546 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 342108005547 active site 342108005548 phosphorylation site [posttranslational modification] 342108005549 intermolecular recognition site; other site 342108005550 dimerization interface [polypeptide binding]; other site 342108005551 PAS domain S-box; Region: sensory_box; TIGR00229 342108005552 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 342108005553 putative active site [active] 342108005554 heme pocket [chemical binding]; other site 342108005555 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108005556 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 342108005557 dimer interface [polypeptide binding]; other site 342108005558 phosphorylation site [posttranslational modification] 342108005559 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 342108005560 ATP binding site [chemical binding]; other site 342108005561 Mg2+ binding site [ion binding]; other site 342108005562 G-X-G motif; other site 342108005563 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 342108005564 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 342108005565 PAS domain; Region: PAS_9; pfam13426 342108005566 putative active site [active] 342108005567 heme pocket [chemical binding]; other site 342108005568 PAS domain S-box; Region: sensory_box; TIGR00229 342108005569 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 342108005570 putative active site [active] 342108005571 heme pocket [chemical binding]; other site 342108005572 PAS domain S-box; Region: sensory_box; TIGR00229 342108005573 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108005574 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108005575 metal binding site [ion binding]; metal-binding site 342108005576 active site 342108005577 I-site; other site 342108005578 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 342108005579 Uncharacterized conserved protein [Function unknown]; Region: COG3025 342108005580 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 342108005581 putative active site [active] 342108005582 putative metal binding residues [ion binding]; other site 342108005583 signature motif; other site 342108005584 putative triphosphate binding site [ion binding]; other site 342108005585 The CHAD domain is an alpha-helical domain functionally associated with some members of the adenylate cyclase family; Region: CHAD; smart00880 342108005586 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 342108005587 Ligand Binding Site [chemical binding]; other site 342108005588 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 342108005589 Ligand Binding Site [chemical binding]; other site 342108005590 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 342108005591 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 342108005592 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 342108005593 dimer interface [polypeptide binding]; other site 342108005594 conserved gate region; other site 342108005595 ABC-ATPase subunit interface; other site 342108005596 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 342108005597 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 342108005598 dimer interface [polypeptide binding]; other site 342108005599 conserved gate region; other site 342108005600 putative PBP binding loops; other site 342108005601 ABC-ATPase subunit interface; other site 342108005602 The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold; Region: PBP2_thermophilic_Hb8_like; cd08513 342108005603 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 342108005604 dimer interface [polypeptide binding]; other site 342108005605 peptide binding site [polypeptide binding]; other site 342108005606 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 342108005607 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 342108005608 hinge; other site 342108005609 active site 342108005610 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108005611 HAMP domain; Region: HAMP; pfam00672 342108005612 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108005613 dimer interface [polypeptide binding]; other site 342108005614 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108005615 putative CheW interface [polypeptide binding]; other site 342108005616 2-dehydropantoate 2-reductase; Provisional; Region: PRK12921 342108005617 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 342108005618 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 342108005619 Hemerythrin family; Region: Hemerythrin-like; cl15774 342108005620 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 342108005621 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 342108005622 dimer interface [polypeptide binding]; other site 342108005623 PYR/PP interface [polypeptide binding]; other site 342108005624 TPP binding site [chemical binding]; other site 342108005625 substrate binding site [chemical binding]; other site 342108005626 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 342108005627 Domain of unknown function; Region: EKR; smart00890 342108005628 4Fe-4S binding domain; Region: Fer4_6; pfam12837 342108005629 4Fe-4S binding domain; Region: Fer4_6; pfam12837 342108005630 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 342108005631 TPP-binding site [chemical binding]; other site 342108005632 dimer interface [polypeptide binding]; other site 342108005633 PAS fold; Region: PAS_4; pfam08448 342108005634 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 342108005635 putative active site [active] 342108005636 heme pocket [chemical binding]; other site 342108005637 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005638 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005639 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005640 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005641 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005642 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005643 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005644 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005645 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005646 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005647 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005648 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005649 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005650 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005651 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005652 Phage DNA packaging protein Nu1; Region: Phage_Nu1; cl01720 342108005653 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005654 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005655 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005656 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005657 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005658 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005659 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005660 Siphovirus protein of unknown function (DUF859); Region: DUF859; pfam05895 342108005661 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005662 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005663 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005664 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005665 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005666 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005667 VCBS repeat; Region: VCBS_repeat; TIGR01965 342108005668 Catalytic domain of Protein Kinases; Region: PKc; cd00180 342108005669 active site 342108005670 ATP binding site [chemical binding]; other site 342108005671 substrate binding site [chemical binding]; other site 342108005672 activation loop (A-loop); other site 342108005673 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07521 342108005674 Nucleoside 2-deoxyribosyltransferase; Region: Nuc_deoxyrib_tr; pfam05014 342108005675 PAS fold; Region: PAS_4; pfam08448 342108005676 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 342108005677 putative active site [active] 342108005678 heme pocket [chemical binding]; other site 342108005679 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 342108005680 dimer interface [polypeptide binding]; other site 342108005681 phosphorylation site [posttranslational modification] 342108005682 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 342108005683 ATP binding site [chemical binding]; other site 342108005684 Mg2+ binding site [ion binding]; other site 342108005685 G-X-G motif; other site 342108005686 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 342108005687 PAS domain S-box; Region: sensory_box; TIGR00229 342108005688 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 342108005689 putative active site [active] 342108005690 heme pocket [chemical binding]; other site 342108005691 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 342108005692 PAS fold; Region: PAS_3; pfam08447 342108005693 putative active site [active] 342108005694 heme pocket [chemical binding]; other site 342108005695 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 342108005696 dimer interface [polypeptide binding]; other site 342108005697 phosphorylation site [posttranslational modification] 342108005698 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 342108005699 ATP binding site [chemical binding]; other site 342108005700 Mg2+ binding site [ion binding]; other site 342108005701 G-X-G motif; other site 342108005702 hypothetical protein; Provisional; Region: PRK09256 342108005703 Domain of unknown function (DUF1476); Region: DUF1476; cl11571 342108005704 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 342108005705 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 342108005706 substrate binding pocket [chemical binding]; other site 342108005707 membrane-bound complex binding site; other site 342108005708 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 342108005709 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 342108005710 dimer interface [polypeptide binding]; other site 342108005711 conserved gate region; other site 342108005712 putative PBP binding loops; other site 342108005713 ABC-ATPase subunit interface; other site 342108005714 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 342108005715 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 342108005716 dimer interface [polypeptide binding]; other site 342108005717 conserved gate region; other site 342108005718 putative PBP binding loops; other site 342108005719 ABC-ATPase subunit interface; other site 342108005720 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108005721 ABC transporter signature motif; other site 342108005722 Walker B; other site 342108005723 D-loop; other site 342108005724 H-loop/switch region; other site 342108005725 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108005726 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 342108005727 dimerization interface [polypeptide binding]; other site 342108005728 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 342108005729 dimer interface [polypeptide binding]; other site 342108005730 phosphorylation site [posttranslational modification] 342108005731 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 342108005732 ATP binding site [chemical binding]; other site 342108005733 Mg2+ binding site [ion binding]; other site 342108005734 G-X-G motif; other site 342108005735 PaaX-like protein; Region: PaaX; pfam07848 342108005736 phenylacetic acid degradation operon negative regulatory protein PaaX; Region: PaaX_trns_reg; TIGR02277 342108005737 PaaX-like protein C-terminal domain; Region: PaaX_C; pfam08223 342108005738 The MopB_Phenylacetyl-CoA-OR CD contains the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), and other related proteins. The phenylacetyl-CoA:acceptor oxidoreductase has been characterized as a membrane-bound molybdenum-iron-sulfur...; Region: MopB_Phenylacetyl-CoA-OR; cd02760 342108005739 DMSO reductase family type II enzyme, molybdopterin subunit; Region: DMSO_red_II_alp; TIGR03479 342108005740 putative molybdopterin cofactor binding site; other site 342108005741 The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme...; Region: MopB_CT_Thiosulfate-R-like; cd02778 342108005742 putative molybdopterin cofactor binding site; other site 342108005743 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 342108005744 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 342108005745 MarR family; Region: MarR; pfam01047 342108005746 4-hydroxybenzoyl-CoA reductase, gamma subunit; Region: 4hydroxCoAred; TIGR03193 342108005747 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 342108005748 catalytic loop [active] 342108005749 iron binding site [ion binding]; other site 342108005750 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 342108005751 4-hydroxybenzoyl-CoA reductase, alpha subunit; Region: 4hydrxCoA_A; TIGR03194 342108005752 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 342108005753 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 342108005754 4-hydroxybenzoyl-CoA reductase, beta subunit; Region: 4hydrxCoA_B; TIGR03195 342108005755 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 342108005756 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 342108005757 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 342108005758 XdhC Rossmann domain; Region: XdhC_C; pfam13478 342108005759 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 342108005760 IHF dimer interface [polypeptide binding]; other site 342108005761 IHF - DNA interface [nucleotide binding]; other site 342108005762 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 342108005763 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 342108005764 active site 342108005765 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 342108005766 feruloyl-CoA synthase; Reviewed; Region: PRK08180 342108005767 Feruloyl-CoA synthetase (FCS); Region: FCS; cd05921 342108005768 acyl-activating enzyme (AAE) consensus motif; other site 342108005769 putative AMP binding site [chemical binding]; other site 342108005770 putative active site [active] 342108005771 putative CoA binding site [chemical binding]; other site 342108005772 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 342108005773 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 342108005774 Walker A/P-loop; other site 342108005775 ATP binding site [chemical binding]; other site 342108005776 Q-loop/lid; other site 342108005777 ABC transporter signature motif; other site 342108005778 Walker B; other site 342108005779 D-loop; other site 342108005780 H-loop/switch region; other site 342108005781 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 342108005782 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 342108005783 Walker A/P-loop; other site 342108005784 ATP binding site [chemical binding]; other site 342108005785 Q-loop/lid; other site 342108005786 ABC transporter signature motif; other site 342108005787 Walker B; other site 342108005788 D-loop; other site 342108005789 H-loop/switch region; other site 342108005790 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 342108005791 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 342108005792 TM-ABC transporter signature motif; other site 342108005793 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 342108005794 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 342108005795 TM-ABC transporter signature motif; other site 342108005796 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 342108005797 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_6; cd06340 342108005798 putative ligand binding site [chemical binding]; other site 342108005799 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 342108005800 ATP binding site [chemical binding]; other site 342108005801 active site 342108005802 substrate binding site [chemical binding]; other site 342108005803 FOG: CBS domain [General function prediction only]; Region: COG0517 342108005804 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 342108005805 Mpr1p, Pad1p N-terminal (MPN) domains; Region: MPN; cl13996 342108005806 Putative inner membrane protein (DUF1819); Region: DUF1819; pfam08849 342108005807 Domain of unknown function (DUF1788); Region: DUF1788; pfam08747 342108005808 HTH-like domain; Region: HTH_21; pfam13276 342108005809 Integrase core domain; Region: rve; pfam00665 342108005810 Integrase core domain; Region: rve_3; pfam13683 342108005811 Transposase; Region: HTH_Tnp_1; pfam01527 342108005812 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108005813 Methyltransferase domain; Region: Methyltransf_26; pfam13659 342108005814 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 342108005815 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 342108005816 TIGR02687 family protein; Region: TIGR02687 342108005817 PglZ domain; Region: PglZ; pfam08665 342108005818 conserved hypothetical protein; Region: Lon_rel_chp; TIGR02653 342108005819 Putative ATP-dependent Lon protease; Region: Lon_2; pfam13337 342108005820 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 342108005821 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 342108005822 active site 342108005823 catalytic site [active] 342108005824 substrate binding site [chemical binding]; other site 342108005825 SpoVG; Region: SpoVG; cl00915 342108005826 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 342108005827 PLD-like domain; Region: PLDc_2; pfam13091 342108005828 putative active site [active] 342108005829 catalytic site [active] 342108005830 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 342108005831 DNA N-6-adenine-methyltransferase (Dam); Region: Dam; cl05442 342108005832 multiple promoter invertase; Provisional; Region: mpi; PRK13413 342108005833 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 342108005834 catalytic residues [active] 342108005835 catalytic nucleophile [active] 342108005836 Presynaptic Site I dimer interface [polypeptide binding]; other site 342108005837 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 342108005838 Synaptic Flat tetramer interface [polypeptide binding]; other site 342108005839 Synaptic Site I dimer interface [polypeptide binding]; other site 342108005840 DNA binding site [nucleotide binding] 342108005841 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 342108005842 DNA-binding interface [nucleotide binding]; DNA binding site 342108005843 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 342108005844 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 342108005845 non-specific DNA binding site [nucleotide binding]; other site 342108005846 salt bridge; other site 342108005847 sequence-specific DNA binding site [nucleotide binding]; other site 342108005848 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 342108005849 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 342108005850 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 342108005851 active site 342108005852 DNA binding site [nucleotide binding] 342108005853 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 342108005854 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 342108005855 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 342108005856 Catalytic site [active] 342108005857 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 342108005858 WYL domain; Region: WYL; pfam13280 342108005859 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 342108005860 Protein of unknown function (DUF3572); Region: DUF3572; pfam12096 342108005861 DNA polymerase III subunit epsilon; Validated; Region: PRK09182 342108005862 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 342108005863 active site 342108005864 catalytic site [active] 342108005865 substrate binding site [chemical binding]; other site 342108005866 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 342108005867 Restriction alleviation protein Lar; Region: Lar_restr_allev; cl08047 342108005868 ATP cone domain; Region: ATP-cone; pfam03477 342108005869 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 342108005870 IHF - DNA interface [nucleotide binding]; other site 342108005871 IHF dimer interface [polypeptide binding]; other site 342108005872 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 342108005873 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108005874 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 342108005875 non-specific DNA binding site [nucleotide binding]; other site 342108005876 salt bridge; other site 342108005877 sequence-specific DNA binding site [nucleotide binding]; other site 342108005878 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 342108005879 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 342108005880 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 342108005881 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 342108005882 active site 342108005883 Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly...; Region: Macro_Appr_pase_like; cd02908 342108005884 putative ADP-ribose binding site [chemical binding]; other site 342108005885 putative active site [active] 342108005886 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 342108005887 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 342108005888 active site 342108005889 metal binding site [ion binding]; metal-binding site 342108005890 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108005891 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 342108005892 NAD(P) binding site [chemical binding]; other site 342108005893 active site 342108005894 amidophosphoribosyltransferase; Provisional; Region: PRK09123 342108005895 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 342108005896 active site 342108005897 tetramer interface [polypeptide binding]; other site 342108005898 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 342108005899 active site 342108005900 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 342108005901 Colicin V production protein; Region: Colicin_V; pfam02674 342108005902 DNA repair protein RadA; Provisional; Region: PRK11823 342108005903 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 342108005904 Walker A motif/ATP binding site; other site 342108005905 ATP binding site [chemical binding]; other site 342108005906 Walker B motif; other site 342108005907 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 342108005908 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 342108005909 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 342108005910 Walker A/P-loop; other site 342108005911 ATP binding site [chemical binding]; other site 342108005912 Q-loop/lid; other site 342108005913 ABC transporter signature motif; other site 342108005914 Walker B; other site 342108005915 D-loop; other site 342108005916 H-loop/switch region; other site 342108005917 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 342108005918 Permease; Region: Permease; pfam02405 342108005919 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 342108005920 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 342108005921 active site 342108005922 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 342108005923 dimer interface [polypeptide binding]; other site 342108005924 substrate binding site [chemical binding]; other site 342108005925 catalytic residues [active] 342108005926 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 342108005927 replicative DNA helicase; Provisional; Region: PRK09165 342108005928 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 342108005929 Walker A motif; other site 342108005930 ATP binding site [chemical binding]; other site 342108005931 Walker B motif; other site 342108005932 DNA binding loops [nucleotide binding] 342108005933 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 342108005934 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 342108005935 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 342108005936 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 342108005937 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 342108005938 Nitrate and nitrite sensing; Region: NIT; pfam08376 342108005939 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 342108005940 dimerization interface [polypeptide binding]; other site 342108005941 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108005942 dimer interface [polypeptide binding]; other site 342108005943 putative CheW interface [polypeptide binding]; other site 342108005944 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 342108005945 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 342108005946 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 342108005947 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108005948 NAD(P) binding site [chemical binding]; other site 342108005949 active site 342108005950 acyl carrier protein; Provisional; Region: acpP; PRK00982 342108005951 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 342108005952 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 342108005953 dimer interface [polypeptide binding]; other site 342108005954 active site 342108005955 YceG-like family; Region: YceG; pfam02618 342108005956 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 342108005957 dimerization interface [polypeptide binding]; other site 342108005958 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 342108005959 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 342108005960 ligand binding site; other site 342108005961 oligomer interface; other site 342108005962 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 342108005963 dimer interface [polypeptide binding]; other site 342108005964 N-terminal domain interface [polypeptide binding]; other site 342108005965 sulfate 1 binding site; other site 342108005966 glycogen synthase; Provisional; Region: glgA; PRK00654 342108005967 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 342108005968 ADP-binding pocket [chemical binding]; other site 342108005969 homodimer interface [polypeptide binding]; other site 342108005970 glucokinase; Provisional; Region: glk; PRK00292 342108005971 glucokinase, proteobacterial type; Region: glk; TIGR00749 342108005972 phosphoribosylformylglycinamidine synthase I; Provisional; Region: PRK03619 342108005973 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 342108005974 putative active site [active] 342108005975 catalytic triad [active] 342108005976 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 342108005977 thiamine-monophosphate kinase; Region: thiL; TIGR01379 342108005978 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 342108005979 dimerization interface [polypeptide binding]; other site 342108005980 ATP binding site [chemical binding]; other site 342108005981 BolA-like protein; Region: BolA; pfam01722 342108005982 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 342108005983 putative GSH binding site [chemical binding]; other site 342108005984 catalytic residues [active] 342108005985 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 342108005986 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 342108005987 active site 342108005988 catalytic residues [active] 342108005989 DNA binding site [nucleotide binding] 342108005990 Int/Topo IB signature motif; other site 342108005991 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108005992 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 342108005993 active site 342108005994 phosphorylation site [posttranslational modification] 342108005995 intermolecular recognition site; other site 342108005996 dimerization interface [polypeptide binding]; other site 342108005997 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 342108005998 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 342108005999 active site 342108006000 catalytic residues [active] 342108006001 DNA binding site [nucleotide binding] 342108006002 Int/Topo IB signature motif; other site 342108006003 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 342108006004 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 342108006005 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 342108006006 RNA binding surface [nucleotide binding]; other site 342108006007 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 342108006008 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 342108006009 putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional; Region: PRK12344 342108006010 Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA3; cd07941 342108006011 active site 342108006012 catalytic residues [active] 342108006013 metal binding site [ion binding]; metal-binding site 342108006014 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 342108006015 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 342108006016 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 342108006017 CoA-transferase family III; Region: CoA_transf_3; pfam02515 342108006018 HAMP domain; Region: HAMP; pfam00672 342108006019 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108006020 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108006021 dimer interface [polypeptide binding]; other site 342108006022 putative CheW interface [polypeptide binding]; other site 342108006023 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 342108006024 S-adenosylmethionine binding site [chemical binding]; other site 342108006025 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108006026 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 342108006027 TPR motif; other site 342108006028 binding surface 342108006029 TPR repeat; Region: TPR_11; pfam13414 342108006030 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 342108006031 TPR motif; other site 342108006032 binding surface 342108006033 TPR repeat; Region: TPR_11; pfam13414 342108006034 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 342108006035 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 342108006036 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 342108006037 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 342108006038 benzoyl-CoA reductase, bcr type, subunit B; Region: benz_CoA_red_B; TIGR02260 342108006039 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 342108006040 benzoyl-CoA reductase, subunit C; Region: benz_CoA_red_C; TIGR02263 342108006041 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 342108006042 cyclohexa-1,5-dienecarbonyl-CoA hydratase; Region: dienoyl_CoA_hyt; TIGR03189 342108006043 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 342108006044 substrate binding site [chemical binding]; other site 342108006045 oxyanion hole (OAH) forming residues; other site 342108006046 trimer interface [polypeptide binding]; other site 342108006047 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; Region: dearomat_oah; TIGR03200 342108006048 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 342108006049 substrate binding site [chemical binding]; other site 342108006050 oxyanion hole (OAH) forming residues; other site 342108006051 trimer interface [polypeptide binding]; other site 342108006052 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase, and other MDR family members; Region: hydroxyacyl_CoA_DH; cd08254 342108006053 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Region: dearomat_had; TIGR03201 342108006054 putative NAD(P) binding site [chemical binding]; other site 342108006055 catalytic Zn binding site [ion binding]; other site 342108006056 structural Zn binding site [ion binding]; other site 342108006057 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 342108006058 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; pfam01558 342108006059 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 342108006060 dimer interface [polypeptide binding]; other site 342108006061 PYR/PP interface [polypeptide binding]; other site 342108006062 TPP binding site [chemical binding]; other site 342108006063 substrate binding site [chemical binding]; other site 342108006064 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 342108006065 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 342108006066 TPP-binding site [chemical binding]; other site 342108006067 Uncharacterized conserved protein [Function unknown]; Region: COG1633 342108006068 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 342108006069 diiron binding motif [ion binding]; other site 342108006070 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 342108006071 homotrimer interaction site [polypeptide binding]; other site 342108006072 putative active site [active] 342108006073 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 342108006074 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 342108006075 Coenzyme A binding pocket [chemical binding]; other site 342108006076 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 342108006077 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108006078 NAD(P) binding site [chemical binding]; other site 342108006079 active site 342108006080 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 342108006081 Domain of unknown function DUF21; Region: DUF21; pfam01595 342108006082 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 342108006083 Transporter associated domain; Region: CorC_HlyC; smart01091 342108006084 PrkA family serine protein kinase; Provisional; Region: PRK15455 342108006085 AAA ATPase domain; Region: AAA_16; pfam13191 342108006086 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 342108006087 hypothetical protein; Provisional; Region: PRK05325 342108006088 SpoVR family protein; Provisional; Region: PRK11767 342108006089 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 342108006090 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 342108006091 TPR motif; other site 342108006092 binding surface 342108006093 TPR repeat; Region: TPR_11; pfam13414 342108006094 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 342108006095 binding surface 342108006096 TPR motif; other site 342108006097 TPR repeat; Region: TPR_11; pfam13414 342108006098 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 342108006099 TPR repeat; Region: TPR_11; pfam13414 342108006100 TPR motif; other site 342108006101 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 342108006102 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 342108006103 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 342108006104 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 342108006105 TPP-binding site [chemical binding]; other site 342108006106 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 342108006107 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 342108006108 dimer interface [polypeptide binding]; other site 342108006109 PYR/PP interface [polypeptide binding]; other site 342108006110 TPP binding site [chemical binding]; other site 342108006111 substrate binding site [chemical binding]; other site 342108006112 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108006113 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 342108006114 putative NAD(P) binding site [chemical binding]; other site 342108006115 active site 342108006116 putative substrate binding site [chemical binding]; other site 342108006117 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 342108006118 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 342108006119 substrate binding pocket [chemical binding]; other site 342108006120 chain length determination region; other site 342108006121 substrate-Mg2+ binding site; other site 342108006122 catalytic residues [active] 342108006123 aspartate-rich region 1; other site 342108006124 active site lid residues [active] 342108006125 aspartate-rich region 2; other site 342108006126 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 342108006127 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 342108006128 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 342108006129 PAS fold; Region: PAS; pfam00989 342108006130 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 342108006131 putative active site [active] 342108006132 heme pocket [chemical binding]; other site 342108006133 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 342108006134 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 342108006135 putative active site [active] 342108006136 heme pocket [chemical binding]; other site 342108006137 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 342108006138 dimer interface [polypeptide binding]; other site 342108006139 phosphorylation site [posttranslational modification] 342108006140 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 342108006141 ATP binding site [chemical binding]; other site 342108006142 Mg2+ binding site [ion binding]; other site 342108006143 G-X-G motif; other site 342108006144 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108006145 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 342108006146 active site 342108006147 phosphorylation site [posttranslational modification] 342108006148 intermolecular recognition site; other site 342108006149 dimerization interface [polypeptide binding]; other site 342108006150 Response regulator receiver domain; Region: Response_reg; pfam00072 342108006151 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 342108006152 active site 342108006153 phosphorylation site [posttranslational modification] 342108006154 intermolecular recognition site; other site 342108006155 dimerization interface [polypeptide binding]; other site 342108006156 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 342108006157 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 342108006158 Subunit III/VIIa interface [polypeptide binding]; other site 342108006159 Phospholipid binding site [chemical binding]; other site 342108006160 Subunit I/III interface [polypeptide binding]; other site 342108006161 Subunit III/VIb interface [polypeptide binding]; other site 342108006162 Subunit III/VIa interface; other site 342108006163 Subunit III/Vb interface [polypeptide binding]; other site 342108006164 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 342108006165 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 342108006166 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 342108006167 Subunit I/III interface [polypeptide binding]; other site 342108006168 D-pathway; other site 342108006169 Subunit I/VIIc interface [polypeptide binding]; other site 342108006170 Subunit I/IV interface [polypeptide binding]; other site 342108006171 Subunit I/II interface [polypeptide binding]; other site 342108006172 Low-spin heme (heme a) binding site [chemical binding]; other site 342108006173 Subunit I/VIIa interface [polypeptide binding]; other site 342108006174 Dimer interface; other site 342108006175 Subunit I/VIa interface [polypeptide binding]; other site 342108006176 Putative water exit pathway; other site 342108006177 Binuclear center (heme a3/CuB) [ion binding]; other site 342108006178 K-pathway; other site 342108006179 Subunit I/Vb interface [polypeptide binding]; other site 342108006180 Putative proton exit pathway; other site 342108006181 Subunit I/VIb interface; other site 342108006182 Subunit I/VIc interface [polypeptide binding]; other site 342108006183 Electron transfer pathway; other site 342108006184 Subunit I/VIIIb interface [polypeptide binding]; other site 342108006185 Subunit I/VIIb interface [polypeptide binding]; other site 342108006186 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 342108006187 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 342108006188 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 342108006189 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 342108006190 active site residue [active] 342108006191 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 342108006192 lycopene cyclase; Region: lycopene_cycl; TIGR01789 342108006193 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 342108006194 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; pfam01258 342108006195 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 342108006196 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 342108006197 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 342108006198 Coenzyme A binding pocket [chemical binding]; other site 342108006199 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108006200 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 342108006201 dimer interface [polypeptide binding]; other site 342108006202 phosphorylation site [posttranslational modification] 342108006203 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 342108006204 ATP binding site [chemical binding]; other site 342108006205 Mg2+ binding site [ion binding]; other site 342108006206 G-X-G motif; other site 342108006207 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108006208 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 342108006209 non-specific DNA binding site [nucleotide binding]; other site 342108006210 salt bridge; other site 342108006211 sequence-specific DNA binding site [nucleotide binding]; other site 342108006212 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 342108006213 IHF - DNA interface [nucleotide binding]; other site 342108006214 IHF dimer interface [polypeptide binding]; other site 342108006215 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 342108006216 Protein of unknown function, DUF486; Region: DUF486; cl01236 342108006217 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108006218 dimer interface [polypeptide binding]; other site 342108006219 putative CheW interface [polypeptide binding]; other site 342108006220 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 342108006221 PAS domain; Region: PAS_9; pfam13426 342108006222 putative active site [active] 342108006223 heme pocket [chemical binding]; other site 342108006224 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 342108006225 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 342108006226 N-acetyl-D-glucosamine binding site [chemical binding]; other site 342108006227 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 342108006228 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 342108006229 phosphoribosylaminoimidazole carboxylase, PurK protein; Region: purK; TIGR01161 342108006230 ATP-grasp domain; Region: ATP-grasp; pfam02222 342108006231 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 342108006232 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108006233 metal binding site [ion binding]; metal-binding site 342108006234 active site 342108006235 I-site; other site 342108006236 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 342108006237 GAF domain; Region: GAF; cl17456 342108006238 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 342108006239 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 342108006240 putative active site [active] 342108006241 heme pocket [chemical binding]; other site 342108006242 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 342108006243 dimer interface [polypeptide binding]; other site 342108006244 phosphorylation site [posttranslational modification] 342108006245 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 342108006246 ATP binding site [chemical binding]; other site 342108006247 Mg2+ binding site [ion binding]; other site 342108006248 G-X-G motif; other site 342108006249 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 342108006250 active site 342108006251 phosphorylation site [posttranslational modification] 342108006252 intermolecular recognition site; other site 342108006253 dimerization interface [polypeptide binding]; other site 342108006254 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 342108006255 Peptidase M15; Region: Peptidase_M15_3; cl01194 342108006256 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 342108006257 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 342108006258 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 342108006259 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 342108006260 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 342108006261 active site residue [active] 342108006262 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 342108006263 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 342108006264 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 342108006265 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 342108006266 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 342108006267 Active Sites [active] 342108006268 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 342108006269 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 342108006270 Active Sites [active] 342108006271 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 342108006272 CysD dimerization site [polypeptide binding]; other site 342108006273 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 342108006274 G1 box; other site 342108006275 putative GEF interaction site [polypeptide binding]; other site 342108006276 GTP/Mg2+ binding site [chemical binding]; other site 342108006277 Switch I region; other site 342108006278 G2 box; other site 342108006279 G3 box; other site 342108006280 Switch II region; other site 342108006281 G4 box; other site 342108006282 G5 box; other site 342108006283 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 342108006284 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 342108006285 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form...; Region: APSK; cd02027 342108006286 ligand-binding site [chemical binding]; other site 342108006287 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 342108006288 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 342108006289 ATP binding site [chemical binding]; other site 342108006290 Mg2+ binding site [ion binding]; other site 342108006291 G-X-G motif; other site 342108006292 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 342108006293 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 342108006294 membrane-bound complex binding site; other site 342108006295 hinge residues; other site 342108006296 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 342108006297 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 342108006298 putative dimer interface [polypeptide binding]; other site 342108006299 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 342108006300 S-adenosylmethionine binding site [chemical binding]; other site 342108006301 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 342108006302 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 342108006303 catalytic residues [active] 342108006304 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 342108006305 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 342108006306 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 342108006307 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 342108006308 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 342108006309 Low-spin heme binding site [chemical binding]; other site 342108006310 D-pathway; other site 342108006311 Putative water exit pathway; other site 342108006312 Binuclear center (active site) [active] 342108006313 K-pathway; other site 342108006314 Putative proton exit pathway; other site 342108006315 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 342108006316 UbiA prenyltransferase family; Region: UbiA; pfam01040 342108006317 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 342108006318 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 342108006319 Cu(I) binding site [ion binding]; other site 342108006320 heme bH binding site [chemical binding]; other site 342108006321 intrachain domain interface; other site 342108006322 Qi binding site; other site 342108006323 heme bL binding site [chemical binding]; other site 342108006324 interchain domain interface [polypeptide binding]; other site 342108006325 Cytochrome b(N-terminal)/b6/petB; Region: Cytochrom_B_N_2; pfam13631 342108006326 Qo binding site; other site 342108006327 4Fe-4S binding domain; Region: Fer4; pfam00037 342108006328 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 342108006329 Methyl-viologen-reducing hydrogenase, delta subunit; Region: FlpD; pfam02662 342108006330 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 342108006331 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 342108006332 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 342108006333 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 342108006334 ATP-binding cassette domain of peroxisomal transporter, subfamily D; Region: ABCD_peroxisomal_ALDP; cd03223 342108006335 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 342108006336 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 342108006337 CHASE2 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria; Region: CHASE2; smart01080 342108006338 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 342108006339 cyclase homology domain; Region: CHD; cd07302 342108006340 nucleotidyl binding site; other site 342108006341 metal binding site [ion binding]; metal-binding site 342108006342 dimer interface [polypeptide binding]; other site 342108006343 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108006344 Tetratricopeptide repeat; Region: TPR_10; cl17452 342108006345 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108006346 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108006347 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108006348 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 342108006349 TPR motif; other site 342108006350 binding surface 342108006351 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108006352 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108006353 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 342108006354 TPR motif; other site 342108006355 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108006356 binding surface 342108006357 CHAT domain; Region: CHAT; pfam12770 342108006358 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 342108006359 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108006360 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 342108006361 ligand binding site [chemical binding]; other site 342108006362 flexible hinge region; other site 342108006363 Hemerythrin; Region: Hemerythrin; cd12107 342108006364 Fe binding site [ion binding]; other site 342108006365 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 342108006366 Sel1-like repeats; Region: SEL1; smart00671 342108006367 Sel1-like repeats; Region: SEL1; smart00671 342108006368 Sel1-like repeats; Region: SEL1; smart00671 342108006369 Sel1-like repeats; Region: SEL1; smart00671 342108006370 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 342108006371 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 342108006372 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108006373 putative CheW interface [polypeptide binding]; other site 342108006374 methylmalonyl-CoA decarboxylase; Provisional; Region: PRK11423 342108006375 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 342108006376 substrate binding site [chemical binding]; other site 342108006377 oxyanion hole (OAH) forming residues; other site 342108006378 trimer interface [polypeptide binding]; other site 342108006379 Exostosin family; Region: Exostosin; pfam03016 342108006380 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 342108006381 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 342108006382 Protein of unknown function (DUF2497); Region: DUF2497; pfam10691 342108006383 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 342108006384 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 342108006385 HIGH motif; other site 342108006386 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 342108006387 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 342108006388 active site 342108006389 KMSKS motif; other site 342108006390 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 342108006391 tRNA binding surface [nucleotide binding]; other site 342108006392 anticodon binding site; other site 342108006393 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 342108006394 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 342108006395 PAS domain; Region: PAS_9; pfam13426 342108006396 putative active site [active] 342108006397 heme pocket [chemical binding]; other site 342108006398 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 342108006399 PAS domain; Region: PAS_9; pfam13426 342108006400 putative active site [active] 342108006401 heme pocket [chemical binding]; other site 342108006402 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108006403 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108006404 metal binding site [ion binding]; metal-binding site 342108006405 active site 342108006406 I-site; other site 342108006407 Hemerythrin; Region: Hemerythrin; cd12107 342108006408 Fe binding site [ion binding]; other site 342108006409 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 342108006410 Fe-S cluster binding site [ion binding]; other site 342108006411 DNA binding site [nucleotide binding] 342108006412 active site 342108006413 Uncharacterized conserved protein [Function unknown]; Region: COG1432 342108006414 LabA_like proteins; Region: LabA; cd10911 342108006415 putative metal binding site [ion binding]; other site 342108006416 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 342108006417 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 342108006418 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108006419 Zn2+ binding site [ion binding]; other site 342108006420 Mg2+ binding site [ion binding]; other site 342108006421 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 342108006422 synthetase active site [active] 342108006423 NTP binding site [chemical binding]; other site 342108006424 metal binding site [ion binding]; metal-binding site 342108006425 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 342108006426 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 342108006427 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 342108006428 active site 342108006429 hydrophilic channel; other site 342108006430 dimerization interface [polypeptide binding]; other site 342108006431 catalytic residues [active] 342108006432 active site lid [active] 342108006433 SnoaL-like domain; Region: SnoaL_2; pfam12680 342108006434 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 342108006435 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 342108006436 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 342108006437 Catalytic site [active] 342108006438 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 342108006439 ribonuclease III; Reviewed; Region: rnc; PRK00102 342108006440 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 342108006441 dimerization interface [polypeptide binding]; other site 342108006442 active site 342108006443 metal binding site [ion binding]; metal-binding site 342108006444 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 342108006445 GTPase Era; Reviewed; Region: era; PRK00089 342108006446 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 342108006447 G1 box; other site 342108006448 GTP/Mg2+ binding site [chemical binding]; other site 342108006449 Switch I region; other site 342108006450 G2 box; other site 342108006451 Switch II region; other site 342108006452 G3 box; other site 342108006453 G4 box; other site 342108006454 G5 box; other site 342108006455 KH domain; Region: KH_2; pfam07650 342108006456 Recombination protein O N terminal; Region: RecO_N; pfam11967 342108006457 2-aminobenzoate-CoA ligase (ABCL); Region: ABCL; cd05958 342108006458 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 342108006459 putative dimer interface [polypeptide binding]; other site 342108006460 acyl-activating enzyme (AAE) consensus motif; other site 342108006461 putative active site [active] 342108006462 putative AMP binding site [chemical binding]; other site 342108006463 putative CoA binding site [chemical binding]; other site 342108006464 putative chemical substrate binding site [chemical binding]; other site 342108006465 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 342108006466 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 342108006467 putative substrate translocation pore; other site 342108006468 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108006469 Transcriptional regulator [Transcription]; Region: LysR; COG0583 342108006470 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 342108006471 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 342108006472 dimerization interface [polypeptide binding]; other site 342108006473 Homospermidine synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG5310 342108006474 Saccharopine dehydrogenase; Region: Saccharop_dh; pfam03435 342108006475 Ribbon-helix-helix domain; Region: RHH_4; pfam13467 342108006476 Transcriptional regulator [Transcription]; Region: LysR; COG0583 342108006477 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 342108006478 Transcriptional regulator [Transcription]; Region: LysR; COG0583 342108006479 LysR substrate binding domain; Region: LysR_substrate; pfam03466 342108006480 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108006481 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 342108006482 sequence-specific DNA binding site [nucleotide binding]; other site 342108006483 salt bridge; other site 342108006484 Helix-turn-helix domain; Region: HTH_17; pfam12728 342108006485 PBP superfamily domain; Region: PBP_like; pfam12727 342108006486 Protein of unknown function (DUF2478); Region: DUF2478; pfam10649 342108006487 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 342108006488 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 342108006489 PAS domain; Region: PAS_9; pfam13426 342108006490 putative active site [active] 342108006491 heme pocket [chemical binding]; other site 342108006492 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108006493 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108006494 metal binding site [ion binding]; metal-binding site 342108006495 active site 342108006496 I-site; other site 342108006497 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 342108006498 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 342108006499 Chromate transporter; Region: Chromate_transp; pfam02417 342108006500 MFS_1 like family; Region: MFS_1_like; pfam12832 342108006501 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 342108006502 uncharacterized YdjC-like family proteins from bacteria; Region: YdjC_like_3; cd10807 342108006503 putative homodimer interface [polypeptide binding]; other site 342108006504 putative active site [active] 342108006505 YdjC motif; other site 342108006506 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 342108006507 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108006508 putative active site [active] 342108006509 heme pocket [chemical binding]; other site 342108006510 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 342108006511 dimer interface [polypeptide binding]; other site 342108006512 phosphorylation site [posttranslational modification] 342108006513 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 342108006514 ATP binding site [chemical binding]; other site 342108006515 Mg2+ binding site [ion binding]; other site 342108006516 G-X-G motif; other site 342108006517 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108006518 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 342108006519 binding surface 342108006520 TPR motif; other site 342108006521 TPR repeat; Region: TPR_11; pfam13414 342108006522 Methyltransferase domain; Region: Methyltransf_24; pfam13578 342108006523 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 342108006524 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 342108006525 active site 342108006526 phosphorylation site [posttranslational modification] 342108006527 intermolecular recognition site; other site 342108006528 dimerization interface [polypeptide binding]; other site 342108006529 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 342108006530 Walker A motif; other site 342108006531 ATP binding site [chemical binding]; other site 342108006532 Walker B motif; other site 342108006533 arginine finger; other site 342108006534 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 342108006535 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 342108006536 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 342108006537 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108006538 putative CheW interface [polypeptide binding]; other site 342108006539 Predicted permeases [General function prediction only]; Region: COG0679 342108006540 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 342108006541 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 342108006542 MOFRL family; Region: MOFRL; pfam05161 342108006543 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 342108006544 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 342108006545 inhibitor site; inhibition site 342108006546 active site 342108006547 dimer interface [polypeptide binding]; other site 342108006548 catalytic residue [active] 342108006549 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 342108006550 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 342108006551 substrate binding pocket [chemical binding]; other site 342108006552 membrane-bound complex binding site; other site 342108006553 hinge residues; other site 342108006554 PAS domain; Region: PAS_9; pfam13426 342108006555 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 342108006556 putative active site [active] 342108006557 heme pocket [chemical binding]; other site 342108006558 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 342108006559 ATP binding site [chemical binding]; other site 342108006560 Mg2+ binding site [ion binding]; other site 342108006561 G-X-G motif; other site 342108006562 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108006563 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 342108006564 binding surface 342108006565 TPR motif; other site 342108006566 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 342108006567 FeS/SAM binding site; other site 342108006568 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 342108006569 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 342108006570 dimerization interface [polypeptide binding]; other site 342108006571 PAS domain; Region: PAS_9; pfam13426 342108006572 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 342108006573 dimer interface [polypeptide binding]; other site 342108006574 phosphorylation site [posttranslational modification] 342108006575 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 342108006576 ATP binding site [chemical binding]; other site 342108006577 Mg2+ binding site [ion binding]; other site 342108006578 G-X-G motif; other site 342108006579 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 342108006580 Response regulator receiver domain; Region: Response_reg; pfam00072 342108006581 active site 342108006582 phosphorylation site [posttranslational modification] 342108006583 intermolecular recognition site; other site 342108006584 dimerization interface [polypeptide binding]; other site 342108006585 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 342108006586 N-formylglutamate amidohydrolase; Region: FGase; cl01522 342108006587 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; pfam10073 342108006588 Dihydroneopterin aldolase; Region: FolB; pfam02152 342108006589 active site 342108006590 NMD3 family; Region: NMD3; pfam04981 342108006591 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 342108006592 catalytic center binding site [active] 342108006593 ATP binding site [chemical binding]; other site 342108006594 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]; Region: COG5481 342108006595 6-phosphofructokinase; Provisional; Region: PRK14071 342108006596 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 342108006597 active site 342108006598 ADP/pyrophosphate binding site [chemical binding]; other site 342108006599 dimerization interface [polypeptide binding]; other site 342108006600 allosteric effector site; other site 342108006601 fructose-1,6-bisphosphate binding site; other site 342108006602 3-polyprenyl-4-hydroxybenzoate decarboxylase [Coenzyme metabolism]; Region: UbiX; COG0163 342108006603 Flavoprotein; Region: Flavoprotein; pfam02441 342108006604 Protein of unknown function (DUF465); Region: DUF465; pfam04325 342108006605 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 342108006606 Propionyl-CoA synthetase (PrpE); Region: PrpE; cd05967 342108006607 acyl-activating enzyme (AAE) consensus motif; other site 342108006608 putative AMP binding site [chemical binding]; other site 342108006609 putative active site [active] 342108006610 putative CoA binding site [chemical binding]; other site 342108006611 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 342108006612 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 342108006613 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 342108006614 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 342108006615 ABC-type Zn2+ transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: ZnuA; COG4531 342108006616 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 342108006617 metal binding site [ion binding]; metal-binding site 342108006618 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 342108006619 metal binding site 2 [ion binding]; metal-binding site 342108006620 putative DNA binding helix; other site 342108006621 metal binding site 1 [ion binding]; metal-binding site 342108006622 dimer interface [polypeptide binding]; other site 342108006623 structural Zn2+ binding site [ion binding]; other site 342108006624 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 342108006625 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108006626 Walker A/P-loop; other site 342108006627 ATP binding site [chemical binding]; other site 342108006628 Q-loop/lid; other site 342108006629 ABC transporter signature motif; other site 342108006630 Walker B; other site 342108006631 D-loop; other site 342108006632 H-loop/switch region; other site 342108006633 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 342108006634 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; cl00462 342108006635 putative PBP binding regions; other site 342108006636 ABC-ATPase subunit interface; other site 342108006637 CHASE domain; Region: CHASE; cl01369 342108006638 PAS domain S-box; Region: sensory_box; TIGR00229 342108006639 PAS domain; Region: PAS; smart00091 342108006640 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 342108006641 dimer interface [polypeptide binding]; other site 342108006642 phosphorylation site [posttranslational modification] 342108006643 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 342108006644 ATP binding site [chemical binding]; other site 342108006645 Mg2+ binding site [ion binding]; other site 342108006646 G-X-G motif; other site 342108006647 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 342108006648 MgtC family; Region: MgtC; pfam02308 342108006649 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 342108006650 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 342108006651 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 342108006652 tetramer interface [polypeptide binding]; other site 342108006653 TPP-binding site [chemical binding]; other site 342108006654 heterodimer interface [polypeptide binding]; other site 342108006655 phosphorylation loop region [posttranslational modification] 342108006656 pyruvate dehydrogenase subunit beta; Provisional; Region: PRK11892 342108006657 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 342108006658 E3 interaction surface; other site 342108006659 lipoyl attachment site [posttranslational modification]; other site 342108006660 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 342108006661 alpha subunit interface [polypeptide binding]; other site 342108006662 TPP binding site [chemical binding]; other site 342108006663 heterodimer interface [polypeptide binding]; other site 342108006664 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 342108006665 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 342108006666 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 342108006667 E3 interaction surface; other site 342108006668 lipoyl attachment site [posttranslational modification]; other site 342108006669 e3 binding domain; Region: E3_binding; pfam02817 342108006670 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 342108006671 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 342108006672 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108006673 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 342108006674 lipoyl synthase; Provisional; Region: PRK05481 342108006675 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 342108006676 FeS/SAM binding site; other site 342108006677 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 342108006678 putative coenzyme Q binding site [chemical binding]; other site 342108006679 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108006680 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 342108006681 ligand binding site [chemical binding]; other site 342108006682 flexible hinge region; other site 342108006683 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 342108006684 non-specific DNA interactions [nucleotide binding]; other site 342108006685 DNA binding site [nucleotide binding] 342108006686 sequence specific DNA binding site [nucleotide binding]; other site 342108006687 putative cAMP binding site [chemical binding]; other site 342108006688 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 342108006689 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 342108006690 TM-ABC transporter signature motif; other site 342108006691 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 342108006692 TM-ABC transporter signature motif; other site 342108006693 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 342108006694 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 342108006695 putative ligand binding site [chemical binding]; other site 342108006696 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 342108006697 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 342108006698 Walker A/P-loop; other site 342108006699 ATP binding site [chemical binding]; other site 342108006700 Q-loop/lid; other site 342108006701 ABC transporter signature motif; other site 342108006702 Walker B; other site 342108006703 D-loop; other site 342108006704 H-loop/switch region; other site 342108006705 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 342108006706 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 342108006707 Walker A/P-loop; other site 342108006708 ATP binding site [chemical binding]; other site 342108006709 Q-loop/lid; other site 342108006710 ABC transporter signature motif; other site 342108006711 Walker B; other site 342108006712 D-loop; other site 342108006713 H-loop/switch region; other site 342108006714 Glutamate synthase domain 1 [Amino acid transport and metabolism]; Region: GltB; COG0067 342108006715 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 342108006716 active site 342108006717 dimer interface [polypeptide binding]; other site 342108006718 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 342108006719 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 342108006720 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 342108006721 active site 342108006722 FMN binding site [chemical binding]; other site 342108006723 substrate binding site [chemical binding]; other site 342108006724 3Fe-4S cluster binding site [ion binding]; other site 342108006725 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 342108006726 domain interface; other site 342108006727 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 342108006728 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108006729 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 342108006730 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108006731 dimer interface [polypeptide binding]; other site 342108006732 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108006733 putative CheW interface [polypeptide binding]; other site 342108006734 NnrS protein; Region: NnrS; pfam05940 342108006735 S-adenosyl-l-methionine hydroxide adenosyltransferase; Region: SAM_adeno_trans; pfam01887 342108006736 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 342108006737 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 342108006738 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 342108006739 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 342108006740 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 342108006741 dimer interface [polypeptide binding]; other site 342108006742 active site 342108006743 glycine-pyridoxal phosphate binding site [chemical binding]; other site 342108006744 folate binding site [chemical binding]; other site 342108006745 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 342108006746 Restriction alleviation protein Lar; Region: Lar_restr_allev; cl08047 342108006747 ATP cone domain; Region: ATP-cone; pfam03477 342108006748 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 342108006749 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 342108006750 catalytic motif [active] 342108006751 Zn binding site [ion binding]; other site 342108006752 RibD C-terminal domain; Region: RibD_C; cl17279 342108006753 Lumazine binding domain; Region: Lum_binding; pfam00677 342108006754 Lumazine binding domain; Region: Lum_binding; pfam00677 342108006755 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 342108006756 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 342108006757 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 342108006758 dimerization interface [polypeptide binding]; other site 342108006759 active site 342108006760 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 342108006761 homopentamer interface [polypeptide binding]; other site 342108006762 active site 342108006763 transcription antitermination factor NusB; Region: nusB; TIGR01951 342108006764 putative RNA binding site [nucleotide binding]; other site 342108006765 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 342108006766 ATP binding site [chemical binding]; other site 342108006767 dimerization interface [polypeptide binding]; other site 342108006768 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 342108006769 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 342108006770 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 342108006771 Ubiquinol-cytochrome C chaperone; Region: Ubiq_cyt_C_chap; pfam03981 342108006772 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 342108006773 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 342108006774 putative phosphate acyltransferase; Provisional; Region: PRK05331 342108006775 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 342108006776 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 342108006777 dimer interface [polypeptide binding]; other site 342108006778 active site 342108006779 CoA binding pocket [chemical binding]; other site 342108006780 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 342108006781 IHF dimer interface [polypeptide binding]; other site 342108006782 IHF - DNA interface [nucleotide binding]; other site 342108006783 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 342108006784 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 342108006785 DNA binding residues [nucleotide binding] 342108006786 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 342108006787 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 342108006788 binding surface 342108006789 TPR motif; other site 342108006790 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 342108006791 binding surface 342108006792 TPR motif; other site 342108006793 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 342108006794 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 342108006795 binding surface 342108006796 TPR motif; other site 342108006797 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK07565 342108006798 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 342108006799 phosphate binding site [ion binding]; other site 342108006800 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 342108006801 UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase [Cell envelope biogenesis, outer membrane]; Region: MurG; COG0707 342108006802 CutA1 divalent ion tolerance protein; Region: CutA1; pfam03091 342108006803 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 342108006804 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 342108006805 substrate binding site; other site 342108006806 dimer interface; other site 342108006807 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 342108006808 homotrimer interaction site [polypeptide binding]; other site 342108006809 zinc binding site [ion binding]; other site 342108006810 CDP-binding sites; other site 342108006811 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 342108006812 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 342108006813 FMN binding site [chemical binding]; other site 342108006814 active site 342108006815 catalytic residues [active] 342108006816 substrate binding site [chemical binding]; other site 342108006817 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 342108006818 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 342108006819 putative active site [active] 342108006820 heme pocket [chemical binding]; other site 342108006821 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 342108006822 dimer interface [polypeptide binding]; other site 342108006823 phosphorylation site [posttranslational modification] 342108006824 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 342108006825 ATP binding site [chemical binding]; other site 342108006826 Mg2+ binding site [ion binding]; other site 342108006827 G-X-G motif; other site 342108006828 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 342108006829 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 342108006830 active site 342108006831 phosphorylation site [posttranslational modification] 342108006832 intermolecular recognition site; other site 342108006833 dimerization interface [polypeptide binding]; other site 342108006834 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 342108006835 Walker A motif; other site 342108006836 ATP binding site [chemical binding]; other site 342108006837 Walker B motif; other site 342108006838 arginine finger; other site 342108006839 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 342108006840 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 342108006841 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 342108006842 dimerization interface [polypeptide binding]; other site 342108006843 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 342108006844 putative active site [active] 342108006845 heme pocket [chemical binding]; other site 342108006846 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 342108006847 dimer interface [polypeptide binding]; other site 342108006848 phosphorylation site [posttranslational modification] 342108006849 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 342108006850 ATP binding site [chemical binding]; other site 342108006851 Mg2+ binding site [ion binding]; other site 342108006852 G-X-G motif; other site 342108006853 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 342108006854 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 342108006855 active site 342108006856 phosphorylation site [posttranslational modification] 342108006857 intermolecular recognition site; other site 342108006858 dimerization interface [polypeptide binding]; other site 342108006859 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 342108006860 Walker A motif; other site 342108006861 ATP binding site [chemical binding]; other site 342108006862 Walker B motif; other site 342108006863 arginine finger; other site 342108006864 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 342108006865 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 342108006866 TrkA-N domain; Region: TrkA_N; pfam02254 342108006867 TrkA-C domain; Region: TrkA_C; pfam02080 342108006868 TrkA-N domain; Region: TrkA_N; pfam02254 342108006869 TrkA-C domain; Region: TrkA_C; pfam02080 342108006870 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 342108006871 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 342108006872 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 342108006873 motif II; other site 342108006874 bacterial Hfq-like; Region: Hfq; cd01716 342108006875 hexamer interface [polypeptide binding]; other site 342108006876 Sm1 motif; other site 342108006877 RNA binding site [nucleotide binding]; other site 342108006878 Sm2 motif; other site 342108006879 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 342108006880 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 342108006881 HflX GTPase family; Region: HflX; cd01878 342108006882 G1 box; other site 342108006883 GTP/Mg2+ binding site [chemical binding]; other site 342108006884 Switch I region; other site 342108006885 G2 box; other site 342108006886 G3 box; other site 342108006887 Switch II region; other site 342108006888 G4 box; other site 342108006889 G5 box; other site 342108006890 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 342108006891 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 342108006892 active site 342108006893 acetylornithine deacetylase; Provisional; Region: PRK07522 342108006894 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 342108006895 metal binding site [ion binding]; metal-binding site 342108006896 putative dimer interface [polypeptide binding]; other site 342108006897 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 342108006898 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 342108006899 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108006900 Walker A/P-loop; other site 342108006901 ATP binding site [chemical binding]; other site 342108006902 Q-loop/lid; other site 342108006903 ABC transporter signature motif; other site 342108006904 Walker B; other site 342108006905 D-loop; other site 342108006906 H-loop/switch region; other site 342108006907 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 342108006908 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic); Region: Peptidase_C39_like; cl00296 342108006909 putative active site [active] 342108006910 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 342108006911 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108006912 Walker A/P-loop; other site 342108006913 ATP binding site [chemical binding]; other site 342108006914 Q-loop/lid; other site 342108006915 ABC transporter signature motif; other site 342108006916 Walker B; other site 342108006917 D-loop; other site 342108006918 H-loop/switch region; other site 342108006919 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 342108006920 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108006921 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 342108006922 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 342108006923 dimer interface [polypeptide binding]; other site 342108006924 ssDNA binding site [nucleotide binding]; other site 342108006925 tetramer (dimer of dimers) interface [polypeptide binding]; other site 342108006926 DNA gyrase subunit A; Validated; Region: PRK05560 342108006927 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 342108006928 CAP-like domain; other site 342108006929 active site 342108006930 primary dimer interface [polypeptide binding]; other site 342108006931 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 342108006932 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 342108006933 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 342108006934 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 342108006935 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 342108006936 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 342108006937 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 342108006938 active site 342108006939 (T/H)XGH motif; other site 342108006940 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 342108006941 active site 342108006942 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 342108006943 active site 342108006944 HTH domain; Region: HTH_11; pfam08279 342108006945 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 342108006946 BON domain; Region: BON; pfam04972 342108006947 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 342108006948 EamA-like transporter family; Region: EamA; pfam00892 342108006949 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 342108006950 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108006951 NAD(P) binding site [chemical binding]; other site 342108006952 active site 342108006953 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 342108006954 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 342108006955 homodimer interface [polypeptide binding]; other site 342108006956 metal binding site [ion binding]; metal-binding site 342108006957 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 342108006958 homodimer interface [polypeptide binding]; other site 342108006959 active site 342108006960 putative chemical substrate binding site [chemical binding]; other site 342108006961 metal binding site [ion binding]; metal-binding site 342108006962 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 342108006963 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 342108006964 Protein of unknown function (DUF736); Region: DUF736; pfam05284 342108006965 Replication protein; Region: Rep_1; cl02412 342108006966 Domain of unknown function DUF87; Region: DUF87; pfam01935 342108006967 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 342108006968 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 342108006969 Helix-turn-helix domain; Region: HTH_38; pfam13936 342108006970 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 342108006971 Domain of unknown function DUF87; Region: DUF87; pfam01935 342108006972 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 342108006973 Replication protein; Region: Rep_1; cl02412 342108006974 Protein of unknown function (DUF736); Region: DUF736; pfam05284 342108006975 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09560 342108006976 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 342108006977 putative hydrolase; Provisional; Region: PRK02113 342108006978 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 342108006979 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 342108006980 active site 342108006981 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 342108006982 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 342108006983 active site 342108006984 HIGH motif; other site 342108006985 KMSKS motif; other site 342108006986 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 342108006987 tRNA binding surface [nucleotide binding]; other site 342108006988 anticodon binding site; other site 342108006989 DNA polymerase III subunit delta'; Validated; Region: PRK07471 342108006990 DNA polymerase III subunit delta'; Validated; Region: PRK08485 342108006991 thymidylate kinase; Validated; Region: tmk; PRK00698 342108006992 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 342108006993 TMP-binding site; other site 342108006994 ATP-binding site [chemical binding]; other site 342108006995 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 342108006996 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 342108006997 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 342108006998 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 342108006999 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 342108007000 Cell division protein [Cell division and chromosome partitioning]; Region: FtsN; COG3087 342108007001 Sporulation related domain; Region: SPOR; pfam05036 342108007002 Transglycosylase SLT domain; Region: SLT_2; pfam13406 342108007003 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 342108007004 N-acetyl-D-glucosamine binding site [chemical binding]; other site 342108007005 Uncharacterized conserved protein [Function unknown]; Region: COG1434 342108007006 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 342108007007 putative active site [active] 342108007008 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 342108007009 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 342108007010 putative ligand binding site [chemical binding]; other site 342108007011 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 342108007012 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 342108007013 active site 342108007014 catalytic tetrad [active] 342108007015 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 342108007016 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 342108007017 Walker A/P-loop; other site 342108007018 ATP binding site [chemical binding]; other site 342108007019 Q-loop/lid; other site 342108007020 ABC transporter signature motif; other site 342108007021 Walker B; other site 342108007022 D-loop; other site 342108007023 H-loop/switch region; other site 342108007024 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 342108007025 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 342108007026 Walker A/P-loop; other site 342108007027 ATP binding site [chemical binding]; other site 342108007028 Q-loop/lid; other site 342108007029 ABC transporter signature motif; other site 342108007030 Walker B; other site 342108007031 D-loop; other site 342108007032 H-loop/switch region; other site 342108007033 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 342108007034 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 342108007035 TM-ABC transporter signature motif; other site 342108007036 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 342108007037 TM-ABC transporter signature motif; other site 342108007038 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 342108007039 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_6; cd06340 342108007040 putative ligand binding site [chemical binding]; other site 342108007041 response regulator PleD; Reviewed; Region: pleD; PRK09581 342108007042 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108007043 metal binding site [ion binding]; metal-binding site 342108007044 active site 342108007045 I-site; other site 342108007046 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 342108007047 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 342108007048 catalytic residues [active] 342108007049 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 342108007050 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108007051 catalytic residue [active] 342108007052 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 342108007053 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 342108007054 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 342108007055 ATP binding site [chemical binding]; other site 342108007056 putative Mg++ binding site [ion binding]; other site 342108007057 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 342108007058 nucleotide binding region [chemical binding]; other site 342108007059 ATP-binding site [chemical binding]; other site 342108007060 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 342108007061 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 342108007062 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 342108007063 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 342108007064 generic binding surface II; other site 342108007065 ssDNA binding site; other site 342108007066 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 342108007067 ATP binding site [chemical binding]; other site 342108007068 putative Mg++ binding site [ion binding]; other site 342108007069 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 342108007070 nucleotide binding region [chemical binding]; other site 342108007071 ATP-binding site [chemical binding]; other site 342108007072 Predicted membrane protein [Function unknown]; Region: COG2119 342108007073 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 342108007074 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 342108007075 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 342108007076 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 342108007077 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108007078 ABC transporter signature motif; other site 342108007079 Walker B; other site 342108007080 D-loop; other site 342108007081 H-loop/switch region; other site 342108007082 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 342108007083 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 342108007084 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 342108007085 ligand binding site [chemical binding]; other site 342108007086 Pseudouridine synthase, Escherichia coli RluE; Region: PseudoU_synth_RluE; cd02566 342108007087 pseudouridine synthase; Region: TIGR00093 342108007088 probable active site [active] 342108007089 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 342108007090 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 342108007091 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 342108007092 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 342108007093 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 342108007094 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 342108007095 RNA binding surface [nucleotide binding]; other site 342108007096 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 342108007097 active site 342108007098 uracil binding [chemical binding]; other site 342108007099 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 342108007100 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 342108007101 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 342108007102 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 342108007103 dimer interface [polypeptide binding]; other site 342108007104 [2Fe-2S] cluster binding site [ion binding]; other site 342108007105 Domain of unknown function (DUF4170); Region: DUF4170; pfam13773 342108007106 Domain of unknown function (DUF4170); Region: DUF4170; pfam13773 342108007107 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 342108007108 Glucose inhibited division protein A; Region: GIDA; pfam01134 342108007109 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 342108007110 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 342108007111 dimer interface [polypeptide binding]; other site 342108007112 active site 342108007113 metal binding site [ion binding]; metal-binding site 342108007114 glutathione binding site [chemical binding]; other site 342108007115 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 342108007116 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 342108007117 Protein of unknown function (DUF1009); Region: DUF1009; pfam06230 342108007118 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 342108007119 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 342108007120 active site 342108007121 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 342108007122 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 342108007123 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 342108007124 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 342108007125 trimer interface [polypeptide binding]; other site 342108007126 active site 342108007127 UDP-GlcNAc binding site [chemical binding]; other site 342108007128 lipid binding site [chemical binding]; lipid-binding site 342108007129 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 342108007130 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 342108007131 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 342108007132 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 342108007133 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 342108007134 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 342108007135 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 342108007136 Surface antigen; Region: Bac_surface_Ag; pfam01103 342108007137 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 342108007138 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 342108007139 active site 342108007140 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 342108007141 protein binding site [polypeptide binding]; other site 342108007142 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 342108007143 putative substrate binding region [chemical binding]; other site 342108007144 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 342108007145 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 342108007146 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 342108007147 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 342108007148 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 342108007149 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 342108007150 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 342108007151 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 342108007152 catalytic residue [active] 342108007153 putative FPP diphosphate binding site; other site 342108007154 putative FPP binding hydrophobic cleft; other site 342108007155 dimer interface [polypeptide binding]; other site 342108007156 putative IPP diphosphate binding site; other site 342108007157 ribosome recycling factor; Reviewed; Region: frr; PRK00083 342108007158 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 342108007159 hinge region; other site 342108007160 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 342108007161 putative nucleotide binding site [chemical binding]; other site 342108007162 uridine monophosphate binding site [chemical binding]; other site 342108007163 homohexameric interface [polypeptide binding]; other site 342108007164 elongation factor Ts; Provisional; Region: tsf; PRK09377 342108007165 UBA/TS-N domain; Region: UBA; pfam00627 342108007166 Elongation factor TS; Region: EF_TS; pfam00889 342108007167 Elongation factor TS; Region: EF_TS; pfam00889 342108007168 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 342108007169 rRNA interaction site [nucleotide binding]; other site 342108007170 S8 interaction site; other site 342108007171 putative laminin-1 binding site; other site 342108007172 penicillin-insensitive murein endopeptidase; Reviewed; Region: mepA; PRK09429 342108007173 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108007174 Zn2+ binding site [ion binding]; other site 342108007175 Mg2+ binding site [ion binding]; other site 342108007176 acyl-CoA synthetase; Validated; Region: PRK08162 342108007177 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 342108007178 acyl-activating enzyme (AAE) consensus motif; other site 342108007179 putative active site [active] 342108007180 AMP binding site [chemical binding]; other site 342108007181 putative CoA binding site [chemical binding]; other site 342108007182 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 342108007183 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 342108007184 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 342108007185 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 342108007186 active site 342108007187 metal binding site [ion binding]; metal-binding site 342108007188 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108007189 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 342108007190 binding surface 342108007191 TPR motif; other site 342108007192 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 342108007193 binding surface 342108007194 TPR motif; other site 342108007195 TPR repeat; Region: TPR_11; pfam13414 342108007196 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 342108007197 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 342108007198 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cd02116 342108007199 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 342108007200 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 342108007201 Proline dehydrogenase; Region: Pro_dh; pfam01619 342108007202 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 342108007203 Glutamate binding site [chemical binding]; other site 342108007204 NAD binding site [chemical binding]; other site 342108007205 catalytic residues [active] 342108007206 Squalene/phytoene synthase; Region: SQS_PSY; pfam00494 342108007207 substrate binding pocket [chemical binding]; other site 342108007208 aspartate-rich region 2; other site 342108007209 substrate-Mg2+ binding site; other site 342108007210 squalene synthase HpnC; Region: HpnC; TIGR03464 342108007211 substrate binding pocket [chemical binding]; other site 342108007212 substrate-Mg2+ binding site; other site 342108007213 aspartate-rich region 1; other site 342108007214 aspartate-rich region 2; other site 342108007215 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 342108007216 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 342108007217 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 342108007218 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 342108007219 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 342108007220 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 342108007221 Protein export membrane protein; Region: SecD_SecF; pfam02355 342108007222 SecD export protein N-terminal TM region; Region: SecD-TM1; cl08136 342108007223 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 342108007224 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 342108007225 Preprotein translocase subunit; Region: YajC; pfam02699 342108007226 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 342108007227 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 342108007228 Walker A motif; other site 342108007229 ATP binding site [chemical binding]; other site 342108007230 Walker B motif; other site 342108007231 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 342108007232 heme-binding site [chemical binding]; other site 342108007233 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108007234 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108007235 dimer interface [polypeptide binding]; other site 342108007236 putative CheW interface [polypeptide binding]; other site 342108007237 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 342108007238 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 342108007239 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 342108007240 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 342108007241 Peptidase family M23; Region: Peptidase_M23; pfam01551 342108007242 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 342108007243 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 342108007244 S-adenosylmethionine binding site [chemical binding]; other site 342108007245 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 342108007246 seryl-tRNA synthetase; Provisional; Region: PRK05431 342108007247 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 342108007248 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 342108007249 dimer interface [polypeptide binding]; other site 342108007250 active site 342108007251 motif 1; other site 342108007252 motif 2; other site 342108007253 motif 3; other site 342108007254 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 342108007255 twin arginine-targeting protein translocase TatB; Region: tatB; TIGR01410 342108007256 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2832 342108007257 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 342108007258 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 342108007259 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 342108007260 Peptidase family M50; Region: Peptidase_M50; pfam02163 342108007261 putative substrate binding region [chemical binding]; other site 342108007262 Sporulation related domain; Region: SPOR; pfam05036 342108007263 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 342108007264 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 342108007265 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 342108007266 active site 342108007267 HIGH motif; other site 342108007268 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 342108007269 KMSK motif region; other site 342108007270 tRNA binding surface [nucleotide binding]; other site 342108007271 DALR anticodon binding domain; Region: DALR_1; smart00836 342108007272 anticodon binding site; other site 342108007273 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108007274 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108007275 metal binding site [ion binding]; metal-binding site 342108007276 active site 342108007277 I-site; other site 342108007278 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 342108007279 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 342108007280 putative catalytic site [active] 342108007281 putative phosphate binding site [ion binding]; other site 342108007282 active site 342108007283 metal binding site A [ion binding]; metal-binding site 342108007284 DNA binding site [nucleotide binding] 342108007285 putative AP binding site [nucleotide binding]; other site 342108007286 putative metal binding site B [ion binding]; other site 342108007287 Hemerythrin; Region: Hemerythrin; cd12107 342108007288 Fe binding site [ion binding]; other site 342108007289 Response regulator receiver domain; Region: Response_reg; pfam00072 342108007290 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 342108007291 active site 342108007292 phosphorylation site [posttranslational modification] 342108007293 intermolecular recognition site; other site 342108007294 dimerization interface [polypeptide binding]; other site 342108007295 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 342108007296 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 342108007297 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 342108007298 motif II; other site 342108007299 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 342108007300 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 342108007301 N-acetyl-D-glucosamine binding site [chemical binding]; other site 342108007302 catalytic residue [active] 342108007303 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 342108007304 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 342108007305 Walker A/P-loop; other site 342108007306 ATP binding site [chemical binding]; other site 342108007307 Q-loop/lid; other site 342108007308 ABC transporter signature motif; other site 342108007309 Walker B; other site 342108007310 D-loop; other site 342108007311 H-loop/switch region; other site 342108007312 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 342108007313 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 342108007314 FtsX-like permease family; Region: FtsX; pfam02687 342108007315 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 342108007316 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 342108007317 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108007318 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 342108007319 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 342108007320 dimer interface [polypeptide binding]; other site 342108007321 active site 342108007322 catalytic residue [active] 342108007323 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 342108007324 SmpB-tmRNA interface; other site 342108007325 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 342108007326 bacterial and archael members of the sulfite oxidase (SO) family of molybdopterin binding domains. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and...; Region: arch_bact_SO_family_Moco; cd02109 342108007327 Moco binding site; other site 342108007328 metal coordination site [ion binding]; other site 342108007329 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 342108007330 dimer interface [polypeptide binding]; other site 342108007331 phosphorylation site [posttranslational modification] 342108007332 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 342108007333 ATP binding site [chemical binding]; other site 342108007334 Mg2+ binding site [ion binding]; other site 342108007335 G-X-G motif; other site 342108007336 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 342108007337 tetramer interfaces [polypeptide binding]; other site 342108007338 binuclear metal-binding site [ion binding]; other site 342108007339 Competence-damaged protein; Region: CinA; pfam02464 342108007340 thiamine pyrophosphate protein; Validated; Region: PRK08199 342108007341 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 342108007342 PYR/PP interface [polypeptide binding]; other site 342108007343 dimer interface [polypeptide binding]; other site 342108007344 TPP binding site [chemical binding]; other site 342108007345 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 342108007346 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; cd00568 342108007347 TPP-binding site [chemical binding]; other site 342108007348 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108007349 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 342108007350 ligand binding site [chemical binding]; other site 342108007351 flexible hinge region; other site 342108007352 Cyclophilin-like; Region: Cyclophil_like; pfam04126 342108007353 Acetokinase family; Region: Acetate_kinase; cl17229 342108007354 propionate/acetate kinase; Provisional; Region: PRK12379 342108007355 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 342108007356 (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 342108007357 dimer interaction site [polypeptide binding]; other site 342108007358 substrate-binding tunnel; other site 342108007359 active site 342108007360 catalytic site [active] 342108007361 substrate binding site [chemical binding]; other site 342108007362 phosphate acetyltransferase; Provisional; Region: PRK11890 342108007363 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 342108007364 CoA binding domain; Region: CoA_binding_2; pfam13380 342108007365 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 342108007366 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 342108007367 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 342108007368 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 342108007369 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 342108007370 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 342108007371 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 342108007372 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 342108007373 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 342108007374 ligand binding site [chemical binding]; other site 342108007375 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 342108007376 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 342108007377 substrate binding site [chemical binding]; other site 342108007378 oxyanion hole (OAH) forming residues; other site 342108007379 trimer interface [polypeptide binding]; other site 342108007380 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 342108007381 OAH/OAS sulfhydrylase; Region: OAH_OAS_sulfhy; TIGR01326 342108007382 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 342108007383 homodimer interface [polypeptide binding]; other site 342108007384 substrate-cofactor binding pocket; other site 342108007385 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108007386 catalytic residue [active] 342108007387 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 342108007388 dimer interface [polypeptide binding]; other site 342108007389 allosteric magnesium binding site [ion binding]; other site 342108007390 active site 342108007391 aspartate-rich active site metal binding site; other site 342108007392 Schiff base residues; other site 342108007393 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 342108007394 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 342108007395 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 342108007396 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 342108007397 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 342108007398 Uncharacterized conserved protein [Function unknown]; Region: COG1262 342108007399 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 342108007400 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 342108007401 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 342108007402 Late embryogenesis abundant protein; Region: LEA_2; pfam03168 342108007403 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 342108007404 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 342108007405 putative active site [active] 342108007406 putative PHP Thumb interface [polypeptide binding]; other site 342108007407 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 342108007408 generic binding surface II; other site 342108007409 generic binding surface I; other site 342108007410 MAPEG family; Region: MAPEG; cl09190 342108007411 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 342108007412 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 342108007413 Walker A/P-loop; other site 342108007414 ATP binding site [chemical binding]; other site 342108007415 Q-loop/lid; other site 342108007416 ABC transporter signature motif; other site 342108007417 Walker B; other site 342108007418 D-loop; other site 342108007419 H-loop/switch region; other site 342108007420 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 342108007421 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 342108007422 FtsX-like permease family; Region: FtsX; pfam02687 342108007423 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 342108007424 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 342108007425 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 342108007426 dimer interface [polypeptide binding]; other site 342108007427 substrate binding site [chemical binding]; other site 342108007428 metal binding site [ion binding]; metal-binding site 342108007429 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 342108007430 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 342108007431 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_PGA_like; cd03747 342108007432 active site 342108007433 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 342108007434 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 342108007435 flagellar motor stator protein MotA; Region: MotA1; TIGR03818 342108007436 flagellar motor protein MotB; Validated; Region: motB; PRK09041 342108007437 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 342108007438 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 342108007439 ligand binding site [chemical binding]; other site 342108007440 RDD family; Region: RDD; pfam06271 342108007441 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 342108007442 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 342108007443 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 342108007444 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT2; COG4665 342108007445 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 342108007446 DctM-like transporters; Region: DctM; pfam06808 342108007447 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 342108007448 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 342108007449 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 342108007450 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 342108007451 CAP-like domain; other site 342108007452 active site 342108007453 primary dimer interface [polypeptide binding]; other site 342108007454 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 342108007455 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 342108007456 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 342108007457 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108007458 NAD(P) binding site [chemical binding]; other site 342108007459 active site 342108007460 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 342108007461 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 342108007462 active site 342108007463 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 342108007464 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 342108007465 substrate binding site [chemical binding]; other site 342108007466 oxyanion hole (OAH) forming residues; other site 342108007467 trimer interface [polypeptide binding]; other site 342108007468 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 342108007469 classical (c) SDRs; Region: SDR_c; cd05233 342108007470 NAD(P) binding site [chemical binding]; other site 342108007471 active site 342108007472 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 342108007473 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 342108007474 substrate binding site [chemical binding]; other site 342108007475 oxyanion hole (OAH) forming residues; other site 342108007476 trimer interface [polypeptide binding]; other site 342108007477 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 342108007478 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 342108007479 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 342108007480 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 342108007481 NAD binding site [chemical binding]; other site 342108007482 catalytic residues [active] 342108007483 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 342108007484 Ligand Binding Site [chemical binding]; other site 342108007485 acetyl-CoA acetyltransferase; Provisional; Region: PRK08131 342108007486 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 342108007487 dimer interface [polypeptide binding]; other site 342108007488 active site 342108007489 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 342108007490 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 342108007491 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 342108007492 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 342108007493 enoyl-CoA hydratase; Provisional; Region: PRK08138 342108007494 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 342108007495 substrate binding site [chemical binding]; other site 342108007496 oxyanion hole (OAH) forming residues; other site 342108007497 trimer interface [polypeptide binding]; other site 342108007498 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 342108007499 Transcriptional regulator [Transcription]; Region: IclR; COG1414 342108007500 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 342108007501 Bacterial transcriptional regulator; Region: IclR; pfam01614 342108007502 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 342108007503 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 342108007504 active site 342108007505 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 342108007506 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 342108007507 acyl-activating enzyme (AAE) consensus motif; other site 342108007508 AMP binding site [chemical binding]; other site 342108007509 active site 342108007510 CoA binding site [chemical binding]; other site 342108007511 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 342108007512 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 342108007513 ligand binding site [chemical binding]; other site 342108007514 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 342108007515 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 342108007516 TM-ABC transporter signature motif; other site 342108007517 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 342108007518 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 342108007519 TM-ABC transporter signature motif; other site 342108007520 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 342108007521 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 342108007522 Walker A/P-loop; other site 342108007523 ATP binding site [chemical binding]; other site 342108007524 Q-loop/lid; other site 342108007525 ABC transporter signature motif; other site 342108007526 Walker B; other site 342108007527 D-loop; other site 342108007528 H-loop/switch region; other site 342108007529 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 342108007530 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 342108007531 Walker A/P-loop; other site 342108007532 ATP binding site [chemical binding]; other site 342108007533 Q-loop/lid; other site 342108007534 ABC transporter signature motif; other site 342108007535 Walker B; other site 342108007536 D-loop; other site 342108007537 H-loop/switch region; other site 342108007538 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 342108007539 CoenzymeA binding site [chemical binding]; other site 342108007540 subunit interaction site [polypeptide binding]; other site 342108007541 PHB binding site; other site 342108007542 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 342108007543 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 342108007544 FMN binding site [chemical binding]; other site 342108007545 substrate binding site [chemical binding]; other site 342108007546 putative catalytic residue [active] 342108007547 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 342108007548 CoA-transferase family III; Region: CoA_transf_3; pfam02515 342108007549 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 342108007550 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 342108007551 TPR motif; other site 342108007552 binding surface 342108007553 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 342108007554 binding surface 342108007555 TPR motif; other site 342108007556 TPR repeat; Region: TPR_11; pfam13414 342108007557 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 342108007558 binding surface 342108007559 TPR motif; other site 342108007560 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 342108007561 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 342108007562 ApbE family; Region: ApbE; pfam02424 342108007563 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 342108007564 electron transport complex protein RsxA; Provisional; Region: PRK05151 342108007565 electron transport complex protein RnfB; Provisional; Region: PRK05113 342108007566 Putative Fe-S cluster; Region: FeS; cl17515 342108007567 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 342108007568 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 342108007569 SLBB domain; Region: SLBB; pfam10531 342108007570 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 342108007571 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 342108007572 electron transport complex, RnfABCDGE type, G subunit; Region: rnfG; TIGR01947 342108007573 electron transport complex RsxE subunit; Provisional; Region: PRK12405 342108007574 RnfH family Ubiquitin; Region: Ub-RnfH; pfam03658 342108007575 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 342108007576 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 342108007577 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 342108007578 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 342108007579 dimer interface [polypeptide binding]; other site 342108007580 conserved gate region; other site 342108007581 putative PBP binding loops; other site 342108007582 ABC-ATPase subunit interface; other site 342108007583 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 342108007584 dimer interface [polypeptide binding]; other site 342108007585 conserved gate region; other site 342108007586 putative PBP binding loops; other site 342108007587 ABC-ATPase subunit interface; other site 342108007588 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 342108007589 ATP-binding cassette domain of the polyamine transporter; Region: ABC_PotA_N; cd03300 342108007590 Walker A/P-loop; other site 342108007591 ATP binding site [chemical binding]; other site 342108007592 Q-loop/lid; other site 342108007593 ABC transporter signature motif; other site 342108007594 Walker B; other site 342108007595 D-loop; other site 342108007596 H-loop/switch region; other site 342108007597 TOBE domain; Region: TOBE_2; pfam08402 342108007598 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 342108007599 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 342108007600 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 342108007601 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 342108007602 Na binding site [ion binding]; other site 342108007603 Protein of unknown function, DUF485; Region: DUF485; pfam04341 342108007604 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108007605 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108007606 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 342108007607 dimerization interface [polypeptide binding]; other site 342108007608 PAS domain; Region: PAS; smart00091 342108007609 PAS fold; Region: PAS_4; pfam08448 342108007610 putative active site [active] 342108007611 heme pocket [chemical binding]; other site 342108007612 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108007613 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 342108007614 dimer interface [polypeptide binding]; other site 342108007615 phosphorylation site [posttranslational modification] 342108007616 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 342108007617 ATP binding site [chemical binding]; other site 342108007618 G-X-G motif; other site 342108007619 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108007620 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 342108007621 active site 342108007622 phosphorylation site [posttranslational modification] 342108007623 intermolecular recognition site; other site 342108007624 dimerization interface [polypeptide binding]; other site 342108007625 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108007626 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 342108007627 active site 342108007628 phosphorylation site [posttranslational modification] 342108007629 intermolecular recognition site; other site 342108007630 dimerization interface [polypeptide binding]; other site 342108007631 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 342108007632 DNA binding site [nucleotide binding] 342108007633 Cytochrome c; Region: Cytochrom_C; cl11414 342108007634 Cytochrome c; Region: Cytochrom_C; cl11414 342108007635 acyl-CoA synthetase; Validated; Region: PRK08162 342108007636 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 342108007637 acyl-activating enzyme (AAE) consensus motif; other site 342108007638 putative active site [active] 342108007639 AMP binding site [chemical binding]; other site 342108007640 putative CoA binding site [chemical binding]; other site 342108007641 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 342108007642 Ligand binding site [chemical binding]; other site 342108007643 Electron transfer flavoprotein domain; Region: ETF; pfam01012 342108007644 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 342108007645 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 342108007646 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 342108007647 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 342108007648 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 342108007649 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 342108007650 active site 342108007651 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 342108007652 Response regulator receiver domain; Region: Response_reg; pfam00072 342108007653 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 342108007654 active site 342108007655 phosphorylation site [posttranslational modification] 342108007656 intermolecular recognition site; other site 342108007657 dimerization interface [polypeptide binding]; other site 342108007658 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108007659 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 342108007660 dimer interface [polypeptide binding]; other site 342108007661 phosphorylation site [posttranslational modification] 342108007662 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 342108007663 ATP binding site [chemical binding]; other site 342108007664 Mg2+ binding site [ion binding]; other site 342108007665 G-X-G motif; other site 342108007666 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 342108007667 Response regulator receiver domain; Region: Response_reg; pfam00072 342108007668 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 342108007669 active site 342108007670 phosphorylation site [posttranslational modification] 342108007671 intermolecular recognition site; other site 342108007672 dimerization interface [polypeptide binding]; other site 342108007673 PAS domain; Region: PAS_9; pfam13426 342108007674 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 342108007675 dimer interface [polypeptide binding]; other site 342108007676 phosphorylation site [posttranslational modification] 342108007677 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 342108007678 ATP binding site [chemical binding]; other site 342108007679 Mg2+ binding site [ion binding]; other site 342108007680 G-X-G motif; other site 342108007681 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 342108007682 Response regulator receiver domain; Region: Response_reg; pfam00072 342108007683 active site 342108007684 phosphorylation site [posttranslational modification] 342108007685 intermolecular recognition site; other site 342108007686 dimerization interface [polypeptide binding]; other site 342108007687 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 342108007688 Response regulator receiver domain; Region: Response_reg; pfam00072 342108007689 active site 342108007690 phosphorylation site [posttranslational modification] 342108007691 intermolecular recognition site; other site 342108007692 dimerization interface [polypeptide binding]; other site 342108007693 Precorrin-6x reductase [Coenzyme metabolism]; Region: CobK; COG2099 342108007694 Precorrin-6x reductase CbiJ/CobK; Region: CbiJ; pfam02571 342108007695 cobalt-precorrin-6A synthase; Reviewed; Region: cbiD; PRK00075 342108007696 Response regulator receiver domain; Region: Response_reg; pfam00072 342108007697 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 342108007698 active site 342108007699 phosphorylation site [posttranslational modification] 342108007700 intermolecular recognition site; other site 342108007701 dimerization interface [polypeptide binding]; other site 342108007702 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 342108007703 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 342108007704 putative active site [active] 342108007705 heme pocket [chemical binding]; other site 342108007706 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108007707 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 342108007708 putative active site [active] 342108007709 heme pocket [chemical binding]; other site 342108007710 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 342108007711 dimer interface [polypeptide binding]; other site 342108007712 phosphorylation site [posttranslational modification] 342108007713 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 342108007714 ATP binding site [chemical binding]; other site 342108007715 Mg2+ binding site [ion binding]; other site 342108007716 G-X-G motif; other site 342108007717 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 342108007718 RNA polymerase sigma factor; Provisional; Region: PRK12546 342108007719 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 342108007720 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 342108007721 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108007722 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 342108007723 active site 342108007724 phosphorylation site [posttranslational modification] 342108007725 intermolecular recognition site; other site 342108007726 dimerization interface [polypeptide binding]; other site 342108007727 pyruvate phosphate dikinase; Provisional; Region: PRK09279 342108007728 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 342108007729 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 342108007730 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 342108007731 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 342108007732 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 342108007733 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 342108007734 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 342108007735 dimer interface [polypeptide binding]; other site 342108007736 motif 1; other site 342108007737 active site 342108007738 motif 2; other site 342108007739 motif 3; other site 342108007740 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108007741 HAMP domain; Region: HAMP; pfam00672 342108007742 dimerization interface [polypeptide binding]; other site 342108007743 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108007744 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108007745 dimer interface [polypeptide binding]; other site 342108007746 putative CheW interface [polypeptide binding]; other site 342108007747 PilZ domain; Region: PilZ; pfam07238 342108007748 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 342108007749 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108007750 Hemerythrin; Region: Hemerythrin; cd12107 342108007751 Fe binding site [ion binding]; other site 342108007752 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 342108007753 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 342108007754 C-terminal domain interface [polypeptide binding]; other site 342108007755 GSH binding site (G-site) [chemical binding]; other site 342108007756 dimer interface [polypeptide binding]; other site 342108007757 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 342108007758 N-terminal domain interface [polypeptide binding]; other site 342108007759 putative dimer interface [polypeptide binding]; other site 342108007760 active site 342108007761 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 342108007762 anti sigma factor interaction site; other site 342108007763 regulatory phosphorylation site [posttranslational modification]; other site 342108007764 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 342108007765 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 342108007766 Response regulator receiver domain; Region: Response_reg; pfam00072 342108007767 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 342108007768 active site 342108007769 phosphorylation site [posttranslational modification] 342108007770 intermolecular recognition site; other site 342108007771 dimerization interface [polypeptide binding]; other site 342108007772 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 342108007773 HAMP domain; Region: HAMP; pfam00672 342108007774 dimerization interface [polypeptide binding]; other site 342108007775 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108007776 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108007777 dimer interface [polypeptide binding]; other site 342108007778 putative CheW interface [polypeptide binding]; other site 342108007779 fructose-1,6-bisphosphatase family protein; Region: PLN02628 342108007780 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 342108007781 AMP binding site [chemical binding]; other site 342108007782 metal binding site [ion binding]; metal-binding site 342108007783 active site 342108007784 Protein of unknown function (DUF3457); Region: DUF3457; pfam11939 342108007785 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 342108007786 Uncharacterized conserved protein [Function unknown]; Region: COG1262 342108007787 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG3837 342108007788 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 342108007789 4Fe-4S binding domain; Region: Fer4_6; pfam12837 342108007790 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 342108007791 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 342108007792 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional; Region: PRK14489 342108007793 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 342108007794 GTP binding site; other site 342108007795 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 342108007796 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 342108007797 Nitrate reductase delta subunit; Region: Nitrate_red_del; pfam02613 342108007798 formate dehydrogenase, alpha subunit, proteobacterial-type; Region: formate-DH-alph; TIGR01553 342108007799 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 342108007800 [4Fe-4S] binding site [ion binding]; other site 342108007801 molybdopterin cofactor binding site; other site 342108007802 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 342108007803 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 342108007804 molybdopterin cofactor binding site; other site 342108007805 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 342108007806 4Fe-4S binding domain; Region: Fer4; cl02805 342108007807 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 342108007808 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 342108007809 phenylacetic acid degradation protein PaaY; Region: PaaY; TIGR02287 342108007810 paaY-like: This group is composed by uncharacterized proteins with similarity to the protein product of the E. coli paaY gene, which is part of the paa gene cluster responsible for phenylacetic acid degradation. Proteins in this group are expected to...; Region: LbH_paaY_like; cd04745 342108007811 putative trimer interface [polypeptide binding]; other site 342108007812 putative metal binding site [ion binding]; other site 342108007813 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 342108007814 active site 342108007815 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 342108007816 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108007817 NAD(P) binding site [chemical binding]; other site 342108007818 active site 342108007819 Protein of unknown function (DUF1192); Region: DUF1192; pfam06698 342108007820 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 342108007821 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 342108007822 NAD(P) binding site [chemical binding]; other site 342108007823 Protein of unknown function (DUF1013); Region: DUF1013; pfam06242 342108007824 Protein of unknown function; Region: DUF3971; pfam13116 342108007825 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 342108007826 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional; Region: PRK14108 342108007827 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 342108007828 metal binding triad; other site 342108007829 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 342108007830 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 342108007831 metal binding triad; other site 342108007832 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 342108007833 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 342108007834 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 342108007835 catalytic triad [active] 342108007836 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 342108007837 dinuclear metal binding motif [ion binding]; other site 342108007838 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 342108007839 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 342108007840 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 342108007841 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 342108007842 4Fe-4S binding domain; Region: Fer4_5; pfam12801 342108007843 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 342108007844 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 342108007845 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 342108007846 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 342108007847 [4Fe-4S] binding site [ion binding]; other site 342108007848 molybdopterin cofactor binding site; other site 342108007849 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 342108007850 molybdopterin cofactor binding site; other site 342108007851 NapD protein; Region: NapD; pfam03927 342108007852 ferredoxin-type protein NapF; Region: napF; TIGR00402 342108007853 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 342108007854 4Fe-4S binding domain; Region: Fer4; cl02805 342108007855 PAS domain; Region: PAS; smart00091 342108007856 PAS domain; Region: PAS_9; pfam13426 342108007857 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108007858 metal binding site [ion binding]; metal-binding site 342108007859 active site 342108007860 I-site; other site 342108007861 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 342108007862 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 342108007863 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]; Region: NPY1; COG2816 342108007864 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 342108007865 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 342108007866 putative NADH binding site [chemical binding]; other site 342108007867 putative active site [active] 342108007868 nudix motif; other site 342108007869 putative metal binding site [ion binding]; other site 342108007870 Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to...; Region: PRK_like; cd02029 342108007871 active site 342108007872 ribulose bisphosphate carboxylase; Provisional; Region: PRK13475 342108007873 Ribulose bisphosphate carboxylase large chain, Form II; Region: RuBisCO_large_II; cd08211 342108007874 dimer interface [polypeptide binding]; other site 342108007875 active site 342108007876 catalytic residue [active] 342108007877 metal binding site [ion binding]; metal-binding site 342108007878 Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the...; Region: deoxycytidylate_deaminase; cd01286 342108007879 catalytic motif [active] 342108007880 Zn binding site [ion binding]; other site 342108007881 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 342108007882 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 342108007883 FeS/SAM binding site; other site 342108007884 HemN C-terminal domain; Region: HemN_C; pfam06969 342108007885 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 342108007886 B1 nucleotide binding pocket [chemical binding]; other site 342108007887 B2 nucleotide binding pocket [chemical binding]; other site 342108007888 CAS motifs; other site 342108007889 active site 342108007890 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 342108007891 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional; Region: PRK11840 342108007892 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 342108007893 thiS-thiF/thiG interaction site; other site 342108007894 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 342108007895 ThiS interaction site; other site 342108007896 putative active site [active] 342108007897 tetramer interface [polypeptide binding]; other site 342108007898 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 342108007899 ATP binding site [chemical binding]; other site 342108007900 Mg2+ binding site [ion binding]; other site 342108007901 G-X-G motif; other site 342108007902 PBP superfamily domain; Region: PBP_like_2; pfam12849 342108007903 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 342108007904 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 342108007905 Dehydroquinase class II; Region: DHquinase_II; pfam01220 342108007906 active site 342108007907 trimer interface [polypeptide binding]; other site 342108007908 dimer interface [polypeptide binding]; other site 342108007909 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 342108007910 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 342108007911 carboxyltransferase (CT) interaction site; other site 342108007912 biotinylation site [posttranslational modification]; other site 342108007913 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 342108007914 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 342108007915 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 342108007916 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 342108007917 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 342108007918 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 342108007919 active site 342108007920 DNA binding site [nucleotide binding] 342108007921 Int/Topo IB signature motif; other site 342108007922 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 342108007923 non-specific DNA binding site [nucleotide binding]; other site 342108007924 salt bridge; other site 342108007925 Complex I intermediate-associated protein 30 (CIA30); Region: CIA30; pfam08547 342108007926 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 342108007927 sequence-specific DNA binding site [nucleotide binding]; other site 342108007928 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 342108007929 Protein of unknown function (DUF2815); Region: DUF2815; pfam10991 342108007930 Protein of unknown function (DUF2800); Region: DUF2800; pfam10926 342108007931 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 342108007932 active site 342108007933 DNA binding site [nucleotide binding] 342108007934 catalytic site [active] 342108007935 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 342108007936 AAA domain; Region: AAA_25; pfam13481 342108007937 Walker B motif; other site 342108007938 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 342108007939 SPRY domain-like in bacteria; Region: SPRY_like; cd12886 342108007940 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 342108007941 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 342108007942 Na binding site [ion binding]; other site 342108007943 Protein of unknown function, DUF485; Region: DUF485; pfam04341 342108007944 FeoC like transcriptional regulator; Region: FeoC; pfam09012 342108007945 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 342108007946 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 342108007947 G1 box; other site 342108007948 GTP/Mg2+ binding site [chemical binding]; other site 342108007949 Switch I region; other site 342108007950 G2 box; other site 342108007951 G3 box; other site 342108007952 Switch II region; other site 342108007953 G4 box; other site 342108007954 G5 box; other site 342108007955 Nucleoside recognition; Region: Gate; pfam07670 342108007956 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 342108007957 Nucleoside recognition; Region: Gate; pfam07670 342108007958 FeoA domain; Region: FeoA; pfam04023 342108007959 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108007960 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 342108007961 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 342108007962 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or...; Region: GlcN6P_deaminase; cd01399 342108007963 active site 342108007964 trimer interface [polypeptide binding]; other site 342108007965 allosteric site; other site 342108007966 active site lid [active] 342108007967 Glycoside Hydrolases Family 4; Alpha-glucosidases and alpha-galactosidases; Region: GH4_alpha_glucosidase_galactosidase; cd05297 342108007968 alpha-galactosidase; Provisional; Region: PRK15076 342108007969 NAD binding site [chemical binding]; other site 342108007970 sugar binding site [chemical binding]; other site 342108007971 divalent metal binding site [ion binding]; other site 342108007972 putative tetramer (dimer of dimers) interface [polypeptide binding]; other site 342108007973 dimer interface [polypeptide binding]; other site 342108007974 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108007975 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 342108007976 putative active site [active] 342108007977 heme pocket [chemical binding]; other site 342108007978 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 342108007979 dimer interface [polypeptide binding]; other site 342108007980 phosphorylation site [posttranslational modification] 342108007981 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 342108007982 ATP binding site [chemical binding]; other site 342108007983 Mg2+ binding site [ion binding]; other site 342108007984 G-X-G motif; other site 342108007985 putative nicotinate phosphoribosyltransferase; Provisional; Region: PRK09198 342108007986 pre-B-cell colony-enhancing factor (PBEF)-like. The mammalian members of this group of nicotinate phosphoribosyltransferases (NAPRTases) were originally identified as genes whose expression is upregulated upon activation in lymphoid cells. In general; Region: PBEF_like; cd01569 342108007987 active site 342108007988 Hemerythrin; Region: Hemerythrin; cd12107 342108007989 Fe binding site [ion binding]; other site 342108007990 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 342108007991 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; pfam09923 342108007992 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 342108007993 mce related protein; Region: MCE; pfam02470 342108007994 mce related protein; Region: MCE; pfam02470 342108007995 NADH dehydrogenase; Validated; Region: PRK08183 342108007996 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07562 342108007997 Class II vitamin B12-dependent ribonucleotide reductase; Region: Ribonuc_red_2_N; pfam08471 342108007998 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 342108007999 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 342108008000 active site 342108008001 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 342108008002 TSCPD domain; Region: TSCPD; pfam12637 342108008003 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 342108008004 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 342108008005 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 342108008006 catalytic residues [active] 342108008007 Domain of unknown function (DUF1127); Region: DUF1127; pfam06568 342108008008 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 342108008009 homotrimer interaction site [polypeptide binding]; other site 342108008010 putative active site [active] 342108008011 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108008012 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108008013 metal binding site [ion binding]; metal-binding site 342108008014 active site 342108008015 I-site; other site 342108008016 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 342108008017 CoenzymeA binding site [chemical binding]; other site 342108008018 subunit interaction site [polypeptide binding]; other site 342108008019 PHB binding site; other site 342108008020 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 342108008021 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 342108008022 dimer interface [polypeptide binding]; other site 342108008023 active site 342108008024 Phenylacetate-CoA ligase (also known as PaaK); Region: PaaK; cd05913 342108008025 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 342108008026 active site 342108008027 AMP binding site [chemical binding]; other site 342108008028 homodimer interface [polypeptide binding]; other site 342108008029 acyl-activating enzyme (AAE) consensus motif; other site 342108008030 CoA binding site [chemical binding]; other site 342108008031 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 342108008032 MgtC family; Region: MgtC; pfam02308 342108008033 biotin synthase; Region: bioB; TIGR00433 342108008034 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 342108008035 FeS/SAM binding site; other site 342108008036 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 342108008037 DNA gyrase inhibitor [DNA replication, recombination, and repair]; Region: COG3449 342108008038 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 342108008039 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 342108008040 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108008041 catalytic residue [active] 342108008042 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 342108008043 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 342108008044 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 342108008045 AAA domain; Region: AAA_26; pfam13500 342108008046 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 342108008047 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 342108008048 inhibitor-cofactor binding pocket; inhibition site 342108008049 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108008050 catalytic residue [active] 342108008051 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 342108008052 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108008053 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 342108008054 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 342108008055 FtsX-like permease family; Region: FtsX; pfam02687 342108008056 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 342108008057 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 342108008058 Walker A/P-loop; other site 342108008059 ATP binding site [chemical binding]; other site 342108008060 Q-loop/lid; other site 342108008061 ABC transporter signature motif; other site 342108008062 Walker B; other site 342108008063 D-loop; other site 342108008064 H-loop/switch region; other site 342108008065 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 342108008066 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 342108008067 active site 342108008068 phosphorylation site [posttranslational modification] 342108008069 intermolecular recognition site; other site 342108008070 dimerization interface [polypeptide binding]; other site 342108008071 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 342108008072 DNA binding residues [nucleotide binding] 342108008073 dimerization interface [polypeptide binding]; other site 342108008074 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 342108008075 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 342108008076 HAMP domain; Region: HAMP; pfam00672 342108008077 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108008078 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108008079 dimer interface [polypeptide binding]; other site 342108008080 putative CheW interface [polypeptide binding]; other site 342108008081 conserved hypothetical protein; Region: MG423; TIGR00649 342108008082 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 342108008083 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 342108008084 pantothenate kinase; Reviewed; Region: PRK13318 342108008085 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 342108008086 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 342108008087 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 342108008088 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 342108008089 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 342108008090 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 342108008091 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 342108008092 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 342108008093 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 342108008094 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 342108008095 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 342108008096 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 342108008097 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 342108008098 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 342108008099 4Fe-4S binding domain; Region: Fer4; pfam00037 342108008100 4Fe-4S binding domain; Region: Fer4; pfam00037 342108008101 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 342108008102 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 342108008103 NADH dehydrogenase subunit G; Validated; Region: PRK09130 342108008104 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 342108008105 catalytic loop [active] 342108008106 iron binding site [ion binding]; other site 342108008107 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 342108008108 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 342108008109 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 342108008110 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 342108008111 SLBB domain; Region: SLBB; pfam10531 342108008112 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 342108008113 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 342108008114 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 342108008115 putative dimer interface [polypeptide binding]; other site 342108008116 [2Fe-2S] cluster binding site [ion binding]; other site 342108008117 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 342108008118 NADH dehydrogenase subunit D; Validated; Region: PRK06075 342108008119 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 342108008120 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 342108008121 NADH dehydrogenase subunit B; Validated; Region: PRK06411 342108008122 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 342108008123 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108008124 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108008125 dimer interface [polypeptide binding]; other site 342108008126 putative CheW interface [polypeptide binding]; other site 342108008127 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 342108008128 IHF - DNA interface [nucleotide binding]; other site 342108008129 IHF dimer interface [polypeptide binding]; other site 342108008130 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 342108008131 Found in ATP-dependent protease La (LON); Region: LON; smart00464 342108008132 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 342108008133 Walker A motif; other site 342108008134 ATP binding site [chemical binding]; other site 342108008135 Walker B motif; other site 342108008136 arginine finger; other site 342108008137 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 342108008138 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 342108008139 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 342108008140 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 342108008141 Walker A motif; other site 342108008142 ATP binding site [chemical binding]; other site 342108008143 Walker B motif; other site 342108008144 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 342108008145 Clp protease; Region: CLP_protease; pfam00574 342108008146 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 342108008147 oligomer interface [polypeptide binding]; other site 342108008148 active site residues [active] 342108008149 trigger factor; Provisional; Region: tig; PRK01490 342108008150 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 342108008151 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 342108008152 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 342108008153 heme-binding site [chemical binding]; other site 342108008154 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108008155 dimer interface [polypeptide binding]; other site 342108008156 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 342108008157 putative CheW interface [polypeptide binding]; other site 342108008158 Predicted transcriptional regulator [Transcription]; Region: COG2378 342108008159 HTH domain; Region: HTH_11; pfam08279 342108008160 WYL domain; Region: WYL; pfam13280 342108008161 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 342108008162 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 342108008163 putative C-terminal domain interface [polypeptide binding]; other site 342108008164 putative GSH binding site (G-site) [chemical binding]; other site 342108008165 putative dimer interface [polypeptide binding]; other site 342108008166 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 342108008167 dimer interface [polypeptide binding]; other site 342108008168 N-terminal domain interface [polypeptide binding]; other site 342108008169 putative substrate binding pocket (H-site) [chemical binding]; other site 342108008170 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 342108008171 Uncharacterized conserved protein [Function unknown]; Region: COG0062 342108008172 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 342108008173 putative substrate binding site [chemical binding]; other site 342108008174 putative ATP binding site [chemical binding]; other site 342108008175 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 342108008176 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 342108008177 Hemerythrin; Region: Hemerythrin; cd12107 342108008178 Fe binding site [ion binding]; other site 342108008179 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 342108008180 dimer interface [polypeptide binding]; other site 342108008181 phosphorylation site [posttranslational modification] 342108008182 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 342108008183 ATP binding site [chemical binding]; other site 342108008184 Mg2+ binding site [ion binding]; other site 342108008185 G-X-G motif; other site 342108008186 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 342108008187 Competence protein; Region: Competence; pfam03772 342108008188 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 342108008189 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 342108008190 HIGH motif; other site 342108008191 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 342108008192 active site 342108008193 KMSKS motif; other site 342108008194 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 342108008195 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 342108008196 dimer interface [polypeptide binding]; other site 342108008197 active site 342108008198 citrylCoA binding site [chemical binding]; other site 342108008199 NADH binding [chemical binding]; other site 342108008200 cationic pore residues; other site 342108008201 oxalacetate/citrate binding site [chemical binding]; other site 342108008202 coenzyme A binding site [chemical binding]; other site 342108008203 catalytic triad [active] 342108008204 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 342108008205 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108008206 ligand binding site [chemical binding]; other site 342108008207 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 342108008208 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 342108008209 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 342108008210 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 342108008211 DNA binding residues [nucleotide binding] 342108008212 EamA-like transporter family; Region: EamA; pfam00892 342108008213 Carbon monoxide dehydrogenase subunit G (CoxG); Region: CoxG; cd05018 342108008214 putative hydrophobic ligand binding site [chemical binding]; other site 342108008215 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 342108008216 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 342108008217 alpha-amylase; Reviewed; Region: malS; PRK09505 342108008218 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane; Region: Tim44; smart00978 342108008219 peptide chain release factor 2; Validated; Region: prfB; PRK00578 342108008220 This domain is found in peptide chain release factors; Region: PCRF; smart00937 342108008221 RF-1 domain; Region: RF-1; pfam00472 342108008222 Heavy-metal resistance; Region: Metal_resist; pfam13801 342108008223 RNA polymerase sigma factor; Reviewed; Region: PRK05602 342108008224 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 342108008225 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 342108008226 DNA binding residues [nucleotide binding] 342108008227 S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100...; Region: S-100; cl08302 342108008228 Ca2+ binding site [ion binding]; other site 342108008229 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 342108008230 Ca2+ binding site [ion binding]; other site 342108008231 rpsU-divergently transcribed protein; Region: diverge_rpsU; TIGR02396 342108008232 COQ9; Region: COQ9; pfam08511 342108008233 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 342108008234 Nitrate and nitrite sensing; Region: NIT; pfam08376 342108008235 HAMP domain; Region: HAMP; pfam00672 342108008236 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108008237 dimer interface [polypeptide binding]; other site 342108008238 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108008239 putative CheW interface [polypeptide binding]; other site 342108008240 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 342108008241 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 342108008242 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 342108008243 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 342108008244 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 342108008245 ligand binding site [chemical binding]; other site 342108008246 homodimer interface [polypeptide binding]; other site 342108008247 NAD(P) binding site [chemical binding]; other site 342108008248 trimer interface B [polypeptide binding]; other site 342108008249 trimer interface A [polypeptide binding]; other site 342108008250 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 342108008251 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 342108008252 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108008253 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108008254 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108008255 dimer interface [polypeptide binding]; other site 342108008256 putative CheW interface [polypeptide binding]; other site 342108008257 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 342108008258 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 342108008259 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 342108008260 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 342108008261 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 342108008262 active site 342108008263 Zn binding site [ion binding]; other site 342108008264 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108008265 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 342108008266 active site 342108008267 phosphorylation site [posttranslational modification] 342108008268 dimerization interface [polypeptide binding]; other site 342108008269 Response regulator receiver domain; Region: Response_reg; pfam00072 342108008270 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 342108008271 active site 342108008272 phosphorylation site [posttranslational modification] 342108008273 intermolecular recognition site; other site 342108008274 dimerization interface [polypeptide binding]; other site 342108008275 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108008276 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108008277 metal binding site [ion binding]; metal-binding site 342108008278 active site 342108008279 I-site; other site 342108008280 Domain of unknown function (DUF1849); Region: DUF1849; pfam08904 342108008281 Caspase domain; Region: Peptidase_C14; pfam00656 342108008282 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 342108008283 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 342108008284 dimer interface [polypeptide binding]; other site 342108008285 anticodon binding site; other site 342108008286 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 342108008287 homodimer interface [polypeptide binding]; other site 342108008288 motif 1; other site 342108008289 active site 342108008290 motif 2; other site 342108008291 GAD domain; Region: GAD; pfam02938 342108008292 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 342108008293 active site 342108008294 motif 3; other site 342108008295 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 342108008296 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 342108008297 catalytic site [active] 342108008298 putative active site [active] 342108008299 putative substrate binding site [chemical binding]; other site 342108008300 HRDC domain; Region: HRDC; pfam00570 342108008301 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 342108008302 exopolyphosphatase; Region: exo_poly_only; TIGR03706 342108008303 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 342108008304 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 342108008305 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 342108008306 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 342108008307 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 342108008308 putative domain interface [polypeptide binding]; other site 342108008309 putative active site [active] 342108008310 catalytic site [active] 342108008311 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 342108008312 putative domain interface [polypeptide binding]; other site 342108008313 putative active site [active] 342108008314 catalytic site [active] 342108008315 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 342108008316 binding surface 342108008317 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 342108008318 TPR motif; other site 342108008319 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108008320 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 342108008321 TPR motif; other site 342108008322 binding surface 342108008323 TPR repeat; Region: TPR_11; pfam13414 342108008324 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108008325 short chain dehydrogenase; Provisional; Region: PRK06125 342108008326 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 342108008327 putative NAD(P) binding site [chemical binding]; other site 342108008328 putative active site [active] 342108008329 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 342108008330 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 342108008331 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 342108008332 Domain of unknown function DUF20; Region: UPF0118; pfam01594 342108008333 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 342108008334 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 342108008335 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 342108008336 dimerization interface [polypeptide binding]; other site 342108008337 putative ATP binding site [chemical binding]; other site 342108008338 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 342108008339 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 342108008340 active site 342108008341 substrate binding site [chemical binding]; other site 342108008342 cosubstrate binding site; other site 342108008343 catalytic site [active] 342108008344 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 342108008345 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 342108008346 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 342108008347 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 342108008348 active site 342108008349 PAS fold; Region: PAS_7; pfam12860 342108008350 PAS domain S-box; Region: sensory_box; TIGR00229 342108008351 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 342108008352 putative active site [active] 342108008353 heme pocket [chemical binding]; other site 342108008354 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108008355 PAS domain; Region: PAS; smart00091 342108008356 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 342108008357 dimer interface [polypeptide binding]; other site 342108008358 phosphorylation site [posttranslational modification] 342108008359 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 342108008360 ATP binding site [chemical binding]; other site 342108008361 Mg2+ binding site [ion binding]; other site 342108008362 G-X-G motif; other site 342108008363 Predicted CoA-binding protein [General function prediction only]; Region: COG1832 342108008364 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 342108008365 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 342108008366 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 342108008367 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108008368 catalytic residue [active] 342108008369 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 342108008370 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 342108008371 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 342108008372 active site 342108008373 pyrophosphate binding site [ion binding]; other site 342108008374 thiamine phosphate binding site [chemical binding]; other site 342108008375 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 342108008376 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 342108008377 active site 342108008378 cosubstrate binding site; other site 342108008379 substrate binding site [chemical binding]; other site 342108008380 catalytic site [active] 342108008381 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 342108008382 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 342108008383 glutamine binding [chemical binding]; other site 342108008384 catalytic triad [active] 342108008385 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 342108008386 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 342108008387 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 342108008388 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 342108008389 active site 342108008390 ribulose/triose binding site [chemical binding]; other site 342108008391 phosphate binding site [ion binding]; other site 342108008392 substrate (anthranilate) binding pocket [chemical binding]; other site 342108008393 product (indole) binding pocket [chemical binding]; other site 342108008394 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 342108008395 trimer interface [polypeptide binding]; other site 342108008396 dimer interface [polypeptide binding]; other site 342108008397 putative active site [active] 342108008398 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 342108008399 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 342108008400 dimer interface [polypeptide binding]; other site 342108008401 putative functional site; other site 342108008402 putative MPT binding site; other site 342108008403 LexA repressor; Validated; Region: PRK00215 342108008404 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 342108008405 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 342108008406 Catalytic site [active] 342108008407 TIGR03545 family protein; Region: TIGR03545 342108008408 Benzoate CoA ligase (BCL) and 4-Hydroxybenzoate-Coenzyme A Ligase (4-HBA-CoA ligase); Region: BCL_4HBCL; cd05959 342108008409 benzoate-CoA ligase family; Region: benz_CoA_lig; TIGR02262 342108008410 dimer interface [polypeptide binding]; other site 342108008411 acyl-activating enzyme (AAE) consensus motif; other site 342108008412 putative active site [active] 342108008413 putative AMP binding site [chemical binding]; other site 342108008414 putative CoA binding site [chemical binding]; other site 342108008415 chemical substrate binding site [chemical binding]; other site 342108008416 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 342108008417 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 342108008418 Walker A/P-loop; other site 342108008419 ATP binding site [chemical binding]; other site 342108008420 Q-loop/lid; other site 342108008421 ABC transporter signature motif; other site 342108008422 Walker B; other site 342108008423 D-loop; other site 342108008424 H-loop/switch region; other site 342108008425 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 342108008426 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 342108008427 Walker A/P-loop; other site 342108008428 ATP binding site [chemical binding]; other site 342108008429 Q-loop/lid; other site 342108008430 ABC transporter signature motif; other site 342108008431 Walker B; other site 342108008432 D-loop; other site 342108008433 H-loop/switch region; other site 342108008434 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 342108008435 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 342108008436 TM-ABC transporter signature motif; other site 342108008437 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 342108008438 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 342108008439 TM-ABC transporter signature motif; other site 342108008440 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 342108008441 Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; Region: PBP1_alkylbenzenes_like; cd06360 342108008442 putative ligand binding site [chemical binding]; other site 342108008443 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 342108008444 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 342108008445 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 342108008446 Cache domain; Region: Cache_1; pfam02743 342108008447 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 342108008448 dimer interface [polypeptide binding]; other site 342108008449 phosphorylation site [posttranslational modification] 342108008450 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 342108008451 ATP binding site [chemical binding]; other site 342108008452 Mg2+ binding site [ion binding]; other site 342108008453 G-X-G motif; other site 342108008454 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 342108008455 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 342108008456 trimerization site [polypeptide binding]; other site 342108008457 active site 342108008458 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 342108008459 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 342108008460 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108008461 catalytic residue [active] 342108008462 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 342108008463 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 342108008464 Ligand binding site; other site 342108008465 metal-binding site 342108008466 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 342108008467 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 342108008468 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 342108008469 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 342108008470 catalytic loop [active] 342108008471 iron binding site [ion binding]; other site 342108008472 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 342108008473 Protein of unknown function (DUF4065); Region: DUF4065; pfam13274 342108008474 Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues; Region: GH25_muramidase; cd00599 342108008475 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 342108008476 active site 342108008477 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 342108008478 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 342108008479 NodB motif; other site 342108008480 active site 342108008481 catalytic site [active] 342108008482 metal binding site [ion binding]; metal-binding site 342108008483 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 342108008484 putative active site [active] 342108008485 putative catalytic site [active] 342108008486 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 342108008487 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108008488 putative substrate translocation pore; other site 342108008489 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 342108008490 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 342108008491 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 342108008492 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 342108008493 active site 342108008494 FMN binding site [chemical binding]; other site 342108008495 substrate binding site [chemical binding]; other site 342108008496 homotetramer interface [polypeptide binding]; other site 342108008497 catalytic residue [active] 342108008498 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 342108008499 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 342108008500 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 342108008501 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 342108008502 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 342108008503 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108008504 putative substrate translocation pore; other site 342108008505 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108008506 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 342108008507 dimerization interface [polypeptide binding]; other site 342108008508 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 342108008509 dimer interface [polypeptide binding]; other site 342108008510 phosphorylation site [posttranslational modification] 342108008511 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 342108008512 ATP binding site [chemical binding]; other site 342108008513 Mg2+ binding site [ion binding]; other site 342108008514 G-X-G motif; other site 342108008515 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108008516 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 342108008517 active site 342108008518 phosphorylation site [posttranslational modification] 342108008519 intermolecular recognition site; other site 342108008520 dimerization interface [polypeptide binding]; other site 342108008521 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 342108008522 DNA binding site [nucleotide binding] 342108008523 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 342108008524 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 342108008525 putative dimer interface [polypeptide binding]; other site 342108008526 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 342108008527 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 342108008528 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 342108008529 RNA binding surface [nucleotide binding]; other site 342108008530 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 342108008531 S-adenosylmethionine binding site [chemical binding]; other site 342108008532 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 342108008533 TPR motif; other site 342108008534 binding surface 342108008535 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 342108008536 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 342108008537 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 342108008538 substrate binding pocket [chemical binding]; other site 342108008539 chain length determination region; other site 342108008540 substrate-Mg2+ binding site; other site 342108008541 catalytic residues [active] 342108008542 aspartate-rich region 1; other site 342108008543 active site lid residues [active] 342108008544 aspartate-rich region 2; other site 342108008545 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 342108008546 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 342108008547 TPP-binding site; other site 342108008548 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 342108008549 PYR/PP interface [polypeptide binding]; other site 342108008550 dimer interface [polypeptide binding]; other site 342108008551 TPP binding site [chemical binding]; other site 342108008552 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 342108008553 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 342108008554 dimerization interface [polypeptide binding]; other site 342108008555 putative DNA binding site [nucleotide binding]; other site 342108008556 putative Zn2+ binding site [ion binding]; other site 342108008557 Precorrin-6x reductase [Coenzyme metabolism]; Region: CobK; COG2099 342108008558 Bacterial TniB protein; Region: TniB; pfam05621 342108008559 NosL; Region: NosL; cl01769 342108008560 Family description; Region: DsbD_2; pfam13386 342108008561 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 342108008562 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 342108008563 Soluble P-type ATPase [General function prediction only]; Region: COG4087 342108008564 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 342108008565 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 342108008566 catalytic residues [active] 342108008567 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 342108008568 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 342108008569 Walker A/P-loop; other site 342108008570 ATP binding site [chemical binding]; other site 342108008571 Q-loop/lid; other site 342108008572 ABC transporter signature motif; other site 342108008573 Walker B; other site 342108008574 D-loop; other site 342108008575 H-loop/switch region; other site 342108008576 FtsX-like permease family; Region: FtsX; pfam02687 342108008577 Fe-S-cluster-containing hydrogenase components 2 [Energy production and conversion]; Region: HycB; COG1142 342108008578 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 342108008579 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; pfam02730 342108008580 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 342108008581 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 342108008582 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108008583 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 342108008584 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 342108008585 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108008586 ThiS family; Region: ThiS; pfam02597 342108008587 charged pocket; other site 342108008588 hydrophobic patch; other site 342108008589 Ubiquitin-like proteins; Region: UBQ; cl00155 342108008590 CHASE domain; Region: CHASE; pfam03924 342108008591 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 342108008592 dimer interface [polypeptide binding]; other site 342108008593 phosphorylation site [posttranslational modification] 342108008594 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 342108008595 ATP binding site [chemical binding]; other site 342108008596 Mg2+ binding site [ion binding]; other site 342108008597 G-X-G motif; other site 342108008598 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 342108008599 substrate binding pocket [chemical binding]; other site 342108008600 membrane-bound complex binding site; other site 342108008601 hinge residues; other site 342108008602 Nitrate and nitrite sensing; Region: NIT; pfam08376 342108008603 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 342108008604 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 342108008605 PAS fold; Region: PAS; pfam00989 342108008606 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 342108008607 putative active site [active] 342108008608 heme pocket [chemical binding]; other site 342108008609 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 342108008610 dimer interface [polypeptide binding]; other site 342108008611 phosphorylation site [posttranslational modification] 342108008612 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 342108008613 ATP binding site [chemical binding]; other site 342108008614 Mg2+ binding site [ion binding]; other site 342108008615 G-X-G motif; other site 342108008616 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 342108008617 Response regulator receiver domain; Region: Response_reg; pfam00072 342108008618 active site 342108008619 phosphorylation site [posttranslational modification] 342108008620 intermolecular recognition site; other site 342108008621 dimerization interface [polypeptide binding]; other site 342108008622 Response regulator receiver domain; Region: Response_reg; pfam00072 342108008623 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 342108008624 active site 342108008625 phosphorylation site [posttranslational modification] 342108008626 intermolecular recognition site; other site 342108008627 dimerization interface [polypeptide binding]; other site 342108008628 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 342108008629 HAMP domain; Region: HAMP; pfam00672 342108008630 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 342108008631 GAF domain; Region: GAF_3; pfam13492 342108008632 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 342108008633 PAS domain; Region: PAS_9; pfam13426 342108008634 putative active site [active] 342108008635 heme pocket [chemical binding]; other site 342108008636 CheB methylesterase; Region: CheB_methylest; pfam01339 342108008637 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 342108008638 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 342108008639 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 342108008640 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 342108008641 GAF domain; Region: GAF_2; pfam13185 342108008642 PAS fold; Region: PAS; pfam00989 342108008643 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 342108008644 putative active site [active] 342108008645 heme pocket [chemical binding]; other site 342108008646 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 342108008647 putative binding surface; other site 342108008648 active site 342108008649 PAS fold; Region: PAS; pfam00989 342108008650 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 342108008651 putative active site [active] 342108008652 heme pocket [chemical binding]; other site 342108008653 Catalytic domain of Protein Kinases; Region: PKc; cd00180 342108008654 active site 342108008655 substrate binding site [chemical binding]; other site 342108008656 ATP binding site [chemical binding]; other site 342108008657 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 342108008658 activation loop (A-loop); other site 342108008659 AAA ATPase domain; Region: AAA_16; pfam13191 342108008660 Predicted ATPase [General function prediction only]; Region: COG3899 342108008661 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 342108008662 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 342108008663 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 342108008664 ATP binding site [chemical binding]; other site 342108008665 Mg2+ binding site [ion binding]; other site 342108008666 G-X-G motif; other site 342108008667 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 342108008668 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 342108008669 Response regulator receiver domain; Region: Response_reg; pfam00072 342108008670 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 342108008671 active site 342108008672 phosphorylation site [posttranslational modification] 342108008673 intermolecular recognition site; other site 342108008674 dimerization interface [polypeptide binding]; other site 342108008675 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of...; Region: NorE_like; cd02862 342108008676 Subunit I/III interface [polypeptide binding]; other site 342108008677 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 342108008678 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 342108008679 metal ion-dependent adhesion site (MIDAS); other site 342108008680 MoxR-like ATPases [General function prediction only]; Region: COG0714 342108008681 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 342108008682 Walker A motif; other site 342108008683 ATP binding site [chemical binding]; other site 342108008684 Walker B motif; other site 342108008685 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 342108008686 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 342108008687 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 342108008688 D-pathway; other site 342108008689 Low-spin heme binding site [chemical binding]; other site 342108008690 Putative water exit pathway; other site 342108008691 Binuclear center (active site) [active] 342108008692 K-pathway; other site 342108008693 Putative proton exit pathway; other site 342108008694 Cytochrome c; Region: Cytochrom_C; pfam00034 342108008695 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108008696 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 342108008697 ligand binding site [chemical binding]; other site 342108008698 flexible hinge region; other site 342108008699 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 342108008700 Protein of unknown function (DUF2478); Region: DUF2478; pfam10649 342108008701 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 342108008702 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 342108008703 molybdenum-pterin binding domain; Region: Mop; TIGR00638 342108008704 molybdenum-pterin binding domain; Region: Mop; TIGR00638 342108008705 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 342108008706 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 342108008707 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 342108008708 NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein...; Region: NifX; cd00853 342108008709 molybdenum transport protein ModD; Provisional; Region: PRK06096 342108008710 Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate...; Region: PRTase_typeII; cl17275 342108008711 active site 342108008712 PAS domain S-box; Region: sensory_box; TIGR00229 342108008713 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 342108008714 putative active site [active] 342108008715 heme pocket [chemical binding]; other site 342108008716 PAS fold; Region: PAS_4; pfam08448 342108008717 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 342108008718 putative active site [active] 342108008719 heme pocket [chemical binding]; other site 342108008720 PAS fold; Region: PAS_7; pfam12860 342108008721 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 342108008722 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 342108008723 putative active site [active] 342108008724 heme pocket [chemical binding]; other site 342108008725 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 342108008726 putative active site [active] 342108008727 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 342108008728 ATP binding site [chemical binding]; other site 342108008729 Mg2+ binding site [ion binding]; other site 342108008730 G-X-G motif; other site 342108008731 Response regulator receiver domain; Region: Response_reg; pfam00072 342108008732 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 342108008733 active site 342108008734 phosphorylation site [posttranslational modification] 342108008735 intermolecular recognition site; other site 342108008736 dimerization interface [polypeptide binding]; other site 342108008737 HDOD domain; Region: HDOD; pfam08668 342108008738 Response regulator receiver domain; Region: Response_reg; pfam00072 342108008739 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 342108008740 active site 342108008741 phosphorylation site [posttranslational modification] 342108008742 intermolecular recognition site; other site 342108008743 dimerization interface [polypeptide binding]; other site 342108008744 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 342108008745 HD domain; Region: HD_5; pfam13487 342108008746 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 342108008747 metal ion-dependent adhesion site (MIDAS); other site 342108008748 Tubulin like; Region: Tubulin_2; pfam13809 342108008749 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 342108008750 metal ion-dependent adhesion site (MIDAS); other site 342108008751 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 342108008752 metal ion-dependent adhesion site (MIDAS); other site 342108008753 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 342108008754 nucleotide binding site [chemical binding]; other site 342108008755 TIGR02680 family protein; Region: TIGR02680 342108008756 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 342108008757 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 342108008758 Transglycosylase; Region: Transgly; pfam00912 342108008759 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 342108008760 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 342108008761 IgD-like repeat domain of mycobacterial L,D-transpeptidases; Region: LDT_IgD_like; cl17506 342108008762 MG2 domain; Region: A2M_N; pfam01835 342108008763 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 342108008764 Alpha-2-macroglobulin family; Region: A2M; pfam00207 342108008765 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 342108008766 Predicted permeases [General function prediction only]; Region: COG0679 342108008767 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 342108008768 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 342108008769 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 342108008770 putative acyl-acceptor binding pocket; other site 342108008771 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 342108008772 acyl-activating enzyme (AAE) consensus motif; other site 342108008773 putative AMP binding site [chemical binding]; other site 342108008774 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 342108008775 active site 342108008776 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 342108008777 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 342108008778 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 342108008779 transcriptional activator FtrB; Provisional; Region: ftrB; PRK09392 342108008780 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 342108008781 ligand binding site [chemical binding]; other site 342108008782 flexible hinge region; other site 342108008783 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 342108008784 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 342108008785 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 342108008786 E-class dimer interface [polypeptide binding]; other site 342108008787 P-class dimer interface [polypeptide binding]; other site 342108008788 active site 342108008789 Cu2+ binding site [ion binding]; other site 342108008790 Zn2+ binding site [ion binding]; other site 342108008791 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108008792 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 342108008793 active site 342108008794 phosphorylation site [posttranslational modification] 342108008795 intermolecular recognition site; other site 342108008796 dimerization interface [polypeptide binding]; other site 342108008797 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108008798 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 342108008799 active site 342108008800 phosphorylation site [posttranslational modification] 342108008801 intermolecular recognition site; other site 342108008802 dimerization interface [polypeptide binding]; other site 342108008803 PAS domain S-box; Region: sensory_box; TIGR00229 342108008804 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 342108008805 putative active site [active] 342108008806 heme pocket [chemical binding]; other site 342108008807 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 342108008808 PAS domain; Region: PAS_9; pfam13426 342108008809 putative active site [active] 342108008810 heme pocket [chemical binding]; other site 342108008811 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108008812 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108008813 metal binding site [ion binding]; metal-binding site 342108008814 active site 342108008815 I-site; other site 342108008816 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 342108008817 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 342108008818 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 342108008819 dimerization interface [polypeptide binding]; other site 342108008820 ligand binding site [chemical binding]; other site 342108008821 Cysteine-rich 4 helical bundle widely conserved in bacteria; Region: DUF326; cd08026 342108008822 dimerization interface [polypeptide binding]; other site 342108008823 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 342108008824 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108008825 putative substrate translocation pore; other site 342108008826 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 342108008827 FAD binding domain; Region: FAD_binding_4; pfam01565 342108008828 Predicted integral membrane protein (DUF2189); Region: DUF2189; cl02291 342108008829 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 342108008830 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 342108008831 dimer interface [polypeptide binding]; other site 342108008832 active site 342108008833 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 342108008834 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 342108008835 substrate binding site [chemical binding]; other site 342108008836 oxyanion hole (OAH) forming residues; other site 342108008837 trimer interface [polypeptide binding]; other site 342108008838 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 342108008839 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 342108008840 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 342108008841 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 342108008842 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 342108008843 radical SAM enzyme, rSAM/lipoprotein system; Region: rSAM_w_lipo; TIGR04133 342108008844 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 342108008845 FeS/SAM binding site; other site 342108008846 Domain of unknown function (DUF4008); Region: DUF4008; cl14869 342108008847 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 342108008848 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 342108008849 ligand binding site [chemical binding]; other site 342108008850 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108008851 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108008852 dimer interface [polypeptide binding]; other site 342108008853 putative CheW interface [polypeptide binding]; other site 342108008854 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 342108008855 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 342108008856 Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]; Region: DUR1; COG1984 342108008857 LamB/YcsF family of lactam utilization protein; Region: LamB_YcsF_like; cd10787 342108008858 putative active site [active] 342108008859 Uncharacterized conserved protein [Function unknown]; Region: COG4544 342108008860 DNA Polymerase Y-family; Region: PolY_like; cd03468 342108008861 active site 342108008862 DNA binding site [nucleotide binding] 342108008863 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 342108008864 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 342108008865 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 342108008866 putative active site [active] 342108008867 putative PHP Thumb interface [polypeptide binding]; other site 342108008868 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 342108008869 generic binding surface I; other site 342108008870 generic binding surface II; other site 342108008871 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 342108008872 dimerization interface [polypeptide binding]; other site 342108008873 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108008874 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108008875 dimer interface [polypeptide binding]; other site 342108008876 putative CheW interface [polypeptide binding]; other site 342108008877 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 342108008878 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 342108008879 active site 342108008880 phosphorylation site [posttranslational modification] 342108008881 intermolecular recognition site; other site 342108008882 dimerization interface [polypeptide binding]; other site 342108008883 CheB methylesterase; Region: CheB_methylest; pfam01339 342108008884 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 342108008885 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 342108008886 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 342108008887 TPR motif; other site 342108008888 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 342108008889 putative binding surface; other site 342108008890 active site 342108008891 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 342108008892 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 342108008893 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 342108008894 ATP binding site [chemical binding]; other site 342108008895 Mg2+ binding site [ion binding]; other site 342108008896 G-X-G motif; other site 342108008897 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 342108008898 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108008899 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 342108008900 active site 342108008901 phosphorylation site [posttranslational modification] 342108008902 intermolecular recognition site; other site 342108008903 dimerization interface [polypeptide binding]; other site 342108008904 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108008905 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 342108008906 active site 342108008907 phosphorylation site [posttranslational modification] 342108008908 intermolecular recognition site; other site 342108008909 dimerization interface [polypeptide binding]; other site 342108008910 Hpt domain; Region: Hpt; pfam01627 342108008911 putative binding surface; other site 342108008912 active site 342108008913 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 342108008914 active site 342108008915 Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]; Region: PleD; COG3706 342108008916 phosphorylation site [posttranslational modification] 342108008917 intermolecular recognition site; other site 342108008918 dimerization interface [polypeptide binding]; other site 342108008919 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 342108008920 active site 342108008921 phosphorylation site [posttranslational modification] 342108008922 intermolecular recognition site; other site 342108008923 dimerization interface [polypeptide binding]; other site 342108008924 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108008925 metal binding site [ion binding]; metal-binding site 342108008926 active site 342108008927 I-site; other site 342108008928 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 342108008929 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 342108008930 Paraquat-inducible protein A; Region: PqiA; pfam04403 342108008931 Uncharacterized paraquat-inducible protein A [Function unknown]; Region: PqiA; COG2995 342108008932 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 342108008933 Paraquat-inducible protein A; Region: PqiA; pfam04403 342108008934 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 342108008935 mce related protein; Region: MCE; pfam02470 342108008936 mce related protein; Region: MCE; pfam02470 342108008937 mce related protein; Region: MCE; pfam02470 342108008938 Protein of unknown function (DUF330); Region: DUF330; pfam03886 342108008939 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cl03439 342108008940 cytochrome c nitrite reductase, pentaheme subunit; Region: cyt_nit_nrfB; TIGR03146 342108008941 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 342108008942 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108008943 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 342108008944 Prokaryotic cytochrome b561; Region: Ni_hydr_CYTB; pfam01292 342108008945 Ethylbenzene dehydrogenase; Region: EB_dh; smart00887 342108008946 Domon-like ligand-binding domains; Region: DOMON_like; cl14783 342108008947 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 342108008948 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 342108008949 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 342108008950 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; pfam09699 342108008951 decaheme-associated outer membrane protein, MtrB/PioB family; Region: OMP_MtrB_PioB; TIGR03509 342108008952 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 342108008953 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 342108008954 Ligand Binding Site [chemical binding]; other site 342108008955 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108008956 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4627 342108008957 Protein of unknown function, DUF599; Region: DUF599; pfam04654 342108008958 Iron-sulphur cluster assembly; Region: Fe-S_assembly; pfam04384 342108008959 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 342108008960 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 342108008961 catalytic loop [active] 342108008962 iron binding site [ion binding]; other site 342108008963 chaperone protein HscA; Provisional; Region: hscA; PRK05183 342108008964 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 342108008965 nucleotide binding site [chemical binding]; other site 342108008966 putative NEF/HSP70 interaction site [polypeptide binding]; other site 342108008967 SBD interface [polypeptide binding]; other site 342108008968 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 342108008969 HSP70 interaction site [polypeptide binding]; other site 342108008970 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 342108008971 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 342108008972 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 342108008973 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 342108008974 trimerization site [polypeptide binding]; other site 342108008975 active site 342108008976 cysteine desulfurase; Provisional; Region: PRK14012 342108008977 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 342108008978 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108008979 catalytic residue [active] 342108008980 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 342108008981 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 342108008982 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108008983 catalytic residue [active] 342108008984 Transcriptional regulator; Region: Rrf2; cl17282 342108008985 Rrf2 family protein; Region: rrf2_super; TIGR00738 342108008986 serine O-acetyltransferase; Region: cysE; TIGR01172 342108008987 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 342108008988 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 342108008989 trimer interface [polypeptide binding]; other site 342108008990 active site 342108008991 substrate binding site [chemical binding]; other site 342108008992 CoA binding site [chemical binding]; other site 342108008993 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 342108008994 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 342108008995 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 342108008996 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 342108008997 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 342108008998 active site 342108008999 HIGH motif; other site 342108009000 dimer interface [polypeptide binding]; other site 342108009001 KMSKS motif; other site 342108009002 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 342108009003 RNA binding surface [nucleotide binding]; other site 342108009004 Frataxin-like domain; Region: Frataxin_Cyay; pfam01491 342108009005 putative iron binding site [ion binding]; other site 342108009006 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00528 342108009007 cyclase homology domain; Region: CHD; cd07302 342108009008 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 342108009009 nucleotidyl binding site; other site 342108009010 metal binding site [ion binding]; metal-binding site 342108009011 dimer interface [polypeptide binding]; other site 342108009012 Succinate dehydrogenase/Fumarate reductase transmembrane subunit; Region: Sdh_cyt; pfam01127 342108009013 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 342108009014 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 342108009015 catalytic loop [active] 342108009016 iron binding site [ion binding]; other site 342108009017 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 342108009018 cyclase homology domain; Region: CHD; cd07302 342108009019 nucleotidyl binding site; other site 342108009020 metal binding site [ion binding]; metal-binding site 342108009021 dimer interface [polypeptide binding]; other site 342108009022 Protein of unknown function (DUF1465); Region: DUF1465; cl11562 342108009023 PBP superfamily domain; Region: PBP_like_2; pfam12849 342108009024 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 342108009025 PBP superfamily domain; Region: PBP_like_2; pfam12849 342108009026 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 342108009027 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 342108009028 Walker A/P-loop; other site 342108009029 ATP binding site [chemical binding]; other site 342108009030 Q-loop/lid; other site 342108009031 ABC transporter signature motif; other site 342108009032 Walker B; other site 342108009033 D-loop; other site 342108009034 H-loop/switch region; other site 342108009035 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 342108009036 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 342108009037 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 342108009038 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 342108009039 FeS/SAM binding site; other site 342108009040 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 342108009041 PAS domain; Region: PAS_9; pfam13426 342108009042 putative active site [active] 342108009043 heme pocket [chemical binding]; other site 342108009044 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108009045 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 342108009046 dimer interface [polypeptide binding]; other site 342108009047 phosphorylation site [posttranslational modification] 342108009048 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 342108009049 ATP binding site [chemical binding]; other site 342108009050 Mg2+ binding site [ion binding]; other site 342108009051 G-X-G motif; other site 342108009052 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 342108009053 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 342108009054 P-loop; other site 342108009055 Magnesium ion binding site [ion binding]; other site 342108009056 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 342108009057 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 342108009058 adenylosuccinate lyase; Provisional; Region: PRK07492 342108009059 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 342108009060 tetramer interface [polypeptide binding]; other site 342108009061 active site 342108009062 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 342108009063 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 342108009064 NdvC_like proteins in this family are putative bacterial beta-(1,6)-glucosyltransferase; Region: CESA_NdvC_like; cd06435 342108009065 Ligand binding site; other site 342108009066 DXD motif; other site 342108009067 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 342108009068 dimerization interface [polypeptide binding]; other site 342108009069 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108009070 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108009071 dimer interface [polypeptide binding]; other site 342108009072 putative CheW interface [polypeptide binding]; other site 342108009073 TPR repeat; Region: TPR_11; pfam13414 342108009074 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 342108009075 TPR motif; other site 342108009076 binding surface 342108009077 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108009078 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108009079 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 342108009080 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 342108009081 Domain of unknown function (DUF4384); Region: DUF4384; pfam14326 342108009082 TPR repeat; Region: TPR_11; pfam13414 342108009083 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 342108009084 binding surface 342108009085 TPR motif; other site 342108009086 Transcriptional regulators [Transcription]; Region: GntR; COG1802 342108009087 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 342108009088 DNA-binding site [nucleotide binding]; DNA binding site 342108009089 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 342108009090 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 342108009091 TPR motif; other site 342108009092 binding surface 342108009093 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 342108009094 binding surface 342108009095 TPR motif; other site 342108009096 ADP-heptose:LPS heptosyl transferase I; Provisional; Region: PRK10964; cl15782 342108009097 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 342108009098 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 342108009099 homodimer interface [polypeptide binding]; other site 342108009100 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 342108009101 active site pocket [active] 342108009102 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 342108009103 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 342108009104 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 342108009105 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 342108009106 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 342108009107 active site 342108009108 catalytic site [active] 342108009109 glycogen branching enzyme; Provisional; Region: PRK05402 342108009110 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 342108009111 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 342108009112 active site 342108009113 catalytic site [active] 342108009114 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 342108009115 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 342108009116 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 342108009117 dimerization interface [polypeptide binding]; other site 342108009118 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108009119 dimer interface [polypeptide binding]; other site 342108009120 putative CheW interface [polypeptide binding]; other site 342108009121 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 342108009122 TMAO/DMSO reductase; Reviewed; Region: PRK05363 342108009123 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 342108009124 Moco binding site; other site 342108009125 metal coordination site [ion binding]; other site 342108009126 Bacterial protein of unknown function (DUF898); Region: DUF898; pfam05987 342108009127 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 342108009128 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 342108009129 NADP binding site [chemical binding]; other site 342108009130 dimer interface [polypeptide binding]; other site 342108009131 bile acid transporter; Region: bass; TIGR00841 342108009132 Sodium Bile acid symporter family; Region: SBF; cl17470 342108009133 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated; Region: PRK06080 342108009134 UbiA prenyltransferase family; Region: UbiA; pfam01040 342108009135 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 342108009136 ABC-2 family transporter protein; Region: ABC2_membrane_2; cl17866 342108009137 NosL; Region: NosL; cl01769 342108009138 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 342108009139 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 342108009140 Walker A/P-loop; other site 342108009141 ATP binding site [chemical binding]; other site 342108009142 Q-loop/lid; other site 342108009143 ABC transporter signature motif; other site 342108009144 Walker B; other site 342108009145 D-loop; other site 342108009146 H-loop/switch region; other site 342108009147 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 342108009148 4Fe-4S binding domain; Region: Fer4_5; pfam12801 342108009149 MauM/NapG family ferredoxin-type protein; Region: mauM_napG; TIGR00397 342108009150 4Fe-4S binding domain; Region: Fer4; pfam00037 342108009151 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 342108009152 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 342108009153 Cytochrome c; Region: Cytochrom_C; cl11414 342108009154 Cytochrome c; Region: Cytochrom_C; cl11414 342108009155 Cytochrome c553 [Energy production and conversion]; Region: COG2863 342108009156 Cytochrome c; Region: Cytochrom_C; cl11414 342108009157 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 342108009158 nitrous-oxide reductase, Sec-dependent; Region: nitrous_NosZ_Gp; TIGR04246 342108009159 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 342108009160 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 342108009161 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 342108009162 Cu(I) binding site [ion binding]; other site 342108009163 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 342108009164 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 342108009165 catalytic residues [active] 342108009166 Protein of unknown function (DUF461); Region: DUF461; pfam04314 342108009167 Hemerythrin; Region: Hemerythrin; cd12107 342108009168 Fe binding site [ion binding]; other site 342108009169 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 342108009170 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108009171 ligand binding site [chemical binding]; other site 342108009172 flexible hinge region; other site 342108009173 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 342108009174 diguanylate cyclase; Provisional; Region: PRK09894 342108009175 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 342108009176 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108009177 metal binding site [ion binding]; metal-binding site 342108009178 active site 342108009179 I-site; other site 342108009180 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 342108009181 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 342108009182 ligand binding site [chemical binding]; other site 342108009183 flexible hinge region; other site 342108009184 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108009185 Hemerythrin; Region: Hemerythrin; cd12107 342108009186 Fe binding site [ion binding]; other site 342108009187 PAS fold; Region: PAS_7; pfam12860 342108009188 PAS fold; Region: PAS_7; pfam12860 342108009189 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108009190 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 342108009191 putative active site [active] 342108009192 heme pocket [chemical binding]; other site 342108009193 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 342108009194 dimer interface [polypeptide binding]; other site 342108009195 phosphorylation site [posttranslational modification] 342108009196 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 342108009197 ATP binding site [chemical binding]; other site 342108009198 Mg2+ binding site [ion binding]; other site 342108009199 G-X-G motif; other site 342108009200 hypothetical protein; Provisional; Region: PRK01254 342108009201 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 342108009202 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 342108009203 hopanoid biosynthesis associated RND transporter like protein HpnN; Region: HpnN; TIGR03480 342108009204 hopanoid biosynthesis associated protein HpnK and similar proteins; Region: YdjC_HpnK_like; cd10804 342108009205 putative active site [active] 342108009206 YdjC motif; other site 342108009207 Mg binding site [ion binding]; other site 342108009208 putative homodimer interface [polypeptide binding]; other site 342108009209 putative membrane protein; Region: HpnL; TIGR03476 342108009210 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 342108009211 PAS domain; Region: PAS_9; pfam13426 342108009212 putative active site [active] 342108009213 heme pocket [chemical binding]; other site 342108009214 Tar ligand binding domain homologue; Region: TarH; pfam02203 342108009215 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108009216 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108009217 dimer interface [polypeptide binding]; other site 342108009218 putative CheW interface [polypeptide binding]; other site 342108009219 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 342108009220 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 342108009221 motif II; other site 342108009222 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 342108009223 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 342108009224 ATP12 chaperone protein; Region: ATP12; cl02228 342108009225 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108009226 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 342108009227 binding surface 342108009228 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108009229 TPR motif; other site 342108009230 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108009231 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 342108009232 S-adenosylmethionine binding site [chemical binding]; other site 342108009233 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 342108009234 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 342108009235 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 342108009236 alphaNTD homodimer interface [polypeptide binding]; other site 342108009237 alphaNTD - beta interaction site [polypeptide binding]; other site 342108009238 alphaNTD - beta' interaction site [polypeptide binding]; other site 342108009239 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 342108009240 30S ribosomal protein S11; Validated; Region: PRK05309 342108009241 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 342108009242 30S ribosomal protein S13; Region: bact_S13; TIGR03631 342108009243 adenylate kinase; Reviewed; Region: adk; PRK00279 342108009244 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 342108009245 AMP-binding site [chemical binding]; other site 342108009246 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 342108009247 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 342108009248 SecY translocase; Region: SecY; pfam00344 342108009249 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 342108009250 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 342108009251 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 342108009252 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 342108009253 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 342108009254 23S rRNA interface [nucleotide binding]; other site 342108009255 L21e interface [polypeptide binding]; other site 342108009256 5S rRNA interface [nucleotide binding]; other site 342108009257 L27 interface [polypeptide binding]; other site 342108009258 L5 interface [polypeptide binding]; other site 342108009259 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 342108009260 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 342108009261 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 342108009262 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 342108009263 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 342108009264 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 342108009265 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 342108009266 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 342108009267 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 342108009268 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 342108009269 RNA binding site [nucleotide binding]; other site 342108009270 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 342108009271 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 342108009272 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 342108009273 23S rRNA interface [nucleotide binding]; other site 342108009274 putative translocon interaction site; other site 342108009275 signal recognition particle (SRP54) interaction site; other site 342108009276 L23 interface [polypeptide binding]; other site 342108009277 trigger factor interaction site; other site 342108009278 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 342108009279 23S rRNA interface [nucleotide binding]; other site 342108009280 5S rRNA interface [nucleotide binding]; other site 342108009281 putative antibiotic binding site [chemical binding]; other site 342108009282 L25 interface [polypeptide binding]; other site 342108009283 L27 interface [polypeptide binding]; other site 342108009284 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 342108009285 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 342108009286 G-X-X-G motif; other site 342108009287 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 342108009288 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 342108009289 putative translocon binding site; other site 342108009290 protein-rRNA interface [nucleotide binding]; other site 342108009291 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 342108009292 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 342108009293 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 342108009294 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 342108009295 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 342108009296 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 342108009297 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 342108009298 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 342108009299 elongation factor Tu; Reviewed; Region: PRK00049 342108009300 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 342108009301 G1 box; other site 342108009302 GEF interaction site [polypeptide binding]; other site 342108009303 GTP/Mg2+ binding site [chemical binding]; other site 342108009304 Switch I region; other site 342108009305 G2 box; other site 342108009306 G3 box; other site 342108009307 Switch II region; other site 342108009308 G4 box; other site 342108009309 G5 box; other site 342108009310 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 342108009311 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 342108009312 Antibiotic Binding Site [chemical binding]; other site 342108009313 elongation factor G; Reviewed; Region: PRK00007 342108009314 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 342108009315 G1 box; other site 342108009316 putative GEF interaction site [polypeptide binding]; other site 342108009317 GTP/Mg2+ binding site [chemical binding]; other site 342108009318 Switch I region; other site 342108009319 G2 box; other site 342108009320 G3 box; other site 342108009321 Switch II region; other site 342108009322 G4 box; other site 342108009323 G5 box; other site 342108009324 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 342108009325 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 342108009326 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 342108009327 30S ribosomal protein S7; Validated; Region: PRK05302 342108009328 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 342108009329 S17 interaction site [polypeptide binding]; other site 342108009330 S8 interaction site; other site 342108009331 16S rRNA interaction site [nucleotide binding]; other site 342108009332 streptomycin interaction site [chemical binding]; other site 342108009333 23S rRNA interaction site [nucleotide binding]; other site 342108009334 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 342108009335 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 342108009336 N-acetyl-D-glucosamine binding site [chemical binding]; other site 342108009337 catalytic residue [active] 342108009338 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 342108009339 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 342108009340 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 342108009341 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 342108009342 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 342108009343 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 342108009344 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 342108009345 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 342108009346 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 342108009347 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 342108009348 Rpb1 - Rpb5 interaction site [polypeptide binding]; other site 342108009349 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 342108009350 DNA binding site [nucleotide binding] 342108009351 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 342108009352 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 342108009353 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 342108009354 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 342108009355 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 342108009356 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 342108009357 RPB11 interaction site [polypeptide binding]; other site 342108009358 RPB12 interaction site [polypeptide binding]; other site 342108009359 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 342108009360 RPB1 interaction site [polypeptide binding]; other site 342108009361 RPB11 interaction site [polypeptide binding]; other site 342108009362 RPB10 interaction site [polypeptide binding]; other site 342108009363 RPB3 interaction site [polypeptide binding]; other site 342108009364 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 342108009365 L11 interface [polypeptide binding]; other site 342108009366 putative EF-Tu interaction site [polypeptide binding]; other site 342108009367 putative EF-G interaction site [polypeptide binding]; other site 342108009368 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 342108009369 23S rRNA interface [nucleotide binding]; other site 342108009370 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 342108009371 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 342108009372 mRNA/rRNA interface [nucleotide binding]; other site 342108009373 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 342108009374 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 342108009375 L7/L12 interface [polypeptide binding]; other site 342108009376 23S rRNA interface [nucleotide binding]; other site 342108009377 L25 interface [polypeptide binding]; other site 342108009378 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 342108009379 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 342108009380 putative homodimer interface [polypeptide binding]; other site 342108009381 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 342108009382 heterodimer interface [polypeptide binding]; other site 342108009383 homodimer interface [polypeptide binding]; other site 342108009384 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 342108009385 elongation factor Tu; Reviewed; Region: PRK00049 342108009386 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 342108009387 G1 box; other site 342108009388 GEF interaction site [polypeptide binding]; other site 342108009389 GTP/Mg2+ binding site [chemical binding]; other site 342108009390 Switch I region; other site 342108009391 G2 box; other site 342108009392 G3 box; other site 342108009393 Switch II region; other site 342108009394 G4 box; other site 342108009395 G5 box; other site 342108009396 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 342108009397 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 342108009398 Antibiotic Binding Site [chemical binding]; other site 342108009399 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 342108009400 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 342108009401 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 342108009402 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 342108009403 Integrase core domain; Region: rve; pfam00665 342108009404 Integrase core domain; Region: rve_3; pfam13683 342108009405 Transposase; Region: HTH_Tnp_1; pfam01527 342108009406 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 342108009407 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 342108009408 active site 342108009409 DNA binding site [nucleotide binding] 342108009410 Int/Topo IB signature motif; other site 342108009411 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 342108009412 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 342108009413 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 342108009414 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108009415 Walker A/P-loop; other site 342108009416 ATP binding site [chemical binding]; other site 342108009417 Q-loop/lid; other site 342108009418 ABC transporter signature motif; other site 342108009419 Walker B; other site 342108009420 D-loop; other site 342108009421 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 342108009422 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 342108009423 lipoyl-biotinyl attachment site [posttranslational modification]; other site 342108009424 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108009425 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 342108009426 FliG C-terminal domain; Region: FliG_C; pfam01706 342108009427 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 342108009428 FliG C-terminal domain; Region: FliG_C; pfam01706 342108009429 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 342108009430 FliG C-terminal domain; Region: FliG_C; pfam01706 342108009431 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 342108009432 HD domain; Region: HD_4; pfam13328 342108009433 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 342108009434 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 342108009435 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 342108009436 catalytic residues [active] 342108009437 catalytic nucleophile [active] 342108009438 Presynaptic Site I dimer interface [polypeptide binding]; other site 342108009439 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 342108009440 Synaptic Flat tetramer interface [polypeptide binding]; other site 342108009441 Synaptic Site I dimer interface [polypeptide binding]; other site 342108009442 DNA binding site [nucleotide binding] 342108009443 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 342108009444 DNA-binding interface [nucleotide binding]; DNA binding site 342108009445 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 342108009446 putative effector binding pocket; other site 342108009447 dimerization interface [polypeptide binding]; other site 342108009448 Pirin; Region: Pirin; pfam02678 342108009449 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 342108009450 Isochorismatase family; Region: Isochorismatase; pfam00857 342108009451 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 342108009452 catalytic triad [active] 342108009453 conserved cis-peptide bond; other site 342108009454 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 342108009455 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 342108009456 FMN binding site [chemical binding]; other site 342108009457 active site 342108009458 substrate binding site [chemical binding]; other site 342108009459 catalytic residue [active] 342108009460 pyruvate kinase; Provisional; Region: PRK06247 342108009461 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 342108009462 domain interfaces; other site 342108009463 active site 342108009464 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 342108009465 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 342108009466 MOFRL family; Region: MOFRL; pfam05161 342108009467 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 342108009468 tartrate dehydrogenase; Region: TTC; TIGR02089 342108009469 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 342108009470 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 342108009471 putative substrate translocation pore; other site 342108009472 L(+)-tartrate dehydratase subunit beta; Validated; Region: PRK08228 342108009473 tartrate dehydratase subunit alpha; Validated; Region: PRK08230 342108009474 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 342108009475 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 342108009476 dimerization interface [polypeptide binding]; other site 342108009477 substrate binding pocket [chemical binding]; other site 342108009478 Phage associated DNA primase [General function prediction only]; Region: COG3378 342108009479 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 342108009480 Predicted transcriptional regulator [Transcription]; Region: COG4190 342108009481 MarR family; Region: MarR_2; cl17246 342108009482 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 342108009483 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 342108009484 RNA binding surface [nucleotide binding]; other site 342108009485 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 342108009486 active site 342108009487 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 342108009488 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 342108009489 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 342108009490 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 342108009491 DNA binding residues [nucleotide binding] 342108009492 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 342108009493 substrate binding site [chemical binding]; other site 342108009494 activation loop (A-loop); other site 342108009495 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 342108009496 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 342108009497 GDP-binding site [chemical binding]; other site 342108009498 ACT binding site; other site 342108009499 IMP binding site; other site 342108009500 Histidyl-tRNA synthetase; Region: tRNA-synt_His; pfam13393 342108009501 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 342108009502 dimer interface [polypeptide binding]; other site 342108009503 motif 1; other site 342108009504 motif 2; other site 342108009505 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108009506 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108009507 dimer interface [polypeptide binding]; other site 342108009508 putative CheW interface [polypeptide binding]; other site 342108009509 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 342108009510 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 342108009511 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 342108009512 ligand binding site [chemical binding]; other site 342108009513 NAD binding site [chemical binding]; other site 342108009514 dimerization interface [polypeptide binding]; other site 342108009515 catalytic site [active] 342108009516 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 342108009517 putative L-serine binding site [chemical binding]; other site 342108009518 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 342108009519 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 342108009520 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 342108009521 catalytic residue [active] 342108009522 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108009523 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 342108009524 dimer interface [polypeptide binding]; other site 342108009525 phosphorylation site [posttranslational modification] 342108009526 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 342108009527 ATP binding site [chemical binding]; other site 342108009528 Mg2+ binding site [ion binding]; other site 342108009529 G-X-G motif; other site 342108009530 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108009531 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 342108009532 active site 342108009533 phosphorylation site [posttranslational modification] 342108009534 intermolecular recognition site; other site 342108009535 dimerization interface [polypeptide binding]; other site 342108009536 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 342108009537 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 342108009538 dimer interface [polypeptide binding]; other site 342108009539 substrate binding site [chemical binding]; other site 342108009540 ATP binding site [chemical binding]; other site 342108009541 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14315 342108009542 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 342108009543 active site 342108009544 substrate binding site [chemical binding]; other site 342108009545 metal binding site [ion binding]; metal-binding site 342108009546 Domain of unknown function (DUF4405); Region: DUF4405; pfam14358 342108009547 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 342108009548 substrate binding pocket [chemical binding]; other site 342108009549 dimer interface [polypeptide binding]; other site 342108009550 inhibitor binding site; inhibition site 342108009551 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 342108009552 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 342108009553 substrate binding pocket [chemical binding]; other site 342108009554 FtsH Extracellular; Region: FtsH_ext; pfam06480 342108009555 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 342108009556 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 342108009557 Walker A motif; other site 342108009558 ATP binding site [chemical binding]; other site 342108009559 Walker B motif; other site 342108009560 arginine finger; other site 342108009561 Peptidase family M41; Region: Peptidase_M41; pfam01434 342108009562 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 342108009563 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 342108009564 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 342108009565 SlyX; Region: SlyX; cl01090 342108009566 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 342108009567 binding surface 342108009568 TPR motif; other site 342108009569 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 342108009570 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 342108009571 ligand binding site [chemical binding]; other site 342108009572 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 342108009573 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 342108009574 ligand binding site [chemical binding]; other site 342108009575 translocation protein TolB; Provisional; Region: tolB; PRK05137 342108009576 TolB amino-terminal domain; Region: TolB_N; pfam04052 342108009577 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 342108009578 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 342108009579 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 342108009580 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 342108009581 TolR protein; Region: tolR; TIGR02801 342108009582 TolQ protein; Region: tolQ; TIGR02796 342108009583 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 342108009584 active site 342108009585 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 342108009586 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 342108009587 Walker A motif; other site 342108009588 ATP binding site [chemical binding]; other site 342108009589 Walker B motif; other site 342108009590 arginine finger; other site 342108009591 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 342108009592 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 342108009593 RuvA N terminal domain; Region: RuvA_N; pfam01330 342108009594 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 342108009595 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 342108009596 active site 342108009597 putative DNA-binding cleft [nucleotide binding]; other site 342108009598 dimer interface [polypeptide binding]; other site 342108009599 hypothetical protein; Validated; Region: PRK00110 342108009600 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 342108009601 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 342108009602 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 342108009603 putative active site [active] 342108009604 metal binding site [ion binding]; metal-binding site 342108009605 homodimer binding site [polypeptide binding]; other site 342108009606 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 342108009607 Cell division protein ZapA; Region: ZapA; pfam05164 342108009608 Domain of unknown function (DUF4164); Region: DUF4164; pfam13747 342108009609 Protein of unknown function (DUF3124); Region: DUF3124; pfam11322 342108009610 Fructose/tagarose-bisphosphate aldolase class II. This family includes fructose-1,6-bisphosphate (FBP) and tagarose 1,6-bisphosphate (TBP) aldolases. FBP-aldolase is homodimeric and used in gluconeogenesis and glycolysis; the enzyme controls the...; Region: FTBP_aldolase_II; cl17181 342108009611 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 342108009612 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 342108009613 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 342108009614 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 342108009615 Ligand binding site [chemical binding]; other site 342108009616 Electron transfer flavoprotein domain; Region: ETF; pfam01012 342108009617 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 342108009618 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 342108009619 FAD binding site [chemical binding]; other site 342108009620 substrate binding pocket [chemical binding]; other site 342108009621 catalytic base [active] 342108009622 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 342108009623 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 342108009624 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 342108009625 putative dimerization interface [polypeptide binding]; other site 342108009626 indolepyruvate ferredoxin oxidoreductase, alpha subunit; Region: IOR_alpha; TIGR03336 342108009627 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 342108009628 dimer interface [polypeptide binding]; other site 342108009629 PYR/PP interface [polypeptide binding]; other site 342108009630 TPP binding site [chemical binding]; other site 342108009631 substrate binding site [chemical binding]; other site 342108009632 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 342108009633 TPP-binding site; other site 342108009634 indolepyruvate oxidoreductase subunit beta; Reviewed; Region: PRK06853 342108009635 Response regulator receiver domain; Region: Response_reg; pfam00072 342108009636 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 342108009637 active site 342108009638 phosphorylation site [posttranslational modification] 342108009639 intermolecular recognition site; other site 342108009640 dimerization interface [polypeptide binding]; other site 342108009641 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 342108009642 Transglycosylase; Region: Transgly; pfam00912 342108009643 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 342108009644 AMIN domain; Region: AMIN; pfam11741 342108009645 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 342108009646 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 342108009647 active site 342108009648 metal binding site [ion binding]; metal-binding site 342108009649 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108009650 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 342108009651 active site 342108009652 phosphorylation site [posttranslational modification] 342108009653 intermolecular recognition site; other site 342108009654 dimerization interface [polypeptide binding]; other site 342108009655 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 342108009656 DNA binding site [nucleotide binding] 342108009657 H+ Antiporter protein; Region: 2A0121; TIGR00900 342108009658 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 342108009659 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 342108009660 Serine hydrolase; Region: Ser_hydrolase; cl17834 342108009661 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 342108009662 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 342108009663 ligand binding site [chemical binding]; other site 342108009664 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 342108009665 ligand binding site [chemical binding]; other site 342108009666 Tudor-like domain present in plant sequences; Region: Agenet; smart00743 342108009667 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 342108009668 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 342108009669 FeS/SAM binding site; other site 342108009670 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 342108009671 TIR domain; Region: TIR_2; cl17458 342108009672 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 342108009673 B12 binding site [chemical binding]; other site 342108009674 Radical SAM superfamily; Region: Radical_SAM; pfam04055 342108009675 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 342108009676 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 342108009677 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108009678 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108009679 metal binding site [ion binding]; metal-binding site 342108009680 active site 342108009681 I-site; other site 342108009682 Transposase; Region: HTH_Tnp_1; pfam01527 342108009683 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108009684 HTH-like domain; Region: HTH_21; pfam13276 342108009685 Integrase core domain; Region: rve; pfam00665 342108009686 Integrase core domain; Region: rve_3; pfam13683 342108009687 Transposase; Region: HTH_Tnp_1; pfam01527 342108009688 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 342108009689 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cl00144 342108009690 HAMP domain; Region: HAMP; pfam00672 342108009691 dimerization interface [polypeptide binding]; other site 342108009692 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108009693 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108009694 dimer interface [polypeptide binding]; other site 342108009695 putative CheW interface [polypeptide binding]; other site 342108009696 Hemerythrin; Region: Hemerythrin; cd12107 342108009697 Fe binding site [ion binding]; other site 342108009698 Uncharacterized conserved protein [Function unknown]; Region: COG1742 342108009699 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 342108009700 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 342108009701 Presynaptic Site I dimer interface [polypeptide binding]; other site 342108009702 catalytic residues [active] 342108009703 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 342108009704 Synaptic Flat tetramer interface [polypeptide binding]; other site 342108009705 Synaptic Site I dimer interface [polypeptide binding]; other site 342108009706 DNA binding site [nucleotide binding] 342108009707 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 342108009708 DNA-binding interface [nucleotide binding]; DNA binding site 342108009709 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 342108009710 Peptidase family M50; Region: Peptidase_M50; pfam02163 342108009711 active site 342108009712 putative substrate binding region [chemical binding]; other site 342108009713 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 342108009714 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108009715 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 342108009716 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108009717 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 342108009718 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108009719 Domain of unknown function (DUF4347); Region: DUF4347; pfam14252 342108009720 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 342108009721 Ca2+ binding site [ion binding]; other site 342108009722 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 342108009723 Ca2+ binding site [ion binding]; other site 342108009724 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108009725 Cadherin repeat-like domain; Region: CA_like; cl15786 342108009726 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108009727 Cadherin repeat-like domain; Region: CA_like; cl15786 342108009728 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108009729 Cadherin repeat-like domain; Region: CA_like; cl15786 342108009730 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108009731 Cadherin repeat-like domain; Region: CA_like; cl15786 342108009732 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108009733 Cadherin repeat-like domain; Region: CA_like; cl15786 342108009734 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108009735 Cadherin repeat-like domain; Region: CA_like; cl15786 342108009736 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108009737 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108009738 Cadherin repeat-like domain; Region: CA_like; cl15786 342108009739 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108009740 Cadherin repeat-like domain; Region: CA_like; cl15786 342108009741 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108009742 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 342108009743 Domain of unknown function (DUF4347); Region: DUF4347; pfam14252 342108009744 Cadherin repeat-like domain; Region: CA_like; cl15786 342108009745 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 342108009746 Helix-turn-helix domain; Region: HTH_18; pfam12833 342108009747 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 342108009748 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 342108009749 active site 342108009750 catalytic residues [active] 342108009751 DNA binding site [nucleotide binding] 342108009752 Int/Topo IB signature motif; other site 342108009753 Transposase; Region: HTH_Tnp_1; pfam01527 342108009754 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108009755 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108009756 Zn2+ binding site [ion binding]; other site 342108009757 Mg2+ binding site [ion binding]; other site 342108009758 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 342108009759 DNA-binding site [nucleotide binding]; DNA binding site 342108009760 RNA-binding motif; other site 342108009761 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 342108009762 active site 342108009763 catalytic site [active] 342108009764 substrate binding site [chemical binding]; other site 342108009765 tetrathionate reductase subunit A; Provisional; Region: PRK14991 342108009766 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 342108009767 molybdopterin cofactor binding site; other site 342108009768 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 342108009769 This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins; Region: MopB_CT_Tetrathionate_Arsenate-R; cd02780 342108009770 putative molybdopterin cofactor binding site; other site 342108009771 tetrathionate reductase subunit C; Provisional; Region: PRK14992 342108009772 tetrathionate reductase subunit C; Provisional; Region: PRK14992 342108009773 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 342108009774 4Fe-4S binding domain; Region: Fer4; pfam00037 342108009775 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 342108009776 Response regulator receiver domain; Region: Response_reg; pfam00072 342108009777 active site 342108009778 phosphorylation site [posttranslational modification] 342108009779 intermolecular recognition site; other site 342108009780 dimerization interface [polypeptide binding]; other site 342108009781 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 342108009782 DNA binding residues [nucleotide binding] 342108009783 dimerization interface [polypeptide binding]; other site 342108009784 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 342108009785 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 342108009786 dimer interface [polypeptide binding]; other site 342108009787 phosphorylation site [posttranslational modification] 342108009788 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 342108009789 ATP binding site [chemical binding]; other site 342108009790 Mg2+ binding site [ion binding]; other site 342108009791 G-X-G motif; other site 342108009792 SlyX; Region: SlyX; pfam04102 342108009793 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 342108009794 active site 342108009795 catalytic residues [active] 342108009796 DNA binding site [nucleotide binding] 342108009797 Int/Topo IB signature motif; other site 342108009798 MarR family; Region: MarR_2; cl17246 342108009799 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 342108009800 Putative transposase of IS4/5 family (DUF4096); Region: DUF4096; pfam13340 342108009801 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 342108009802 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 342108009803 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 342108009804 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 342108009805 substrate binding pocket [chemical binding]; other site 342108009806 membrane-bound complex binding site; other site 342108009807 hinge residues; other site 342108009808 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108009809 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108009810 metal binding site [ion binding]; metal-binding site 342108009811 active site 342108009812 I-site; other site 342108009813 Porin subfamily; Region: Porin_2; pfam02530 342108009814 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 342108009815 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3666 342108009816 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 342108009817 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 342108009818 FMN binding site [chemical binding]; other site 342108009819 active site 342108009820 substrate binding site [chemical binding]; other site 342108009821 catalytic residue [active] 342108009822 Isochorismatase family; Region: Isochorismatase; pfam00857 342108009823 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 342108009824 catalytic triad [active] 342108009825 conserved cis-peptide bond; other site 342108009826 Pirin; Region: Pirin; pfam02678 342108009827 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 342108009828 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 342108009829 putative effector binding pocket; other site 342108009830 dimerization interface [polypeptide binding]; other site 342108009831 multiple promoter invertase; Provisional; Region: mpi; PRK13413 342108009832 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 342108009833 catalytic residues [active] 342108009834 catalytic nucleophile [active] 342108009835 Presynaptic Site I dimer interface [polypeptide binding]; other site 342108009836 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 342108009837 Synaptic Flat tetramer interface [polypeptide binding]; other site 342108009838 Synaptic Site I dimer interface [polypeptide binding]; other site 342108009839 DNA binding site [nucleotide binding] 342108009840 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 342108009841 DNA-binding interface [nucleotide binding]; DNA binding site 342108009842 Response regulator receiver domain; Region: Response_reg; pfam00072 342108009843 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 342108009844 active site 342108009845 phosphorylation site [posttranslational modification] 342108009846 intermolecular recognition site; other site 342108009847 dimerization interface [polypeptide binding]; other site 342108009848 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 342108009849 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 342108009850 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 342108009851 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 342108009852 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108009853 putative active site [active] 342108009854 heme pocket [chemical binding]; other site 342108009855 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 342108009856 dimer interface [polypeptide binding]; other site 342108009857 phosphorylation site [posttranslational modification] 342108009858 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 342108009859 ATP binding site [chemical binding]; other site 342108009860 Mg2+ binding site [ion binding]; other site 342108009861 G-X-G motif; other site 342108009862 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108009863 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 342108009864 active site 342108009865 phosphorylation site [posttranslational modification] 342108009866 intermolecular recognition site; other site 342108009867 dimerization interface [polypeptide binding]; other site 342108009868 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108009869 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108009870 dimer interface [polypeptide binding]; other site 342108009871 putative CheW interface [polypeptide binding]; other site 342108009872 Transposase; Region: HTH_Tnp_1; pfam01527 342108009873 Transposase; Region: HTH_Tnp_1; pfam01527 342108009874 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108009875 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 342108009876 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 342108009877 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 342108009878 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 342108009879 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 342108009880 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 342108009881 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 342108009882 Plasmid pRiA4b ORF-3-like protein; Region: PRiA4_ORF3; pfam07929 342108009883 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 342108009884 Integrase core domain; Region: rve; pfam00665 342108009885 Integrase core domain; Region: rve_3; pfam13683 342108009886 Transposase; Region: HTH_Tnp_1; pfam01527 342108009887 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108009888 HTH-like domain; Region: HTH_21; pfam13276 342108009889 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 342108009890 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 342108009891 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 342108009892 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 342108009893 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 342108009894 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 342108009895 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 342108009896 Transposase; Region: HTH_Tnp_1; pfam01527 342108009897 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108009898 Integrase core domain; Region: rve; pfam00665 342108009899 Integrase core domain; Region: rve_3; pfam13683 342108009900 Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]; Region: CheB; COG2201 342108009901 CheB methylesterase; Region: CheB_methylest; pfam01339 342108009902 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 342108009903 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 342108009904 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 342108009905 PAS fold; Region: PAS_4; pfam08448 342108009906 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 342108009907 putative active site [active] 342108009908 heme pocket [chemical binding]; other site 342108009909 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 342108009910 PAS domain; Region: PAS_9; pfam13426 342108009911 putative active site [active] 342108009912 heme pocket [chemical binding]; other site 342108009913 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108009914 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108009915 metal binding site [ion binding]; metal-binding site 342108009916 active site 342108009917 I-site; other site 342108009918 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 342108009919 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108009920 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 342108009921 active site 342108009922 phosphorylation site [posttranslational modification] 342108009923 intermolecular recognition site; other site 342108009924 dimerization interface [polypeptide binding]; other site 342108009925 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108009926 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108009927 metal binding site [ion binding]; metal-binding site 342108009928 active site 342108009929 I-site; other site 342108009930 LTXXQ motif family protein; Region: LTXXQ; pfam07813 342108009931 dimer interface [polypeptide binding]; other site 342108009932 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 342108009933 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 342108009934 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 342108009935 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 342108009936 FAD binding pocket [chemical binding]; other site 342108009937 FAD binding motif [chemical binding]; other site 342108009938 phosphate binding motif [ion binding]; other site 342108009939 beta-alpha-beta structure motif; other site 342108009940 NAD binding pocket [chemical binding]; other site 342108009941 Domain of unknown function (DUF329); Region: DUF329; pfam03884 342108009942 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 342108009943 homodimer interface [polypeptide binding]; other site 342108009944 oligonucleotide binding site [chemical binding]; other site 342108009945 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 342108009946 Maf-like protein; Region: Maf; pfam02545 342108009947 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 342108009948 active site 342108009949 dimer interface [polypeptide binding]; other site 342108009950 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 342108009951 rRNA binding site [nucleotide binding]; other site 342108009952 predicted 30S ribosome binding site; other site 342108009953 Low molecular weight phosphatase family; Region: LMWPc; cd00115 342108009954 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 342108009955 active site 342108009956 hypothetical protein; Provisional; Region: PRK02853 342108009957 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 342108009958 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 342108009959 NAD binding site [chemical binding]; other site 342108009960 dimerization interface [polypeptide binding]; other site 342108009961 product binding site; other site 342108009962 substrate binding site [chemical binding]; other site 342108009963 zinc binding site [ion binding]; other site 342108009964 catalytic residues [active] 342108009965 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 342108009966 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 342108009967 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 342108009968 active site 342108009969 phosphorylation site [posttranslational modification] 342108009970 intermolecular recognition site; other site 342108009971 dimerization interface [polypeptide binding]; other site 342108009972 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 342108009973 DNA binding site [nucleotide binding] 342108009974 HAMP domain; Region: HAMP; pfam00672 342108009975 dimerization interface [polypeptide binding]; other site 342108009976 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 342108009977 dimer interface [polypeptide binding]; other site 342108009978 phosphorylation site [posttranslational modification] 342108009979 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 342108009980 ATP binding site [chemical binding]; other site 342108009981 Mg2+ binding site [ion binding]; other site 342108009982 G-X-G motif; other site 342108009983 cyclase homology domain; Region: CHD; cd07302 342108009984 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 342108009985 nucleotidyl binding site; other site 342108009986 metal binding site [ion binding]; metal-binding site 342108009987 dimer interface [polypeptide binding]; other site 342108009988 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 342108009989 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 342108009990 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 342108009991 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 342108009992 Mg2+ binding site [ion binding]; other site 342108009993 G-X-G motif; other site 342108009994 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 342108009995 anchoring element; other site 342108009996 dimer interface [polypeptide binding]; other site 342108009997 ATP binding site [chemical binding]; other site 342108009998 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 342108009999 active site 342108010000 metal binding site [ion binding]; metal-binding site 342108010001 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 342108010002 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108010003 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 342108010004 ligand binding site [chemical binding]; other site 342108010005 flexible hinge region; other site 342108010006 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 342108010007 non-specific DNA interactions [nucleotide binding]; other site 342108010008 DNA binding site [nucleotide binding] 342108010009 sequence specific DNA binding site [nucleotide binding]; other site 342108010010 putative cAMP binding site [chemical binding]; other site 342108010011 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 342108010012 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 342108010013 anti sigma factor interaction site; other site 342108010014 regulatory phosphorylation site [posttranslational modification]; other site 342108010015 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108010016 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108010017 dimer interface [polypeptide binding]; other site 342108010018 putative CheW interface [polypeptide binding]; other site 342108010019 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 342108010020 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 342108010021 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 342108010022 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108010023 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 342108010024 ligand binding site [chemical binding]; other site 342108010025 flexible hinge region; other site 342108010026 helix_turn_helix, cAMP Regulatory protein; Region: HTH_CRP; smart00419 342108010027 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 342108010028 Ion transport protein; Region: Ion_trans; pfam00520 342108010029 Ion channel; Region: Ion_trans_2; pfam07885 342108010030 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 342108010031 active site 342108010032 SAM binding site [chemical binding]; other site 342108010033 homodimer interface [polypeptide binding]; other site 342108010034 hypothetical protein; Provisional; Region: PRK02395 342108010035 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 342108010036 putative active site [active] 342108010037 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 342108010038 putative active site [active] 342108010039 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 342108010040 active site 342108010041 iron coordination sites [ion binding]; other site 342108010042 substrate binding pocket [chemical binding]; other site 342108010043 sulfite reductase, dissimilatory-type alpha subunit; Region: dsrA; TIGR02064 342108010044 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 342108010045 sulfite reductase, dissimilatory-type beta subunit; Region: dsrB; TIGR02066 342108010046 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 342108010047 sulfur relay protein TusD/DsrE; Region: sulf_tusD_dsrE; TIGR03012 342108010048 sulfur relay protein TusC/DsrF; Region: sulf_tusC_dsrF; TIGR03010 342108010049 sulfur relay protein TusB/DsrH; Region: sulf_tusB_dsrH; TIGR03011 342108010050 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]; Region: DsrC; COG2920 342108010051 DsrC like protein; Region: DsrC; pfam04358 342108010052 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 342108010053 putative glutamate synthase (NADPH) small subunit; Provisional; Region: PRK12771 342108010054 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 342108010055 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108010056 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 342108010057 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 342108010058 4Fe-4S binding domain; Region: Fer4; cl02805 342108010059 Polysulphide reductase, NrfD; Region: NrfD; pfam03916 342108010060 Polysulphide reductase [Energy production and conversion]; Region: COG5557; cl17901 342108010061 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 342108010062 Sulfate transporter family; Region: Sulfate_transp; pfam00916 342108010063 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 342108010064 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 342108010065 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108010066 ligand binding site [chemical binding]; other site 342108010067 flexible hinge region; other site 342108010068 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 342108010069 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 342108010070 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 342108010071 DsbD alpha interface [polypeptide binding]; other site 342108010072 catalytic residues [active] 342108010073 Nitrate and nitrite sensing; Region: NIT; pfam08376 342108010074 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108010075 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108010076 dimer interface [polypeptide binding]; other site 342108010077 putative CheW interface [polypeptide binding]; other site 342108010078 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108010079 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 342108010080 active site 342108010081 phosphorylation site [posttranslational modification] 342108010082 intermolecular recognition site; other site 342108010083 dimerization interface [polypeptide binding]; other site 342108010084 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 342108010085 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 342108010086 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 342108010087 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 342108010088 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 342108010089 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 342108010090 Walker A/P-loop; other site 342108010091 ATP binding site [chemical binding]; other site 342108010092 Q-loop/lid; other site 342108010093 ABC transporter signature motif; other site 342108010094 Walker B; other site 342108010095 D-loop; other site 342108010096 H-loop/switch region; other site 342108010097 magnesium chelatase subunit H; Provisional; Region: PLN03241 342108010098 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 342108010099 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108010100 putative active site [active] 342108010101 heme pocket [chemical binding]; other site 342108010102 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 342108010103 dimer interface [polypeptide binding]; other site 342108010104 phosphorylation site [posttranslational modification] 342108010105 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 342108010106 ATP binding site [chemical binding]; other site 342108010107 Mg2+ binding site [ion binding]; other site 342108010108 G-X-G motif; other site 342108010109 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 342108010110 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 342108010111 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108010112 catalytic residue [active] 342108010113 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 342108010114 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 342108010115 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 342108010116 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 342108010117 Type I periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; Region: PBP1_Nba_like; cd06359 342108010118 putative ligand binding site [chemical binding]; other site 342108010119 Rrf2 family protein; Region: rrf2_super; TIGR00738 342108010120 Transcriptional regulator; Region: Rrf2; pfam02082 342108010121 putative acetyltransferase; Provisional; Region: PRK03624 342108010122 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 342108010123 Coenzyme A binding pocket [chemical binding]; other site 342108010124 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 342108010125 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase...; Region: TRX_Fd_NuoE_hoxF; cd03083 342108010126 putative dimer interface [polypeptide binding]; other site 342108010127 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 342108010128 SLBB domain; Region: SLBB; pfam10531 342108010129 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 342108010130 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 342108010131 catalytic loop [active] 342108010132 iron binding site [ion binding]; other site 342108010133 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 342108010134 4Fe-4S single cluster domain; Region: Fer4_15; pfam13459 342108010135 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 342108010136 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 342108010137 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 342108010138 Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit...; Region: H2MP_NAD-link-bidir; cd06066 342108010139 nickel binding site [ion binding]; other site 342108010140 Response regulator receiver domain; Region: Response_reg; pfam00072 342108010141 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 342108010142 active site 342108010143 phosphorylation site [posttranslational modification] 342108010144 intermolecular recognition site; other site 342108010145 dimerization interface [polypeptide binding]; other site 342108010146 ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: ModC; COG4148 342108010147 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108010148 Walker A/P-loop; other site 342108010149 ATP binding site [chemical binding]; other site 342108010150 Q-loop/lid; other site 342108010151 ABC transporter signature motif; other site 342108010152 Walker B; other site 342108010153 D-loop; other site 342108010154 H-loop/switch region; other site 342108010155 TOBE domain; Region: TOBE; cl01440 342108010156 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 342108010157 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 342108010158 dimer interface [polypeptide binding]; other site 342108010159 conserved gate region; other site 342108010160 putative PBP binding loops; other site 342108010161 ABC-ATPase subunit interface; other site 342108010162 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 342108010163 PAS domain; Region: PAS_9; pfam13426 342108010164 putative active site [active] 342108010165 heme pocket [chemical binding]; other site 342108010166 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 342108010167 PAS domain; Region: PAS_9; pfam13426 342108010168 putative active site [active] 342108010169 heme pocket [chemical binding]; other site 342108010170 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108010171 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108010172 metal binding site [ion binding]; metal-binding site 342108010173 active site 342108010174 I-site; other site 342108010175 camphor resistance protein CrcB; Provisional; Region: PRK14206 342108010176 AsmA family; Region: AsmA; pfam05170 342108010177 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 342108010178 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 342108010179 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 342108010180 ligand binding site [chemical binding]; other site 342108010181 TIR domain; Region: TIR_2; pfam13676 342108010182 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 342108010183 TPR motif; other site 342108010184 binding surface 342108010185 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108010186 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108010187 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 342108010188 binding surface 342108010189 TPR motif; other site 342108010190 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108010191 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 342108010192 Ligand Binding Site [chemical binding]; other site 342108010193 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 342108010194 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 342108010195 active site 342108010196 multidrug efflux protein; Reviewed; Region: PRK09579 342108010197 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 342108010198 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 342108010199 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108010200 transcriptional repressor BetI; Region: betaine_BetI; TIGR03384 342108010201 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 342108010202 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 342108010203 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 342108010204 MarR family; Region: MarR; pfam01047 342108010205 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 342108010206 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 342108010207 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 342108010208 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 342108010209 RNA binding site [nucleotide binding]; other site 342108010210 PilZ domain; Region: PilZ; pfam07238 342108010211 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 342108010212 FecR protein; Region: FecR; pfam04773 342108010213 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 342108010214 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 342108010215 Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of...; Region: LamG; cd00110 342108010216 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 342108010217 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 342108010218 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 342108010219 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 342108010220 Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of...; Region: LamG; cd00110 342108010221 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 342108010222 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 342108010223 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 342108010224 intermolecular salt bridges; other site 342108010225 Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of...; Region: LamG; cd00110 342108010226 Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated...; Region: PTX; cl00102 342108010227 intermolecular salt bridges; other site 342108010228 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 342108010229 PAS domain S-box; Region: sensory_box; TIGR00229 342108010230 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 342108010231 putative active site [active] 342108010232 heme pocket [chemical binding]; other site 342108010233 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108010234 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 342108010235 putative active site [active] 342108010236 heme pocket [chemical binding]; other site 342108010237 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 342108010238 dimer interface [polypeptide binding]; other site 342108010239 phosphorylation site [posttranslational modification] 342108010240 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 342108010241 ATP binding site [chemical binding]; other site 342108010242 Mg2+ binding site [ion binding]; other site 342108010243 G-X-G motif; other site 342108010244 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 342108010245 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 342108010246 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108010247 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 342108010248 Cytochrome c; Region: Cytochrom_C; cl11414 342108010249 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 342108010250 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108010251 Rubredoxin [Energy production and conversion]; Region: COG1773 342108010252 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 342108010253 iron binding site [ion binding]; other site 342108010254 Rubredoxin; Region: Rubredoxin; pfam00301 342108010255 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 342108010256 iron binding site [ion binding]; other site 342108010257 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 342108010258 Rubrerythrin [Energy production and conversion]; Region: COG1592 342108010259 binuclear metal center [ion binding]; other site 342108010260 Outer membrane efflux protein; Region: OEP; pfam02321 342108010261 Outer membrane efflux protein; Region: OEP; pfam02321 342108010262 Resolvase, N terminal domain; Region: Resolvase; pfam00239 342108010263 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 342108010264 catalytic residues [active] 342108010265 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 342108010266 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 342108010267 Protein export membrane protein; Region: SecD_SecF; cl14618 342108010268 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 342108010269 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 342108010270 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 342108010271 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108010272 Uncharacterized conserved protein [Function unknown]; Region: COG3287 342108010273 FIST N domain; Region: FIST; pfam08495 342108010274 FIST C domain; Region: FIST_C; pfam10442 342108010275 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 342108010276 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 342108010277 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108010278 putative active site [active] 342108010279 heme pocket [chemical binding]; other site 342108010280 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 342108010281 dimer interface [polypeptide binding]; other site 342108010282 phosphorylation site [posttranslational modification] 342108010283 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 342108010284 ATP binding site [chemical binding]; other site 342108010285 Mg2+ binding site [ion binding]; other site 342108010286 G-X-G motif; other site 342108010287 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108010288 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 342108010289 active site 342108010290 phosphorylation site [posttranslational modification] 342108010291 intermolecular recognition site; other site 342108010292 dimerization interface [polypeptide binding]; other site 342108010293 Response regulator receiver domain; Region: Response_reg; pfam00072 342108010294 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 342108010295 active site 342108010296 phosphorylation site [posttranslational modification] 342108010297 intermolecular recognition site; other site 342108010298 dimerization interface [polypeptide binding]; other site 342108010299 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 342108010300 putative binding surface; other site 342108010301 active site 342108010302 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 342108010303 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 342108010304 active site 342108010305 phosphorylation site [posttranslational modification] 342108010306 intermolecular recognition site; other site 342108010307 dimerization interface [polypeptide binding]; other site 342108010308 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108010309 Zn2+ binding site [ion binding]; other site 342108010310 Mg2+ binding site [ion binding]; other site 342108010311 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 342108010312 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108010313 Zn2+ binding site [ion binding]; other site 342108010314 Mg2+ binding site [ion binding]; other site 342108010315 acyl-CoA esterase; Provisional; Region: PRK10673 342108010316 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 342108010317 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 342108010318 Helix-turn-helix domain; Region: HTH_28; pfam13518 342108010319 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108010320 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 342108010321 active site 342108010322 phosphorylation site [posttranslational modification] 342108010323 intermolecular recognition site; other site 342108010324 dimerization interface [polypeptide binding]; other site 342108010325 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 342108010326 DNA binding site [nucleotide binding] 342108010327 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108010328 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 342108010329 active site 342108010330 phosphorylation site [posttranslational modification] 342108010331 intermolecular recognition site; other site 342108010332 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108010333 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 342108010334 dimer interface [polypeptide binding]; other site 342108010335 phosphorylation site [posttranslational modification] 342108010336 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 342108010337 ATP binding site [chemical binding]; other site 342108010338 Mg2+ binding site [ion binding]; other site 342108010339 G-X-G motif; other site 342108010340 Domain of unknown function (DUF1987); Region: DUF1987; pfam09345 342108010341 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 342108010342 ATP binding site [chemical binding]; other site 342108010343 Mg2+ binding site [ion binding]; other site 342108010344 G-X-G motif; other site 342108010345 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 342108010346 active site 342108010347 phosphorylation site [posttranslational modification] 342108010348 intermolecular recognition site; other site 342108010349 PAS fold; Region: PAS_4; pfam08448 342108010350 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 342108010351 putative active site [active] 342108010352 heme pocket [chemical binding]; other site 342108010353 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108010354 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108010355 metal binding site [ion binding]; metal-binding site 342108010356 active site 342108010357 I-site; other site 342108010358 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 342108010359 substrate binding pocket [chemical binding]; other site 342108010360 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 342108010361 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 342108010362 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 342108010363 active site 342108010364 FMN binding site [chemical binding]; other site 342108010365 2,4-decadienoyl-CoA binding site; other site 342108010366 catalytic residue [active] 342108010367 4Fe-4S cluster binding site [ion binding]; other site 342108010368 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 342108010369 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 342108010370 HI0933-like protein; Region: HI0933_like; pfam03486 342108010371 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 342108010372 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 342108010373 FAD binding domain; Region: FAD_binding_4; pfam01565 342108010374 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 342108010375 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 342108010376 substrate binding pocket [chemical binding]; other site 342108010377 membrane-bound complex binding site; other site 342108010378 Helix-turn-helix domain; Region: HTH_28; pfam13518 342108010379 Nif-specific regulatory protein; Region: nifA; TIGR01817 342108010380 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 342108010381 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 342108010382 Walker A motif; other site 342108010383 ATP binding site [chemical binding]; other site 342108010384 Walker B motif; other site 342108010385 Biopterin-dependent aromatic amino acid hydroxylase; a family of non-heme, iron(II)-dependent enzymes that includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan...; Region: arom_aa_hydroxylase; cl01244 342108010386 cofactor binding site; other site 342108010387 arginine finger; other site 342108010388 metal binding site [ion binding]; metal-binding site 342108010389 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 342108010390 Predicted protein tyrosine phosphatase [General function prediction only]; Region: COG5350 342108010391 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 342108010392 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 342108010393 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 342108010394 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 342108010395 TrkA-N domain; Region: TrkA_N; pfam02254 342108010396 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 342108010397 dimerization interface [polypeptide binding]; other site 342108010398 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108010399 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108010400 dimer interface [polypeptide binding]; other site 342108010401 putative CheW interface [polypeptide binding]; other site 342108010402 2-isopropylmalate synthase; Validated; Region: PRK03739 342108010403 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 342108010404 active site 342108010405 catalytic residues [active] 342108010406 metal binding site [ion binding]; metal-binding site 342108010407 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 342108010408 CHASE domain; Region: CHASE; cl01369 342108010409 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 342108010410 dimer interface [polypeptide binding]; other site 342108010411 phosphorylation site [posttranslational modification] 342108010412 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 342108010413 ATP binding site [chemical binding]; other site 342108010414 Mg2+ binding site [ion binding]; other site 342108010415 G-X-G motif; other site 342108010416 Response regulator receiver domain; Region: Response_reg; pfam00072 342108010417 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 342108010418 active site 342108010419 phosphorylation site [posttranslational modification] 342108010420 intermolecular recognition site; other site 342108010421 dimerization interface [polypeptide binding]; other site 342108010422 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5330 342108010423 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 342108010424 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 342108010425 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 342108010426 catalytic triad [active] 342108010427 CHASE3 domain; Region: CHASE3; cl05000 342108010428 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 342108010429 dimerization interface [polypeptide binding]; other site 342108010430 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108010431 dimer interface [polypeptide binding]; other site 342108010432 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 342108010433 putative CheW interface [polypeptide binding]; other site 342108010434 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 342108010435 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 342108010436 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108010437 Walker A/P-loop; other site 342108010438 ATP binding site [chemical binding]; other site 342108010439 Q-loop/lid; other site 342108010440 ABC transporter signature motif; other site 342108010441 Walker B; other site 342108010442 D-loop; other site 342108010443 H-loop/switch region; other site 342108010444 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 342108010445 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108010446 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 342108010447 Uncharacterized conserved protein [Function unknown]; Region: COG2128 342108010448 RNA polymerase sigma-70 factor, TIGR02957 family; Region: SigX4 342108010449 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 342108010450 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 342108010451 DNA binding residues [nucleotide binding] 342108010452 RNA recognition motif (RRM) superfamily; Region: RRM_SF; cl17169 342108010453 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 342108010454 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 342108010455 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 342108010456 motif II; other site 342108010457 Protein of unknown function (DUF1015); Region: DUF1015; pfam06245 342108010458 Uncharacterized conserved protein [Function unknown]; Region: COG4198 342108010459 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 342108010460 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 342108010461 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 342108010462 protein binding site [polypeptide binding]; other site 342108010463 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 342108010464 protein binding site [polypeptide binding]; other site 342108010465 recombination factor protein RarA; Reviewed; Region: PRK13342 342108010466 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 342108010467 Walker A motif; other site 342108010468 ATP binding site [chemical binding]; other site 342108010469 Walker B motif; other site 342108010470 arginine finger; other site 342108010471 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 342108010472 hopanoid biosynthesis associated radical SAM protein HpnJ; Region: HpnJ; TIGR03471 342108010473 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 342108010474 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 342108010475 FeS/SAM binding site; other site 342108010476 hopanoid biosynthesis associated glycosyl transferase protein HpnI; Region: HpnI; TIGR03472 342108010477 Glucosylceramide synthase catalyzes the first glycosylation step of glycosphingolipid synthesis; Region: Glucosylceramide_synthase; cd02520 342108010478 ligand binding site; other site 342108010479 hopanoid biosynthesis associated membrane protein HpnM; Region: HpnM; TIGR03481 342108010480 Domain of unknown function DUF59; Region: DUF59; pfam01883 342108010481 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 342108010482 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 342108010483 Walker A motif; other site 342108010484 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 342108010485 HflK protein; Region: hflK; TIGR01933 342108010486 HflC protein; Region: hflC; TIGR01932 342108010487 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 342108010488 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 342108010489 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 342108010490 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 342108010491 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 342108010492 protein binding site [polypeptide binding]; other site 342108010493 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 342108010494 protein binding site [polypeptide binding]; other site 342108010495 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12788 342108010496 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 342108010497 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK12786 342108010498 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 342108010499 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 342108010500 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12691 342108010501 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 342108010502 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 342108010503 flagellar hook-basal body protein; Region: FlgEFG_subfam; TIGR03506 342108010504 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 342108010505 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 342108010506 flagellar motor switch protein FliM; Region: fliM_switch; TIGR01397 342108010507 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 342108010508 Uncharacterized conserved protein [Function unknown]; Region: COG3334 342108010509 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 342108010510 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 342108010511 active site 342108010512 phosphorylation site [posttranslational modification] 342108010513 intermolecular recognition site; other site 342108010514 dimerization interface [polypeptide binding]; other site 342108010515 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 342108010516 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 342108010517 NnrS protein; Region: NnrS; pfam05940 342108010518 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 342108010519 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 342108010520 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK09107 342108010521 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 342108010522 PYR/PP interface [polypeptide binding]; other site 342108010523 dimer interface [polypeptide binding]; other site 342108010524 TPP binding site [chemical binding]; other site 342108010525 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 342108010526 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 342108010527 TPP-binding site [chemical binding]; other site 342108010528 dimer interface [polypeptide binding]; other site 342108010529 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 342108010530 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 342108010531 putative valine binding site [chemical binding]; other site 342108010532 dimer interface [polypeptide binding]; other site 342108010533 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 342108010534 ketol-acid reductoisomerase; Provisional; Region: PRK05479 342108010535 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 342108010536 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 342108010537 Conserved hypothetical protein (DUF2461); Region: DUF2461; pfam09365 342108010538 2-isopropylmalate synthase; Validated; Region: PRK00915 342108010539 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 342108010540 active site 342108010541 catalytic residues [active] 342108010542 metal binding site [ion binding]; metal-binding site 342108010543 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 342108010544 rod shape-determining protein MreB; Provisional; Region: PRK13927 342108010545 MreB and similar proteins; Region: MreB_like; cd10225 342108010546 nucleotide binding site [chemical binding]; other site 342108010547 Mg binding site [ion binding]; other site 342108010548 putative protofilament interaction site [polypeptide binding]; other site 342108010549 RodZ interaction site [polypeptide binding]; other site 342108010550 rod shape-determining protein MreC; Provisional; Region: PRK13922 342108010551 rod shape-determining protein MreC; Region: MreC; pfam04085 342108010552 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 342108010553 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 342108010554 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 342108010555 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 342108010556 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 342108010557 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 342108010558 anti sigma factor interaction site; other site 342108010559 regulatory phosphorylation site [posttranslational modification]; other site 342108010560 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 342108010561 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 342108010562 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 342108010563 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 342108010564 Formyl transferase catalytic core domain found in a group of proteins with unknown functions; Region: FMT_core_like_3; cd08653 342108010565 putative active site [active] 342108010566 putative cosubstrate binding site; other site 342108010567 putative substrate binding site [chemical binding]; other site 342108010568 catalytic site [active] 342108010569 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 342108010570 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 342108010571 dimerization interface [polypeptide binding]; other site 342108010572 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 342108010573 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108010574 putative substrate translocation pore; other site 342108010575 glutamate racemase; Provisional; Region: PRK00865 342108010576 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108010577 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 342108010578 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]; Region: COG1525 342108010579 Catalytic site; other site 342108010580 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 342108010581 Uncharacterized conserved protein (DUF2249); Region: DUF2249; cl17719 342108010582 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 342108010583 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 342108010584 motif 1; other site 342108010585 active site 342108010586 motif 2; other site 342108010587 motif 3; other site 342108010588 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 342108010589 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 342108010590 Sulfate transporter family; Region: Sulfate_transp; pfam00916 342108010591 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 342108010592 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 342108010593 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108010594 ligand binding site [chemical binding]; other site 342108010595 flexible hinge region; other site 342108010596 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 342108010597 PAS domain; Region: PAS_9; pfam13426 342108010598 putative active site [active] 342108010599 heme pocket [chemical binding]; other site 342108010600 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108010601 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 342108010602 putative active site [active] 342108010603 heme pocket [chemical binding]; other site 342108010604 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 342108010605 dimer interface [polypeptide binding]; other site 342108010606 phosphorylation site [posttranslational modification] 342108010607 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 342108010608 ATP binding site [chemical binding]; other site 342108010609 Mg2+ binding site [ion binding]; other site 342108010610 G-X-G motif; other site 342108010611 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108010612 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 342108010613 active site 342108010614 phosphorylation site [posttranslational modification] 342108010615 intermolecular recognition site; other site 342108010616 dimerization interface [polypeptide binding]; other site 342108010617 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 342108010618 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 342108010619 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 342108010620 dimerization interface [polypeptide binding]; other site 342108010621 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108010622 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108010623 dimer interface [polypeptide binding]; other site 342108010624 putative CheW interface [polypeptide binding]; other site 342108010625 anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 342108010626 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 342108010627 molybdopterin cofactor binding site; other site 342108010628 The MopB_2 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to...; Region: MopB_2; cd02763 342108010629 putative molybdopterin cofactor binding site [chemical binding]; other site 342108010630 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is...; Region: MopB_CT_2; cd02783 342108010631 putative molybdopterin cofactor binding site; other site 342108010632 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 342108010633 4Fe-4S binding domain; Region: Fer4; pfam00037 342108010634 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl17519 342108010635 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 342108010636 N-terminal plug; other site 342108010637 ligand-binding site [chemical binding]; other site 342108010638 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 342108010639 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 342108010640 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 342108010641 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 342108010642 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 342108010643 TolR protein; Region: tolR; TIGR02801 342108010644 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 342108010645 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 342108010646 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 342108010647 hypothetical protein; Provisional; Region: PRK10621 342108010648 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 342108010649 PAS domain; Region: PAS_9; pfam13426 342108010650 putative active site [active] 342108010651 heme pocket [chemical binding]; other site 342108010652 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 342108010653 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cl00144 342108010654 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108010655 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108010656 dimer interface [polypeptide binding]; other site 342108010657 putative CheW interface [polypeptide binding]; other site 342108010658 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 342108010659 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 342108010660 23S rRNA interface [nucleotide binding]; other site 342108010661 L3 interface [polypeptide binding]; other site 342108010662 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 342108010663 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 342108010664 dimer interface [polypeptide binding]; other site 342108010665 phosphorylation site [posttranslational modification] 342108010666 Histidine kinase-like ATPases; Region: HATPase_c; smart00387 342108010667 ATP binding site [chemical binding]; other site 342108010668 G-X-G motif; other site 342108010669 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 342108010670 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 342108010671 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 342108010672 ABC transporter; Region: ABC_tran_2; pfam12848 342108010673 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 342108010674 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 342108010675 active site 342108010676 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 342108010677 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108010678 sequence-specific DNA binding site [nucleotide binding]; other site 342108010679 salt bridge; other site 342108010680 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 342108010681 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108010682 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108010683 metal binding site [ion binding]; metal-binding site 342108010684 active site 342108010685 I-site; other site 342108010686 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108010687 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 342108010688 putative active site [active] 342108010689 heme pocket [chemical binding]; other site 342108010690 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 342108010691 dimer interface [polypeptide binding]; other site 342108010692 phosphorylation site [posttranslational modification] 342108010693 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 342108010694 ATP binding site [chemical binding]; other site 342108010695 Mg2+ binding site [ion binding]; other site 342108010696 G-X-G motif; other site 342108010697 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 342108010698 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 342108010699 dimer interface [polypeptide binding]; other site 342108010700 conserved gate region; other site 342108010701 putative PBP binding loops; other site 342108010702 ABC-ATPase subunit interface; other site 342108010703 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 342108010704 dimer interface [polypeptide binding]; other site 342108010705 conserved gate region; other site 342108010706 ABC-ATPase subunit interface; other site 342108010707 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 342108010708 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 342108010709 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108010710 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108010711 metal binding site [ion binding]; metal-binding site 342108010712 active site 342108010713 I-site; other site 342108010714 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 342108010715 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108010716 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 342108010717 active site 342108010718 phosphorylation site [posttranslational modification] 342108010719 intermolecular recognition site; other site 342108010720 dimerization interface [polypeptide binding]; other site 342108010721 FecR protein; Region: FecR; pfam04773 342108010722 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 342108010723 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 342108010724 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 342108010725 putative active site [active] 342108010726 putative substrate binding site [chemical binding]; other site 342108010727 putative cosubstrate binding site; other site 342108010728 catalytic site [active] 342108010729 Uncharacterized conserved protein (DUF2249); Region: DUF2249; pfam10006 342108010730 Uncharacterized conserved protein (DUF2249); Region: DUF2249; pfam10006 342108010731 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 342108010732 ligand binding site [chemical binding]; other site 342108010733 flexible hinge region; other site 342108010734 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 342108010735 transcriptional activator FtrB; Provisional; Region: ftrB; PRK09392 342108010736 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 342108010737 ligand binding site [chemical binding]; other site 342108010738 flexible hinge region; other site 342108010739 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 342108010740 glutamate racemase; Provisional; Region: PRK00865 342108010741 Rop-like; Region: Rop-like; pfam05082 342108010742 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 342108010743 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108010744 NAD(P) binding site [chemical binding]; other site 342108010745 active site 342108010746 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 342108010747 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 342108010748 substrate binding site [chemical binding]; other site 342108010749 oxyanion hole (OAH) forming residues; other site 342108010750 trimer interface [polypeptide binding]; other site 342108010751 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 342108010752 malonyl-CoA synthase; Validated; Region: PRK07514 342108010753 Malonyl-CoA synthetase (MCS); Region: MCS; cd05941 342108010754 acyl-activating enzyme (AAE) consensus motif; other site 342108010755 active site 342108010756 AMP binding site [chemical binding]; other site 342108010757 CoA binding site [chemical binding]; other site 342108010758 Transcriptional regulators [Transcription]; Region: FadR; COG2186 342108010759 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 342108010760 DNA-binding site [nucleotide binding]; DNA binding site 342108010761 FCD domain; Region: FCD; pfam07729 342108010762 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 342108010763 Isobutyryl-CoA dehydrogenase; Region: IBD; cd01162 342108010764 substrate binding pocket [chemical binding]; other site 342108010765 FAD binding site [chemical binding]; other site 342108010766 catalytic base [active] 342108010767 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 342108010768 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 342108010769 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 342108010770 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 342108010771 Walker A/P-loop; other site 342108010772 ATP binding site [chemical binding]; other site 342108010773 Q-loop/lid; other site 342108010774 ABC transporter signature motif; other site 342108010775 Walker B; other site 342108010776 D-loop; other site 342108010777 H-loop/switch region; other site 342108010778 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 342108010779 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 342108010780 acyl-activating enzyme (AAE) consensus motif; other site 342108010781 putative AMP binding site [chemical binding]; other site 342108010782 putative active site [active] 342108010783 putative CoA binding site [chemical binding]; other site 342108010784 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 342108010785 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 342108010786 TM-ABC transporter signature motif; other site 342108010787 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 342108010788 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 342108010789 TM-ABC transporter signature motif; other site 342108010790 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 342108010791 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 342108010792 putative ligand binding site [chemical binding]; other site 342108010793 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 342108010794 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 342108010795 Walker A/P-loop; other site 342108010796 ATP binding site [chemical binding]; other site 342108010797 Q-loop/lid; other site 342108010798 ABC transporter signature motif; other site 342108010799 Walker B; other site 342108010800 D-loop; other site 342108010801 H-loop/switch region; other site 342108010802 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 342108010803 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 342108010804 acyl-activating enzyme (AAE) consensus motif; other site 342108010805 active site 342108010806 AMP binding site [chemical binding]; other site 342108010807 CoA binding site [chemical binding]; other site 342108010808 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 342108010809 Magnetospirillum NAD(P)+-dependent aldehyde dehydrogenase MSR-1-like; Region: ALDH_MGR_2402; cd07108 342108010810 NAD(P) binding site [chemical binding]; other site 342108010811 catalytic residues [active] 342108010812 catalytic residues [active] 342108010813 Protein of unknown function DUF86; Region: DUF86; cl01031 342108010814 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 342108010815 active site 342108010816 NTP binding site [chemical binding]; other site 342108010817 metal binding triad [ion binding]; metal-binding site 342108010818 antibiotic binding site [chemical binding]; other site 342108010819 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 342108010820 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 342108010821 dimer interface [polypeptide binding]; other site 342108010822 active site 342108010823 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 342108010824 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 342108010825 FAD binding site [chemical binding]; other site 342108010826 homotetramer interface [polypeptide binding]; other site 342108010827 substrate binding pocket [chemical binding]; other site 342108010828 catalytic base [active] 342108010829 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 342108010830 Ligand Binding Site [chemical binding]; other site 342108010831 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 342108010832 Ligand Binding Site [chemical binding]; other site 342108010833 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 342108010834 CoenzymeA binding site [chemical binding]; other site 342108010835 subunit interaction site [polypeptide binding]; other site 342108010836 PHB binding site; other site 342108010837 PAS domain S-box; Region: sensory_box; TIGR00229 342108010838 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108010839 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108010840 metal binding site [ion binding]; metal-binding site 342108010841 active site 342108010842 I-site; other site 342108010843 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 342108010844 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 342108010845 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 342108010846 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 342108010847 active site 342108010848 metal binding site [ion binding]; metal-binding site 342108010849 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 342108010850 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 342108010851 Hemerythrin; Region: Hemerythrin; cd12107 342108010852 Fe binding site [ion binding]; other site 342108010853 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 342108010854 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 342108010855 active site 342108010856 nucleotide binding site [chemical binding]; other site 342108010857 HIGH motif; other site 342108010858 KMSKS motif; other site 342108010859 Cupin domain; Region: Cupin_2; pfam07883 342108010860 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 342108010861 dihydroorotase; Validated; Region: PRK09059 342108010862 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 342108010863 active site 342108010864 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 342108010865 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 342108010866 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 342108010867 PAS fold; Region: PAS_7; pfam12860 342108010868 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108010869 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 342108010870 putative active site [active] 342108010871 heme pocket [chemical binding]; other site 342108010872 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 342108010873 dimer interface [polypeptide binding]; other site 342108010874 phosphorylation site [posttranslational modification] 342108010875 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 342108010876 ATP binding site [chemical binding]; other site 342108010877 Mg2+ binding site [ion binding]; other site 342108010878 G-X-G motif; other site 342108010879 PAS domain S-box; Region: sensory_box; TIGR00229 342108010880 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 342108010881 putative active site [active] 342108010882 heme pocket [chemical binding]; other site 342108010883 PAS fold; Region: PAS_4; pfam08448 342108010884 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 342108010885 putative active site [active] 342108010886 heme pocket [chemical binding]; other site 342108010887 RNase II stability modulator; Provisional; Region: PRK10060 342108010888 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 342108010889 putative active site [active] 342108010890 heme pocket [chemical binding]; other site 342108010891 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108010892 metal binding site [ion binding]; metal-binding site 342108010893 active site 342108010894 I-site; other site 342108010895 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 342108010896 Cache domain; Region: Cache_1; pfam02743 342108010897 HAMP domain; Region: HAMP; pfam00672 342108010898 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 342108010899 cyclase homology domain; Region: CHD; cd07302 342108010900 nucleotidyl binding site; other site 342108010901 metal binding site [ion binding]; metal-binding site 342108010902 dimer interface [polypeptide binding]; other site 342108010903 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 342108010904 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 342108010905 S-adenosylmethionine binding site [chemical binding]; other site 342108010906 hypothetical protein; Validated; Region: PRK09071 342108010907 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 342108010908 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 342108010909 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 342108010910 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 342108010911 catalytic triad [active] 342108010912 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 342108010913 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108010914 Walker A/P-loop; other site 342108010915 ATP binding site [chemical binding]; other site 342108010916 Q-loop/lid; other site 342108010917 ABC transporter signature motif; other site 342108010918 Walker B; other site 342108010919 D-loop; other site 342108010920 H-loop/switch region; other site 342108010921 ABC-2 type transporter; Region: ABC2_membrane; cl17235 342108010922 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 342108010923 GAF domain; Region: GAF; pfam01590 342108010924 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108010925 Zn2+ binding site [ion binding]; other site 342108010926 Mg2+ binding site [ion binding]; other site 342108010927 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108010928 PAS domain S-box; Region: sensory_box; TIGR00229 342108010929 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 342108010930 putative active site [active] 342108010931 heme pocket [chemical binding]; other site 342108010932 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 342108010933 PAS domain; Region: PAS; smart00091 342108010934 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 342108010935 dimer interface [polypeptide binding]; other site 342108010936 phosphorylation site [posttranslational modification] 342108010937 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 342108010938 ATP binding site [chemical binding]; other site 342108010939 Mg2+ binding site [ion binding]; other site 342108010940 G-X-G motif; other site 342108010941 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 342108010942 catalytic residues [active] 342108010943 dimer interface [polypeptide binding]; other site 342108010944 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 342108010945 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 342108010946 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108010947 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108010948 dimer interface [polypeptide binding]; other site 342108010949 putative CheW interface [polypeptide binding]; other site 342108010950 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 342108010951 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 342108010952 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 342108010953 Mg2+ binding site [ion binding]; other site 342108010954 G-X-G motif; other site 342108010955 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 342108010956 Response regulator receiver domain; Region: Response_reg; pfam00072 342108010957 active site 342108010958 phosphorylation site [posttranslational modification] 342108010959 intermolecular recognition site; other site 342108010960 dimerization interface [polypeptide binding]; other site 342108010961 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 342108010962 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108010963 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 342108010964 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 342108010965 prolyl-tRNA synthetase; Provisional; Region: PRK08661 342108010966 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_arch_euk; cd00778 342108010967 dimer interface [polypeptide binding]; other site 342108010968 motif 1; other site 342108010969 active site 342108010970 motif 2; other site 342108010971 motif 3; other site 342108010972 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for...; Region: HGTP_anticodon; cl00266 342108010973 anticodon binding site; other site 342108010974 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 342108010975 active site 342108010976 catalytic residues [active] 342108010977 DNA binding site [nucleotide binding] 342108010978 Int/Topo IB signature motif; other site 342108010979 Domain of unknown function (DUF955); Region: DUF955; cl01076 342108010980 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 342108010981 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 342108010982 active site 342108010983 DNA binding site [nucleotide binding] 342108010984 Int/Topo IB signature motif; other site 342108010985 fumarate hydratase; Reviewed; Region: fumC; PRK00485 342108010986 Class II fumarases; Region: Fumarase_classII; cd01362 342108010987 active site 342108010988 tetramer interface [polypeptide binding]; other site 342108010989 aconitate hydratase; Validated; Region: PRK09277 342108010990 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 342108010991 substrate binding site [chemical binding]; other site 342108010992 ligand binding site [chemical binding]; other site 342108010993 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 342108010994 substrate binding site [chemical binding]; other site 342108010995 CheB methylesterase; Region: CheB_methylest; pfam01339 342108010996 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 342108010997 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 342108010998 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 342108010999 S-adenosylmethionine binding site [chemical binding]; other site 342108011000 Protein of unknown function (DUF904); Region: DUF904; pfam06005 342108011001 PAS domain; Region: PAS_10; pfam13596 342108011002 PAS domain; Region: PAS_9; pfam13426 342108011003 PAS domain; Region: PAS_9; pfam13426 342108011004 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 342108011005 dimer interface [polypeptide binding]; other site 342108011006 phosphorylation site [posttranslational modification] 342108011007 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 342108011008 ATP binding site [chemical binding]; other site 342108011009 Mg2+ binding site [ion binding]; other site 342108011010 G-X-G motif; other site 342108011011 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 342108011012 B12 binding site [chemical binding]; other site 342108011013 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 342108011014 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 342108011015 FeS/SAM binding site; other site 342108011016 Domain of unknown function (DUF4070); Region: DUF4070; pfam13282 342108011017 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 342108011018 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 342108011019 active site 342108011020 phosphorylation site [posttranslational modification] 342108011021 intermolecular recognition site; other site 342108011022 dimerization interface [polypeptide binding]; other site 342108011023 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 342108011024 DNA binding residues [nucleotide binding] 342108011025 dimerization interface [polypeptide binding]; other site 342108011026 PAS domain S-box; Region: sensory_box; TIGR00229 342108011027 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 342108011028 putative active site [active] 342108011029 heme pocket [chemical binding]; other site 342108011030 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 342108011031 Histidine kinase; Region: HisKA_3; pfam07730 342108011032 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 342108011033 ATP binding site [chemical binding]; other site 342108011034 Mg2+ binding site [ion binding]; other site 342108011035 G-X-G motif; other site 342108011036 Transposase; Region: HTH_Tnp_1; pfam01527 342108011037 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108011038 HTH-like domain; Region: HTH_21; pfam13276 342108011039 Integrase core domain; Region: rve; pfam00665 342108011040 Integrase core domain; Region: rve_3; pfam13683 342108011041 Protein of unknown function (DUF3768); Region: DUF3768; pfam12599 342108011042 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 342108011043 active site 342108011044 catalytic residues [active] 342108011045 Int/Topo IB signature motif; other site 342108011046 DNA binding site [nucleotide binding] 342108011047 DNA polymerase III subunit chi; Validated; Region: PRK05728 342108011048 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 342108011049 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 342108011050 Ligand binding site; other site 342108011051 Putative Catalytic site; other site 342108011052 DXD motif; other site 342108011053 multifunctional aminopeptidase A; Provisional; Region: PRK00913 342108011054 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 342108011055 interface (dimer of trimers) [polypeptide binding]; other site 342108011056 Substrate-binding/catalytic site; other site 342108011057 Zn-binding sites [ion binding]; other site 342108011058 multifunctional aminopeptidase A; Provisional; Region: PRK00913 342108011059 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 342108011060 interface (dimer of trimers) [polypeptide binding]; other site 342108011061 Substrate-binding/catalytic site; other site 342108011062 Zn-binding sites [ion binding]; other site 342108011063 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 342108011064 NACHT domain; Region: NACHT; pfam05729 342108011065 AmmeMemoRadiSam system radical SAM enzyme; Region: AmmeMemoSam_rS; TIGR04337 342108011066 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 342108011067 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 342108011068 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 342108011069 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 342108011070 GTP cyclohydrolase I; Provisional; Region: PLN03044 342108011071 active site 342108011072 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 342108011073 active site 342108011074 catalytic residues [active] 342108011075 DNA binding site [nucleotide binding] 342108011076 Int/Topo IB signature motif; other site 342108011077 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 342108011078 PAS domain S-box; Region: sensory_box; TIGR00229 342108011079 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 342108011080 putative active site [active] 342108011081 heme pocket [chemical binding]; other site 342108011082 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 342108011083 GAF domain; Region: GAF; pfam01590 342108011084 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 342108011085 dimer interface [polypeptide binding]; other site 342108011086 phosphorylation site [posttranslational modification] 342108011087 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 342108011088 ATP binding site [chemical binding]; other site 342108011089 Mg2+ binding site [ion binding]; other site 342108011090 G-X-G motif; other site 342108011091 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 342108011092 dimerization interface [polypeptide binding]; other site 342108011093 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 342108011094 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108011095 dimer interface [polypeptide binding]; other site 342108011096 putative CheW interface [polypeptide binding]; other site 342108011097 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108011098 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 342108011099 ligand binding site [chemical binding]; other site 342108011100 flexible hinge region; other site 342108011101 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 342108011102 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 342108011103 dimerization interface [polypeptide binding]; other site 342108011104 putative DNA binding site [nucleotide binding]; other site 342108011105 putative Zn2+ binding site [ion binding]; other site 342108011106 putative transporter; Provisional; Region: PRK11660 342108011107 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 342108011108 Sulfate transporter family; Region: Sulfate_transp; pfam00916 342108011109 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 342108011110 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 342108011111 active site 342108011112 phosphorylation site [posttranslational modification] 342108011113 intermolecular recognition site; other site 342108011114 Response regulator receiver domain; Region: Response_reg; pfam00072 342108011115 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 342108011116 active site 342108011117 phosphorylation site [posttranslational modification] 342108011118 intermolecular recognition site; other site 342108011119 dimerization interface [polypeptide binding]; other site 342108011120 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 342108011121 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 342108011122 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108011123 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108011124 metal binding site [ion binding]; metal-binding site 342108011125 active site 342108011126 I-site; other site 342108011127 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 342108011128 PAS fold; Region: PAS_3; pfam08447 342108011129 putative active site [active] 342108011130 heme pocket [chemical binding]; other site 342108011131 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108011132 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108011133 dimer interface [polypeptide binding]; other site 342108011134 putative CheW interface [polypeptide binding]; other site 342108011135 Protein of unknown function (DUF3768); Region: DUF3768; pfam12599 342108011136 Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility; Region: MEMO_like; cd07361 342108011137 putative ligand binding pocket/active site [active] 342108011138 putative metal binding site [ion binding]; other site 342108011139 AmmeMemoRadiSam system protein A; Region: AmmeMemoSam_A; TIGR04335 342108011140 AMMECR1; Region: AMMECR1; cl00911 342108011141 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 342108011142 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 342108011143 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 342108011144 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 342108011145 active site 342108011146 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 342108011147 Coenzyme A binding pocket [chemical binding]; other site 342108011148 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; pfam10087 342108011149 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 342108011150 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 342108011151 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 342108011152 FAD binding domain; Region: FAD_binding_4; pfam01565 342108011153 Predicted permeases [General function prediction only]; Region: COG0795 342108011154 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 342108011155 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 342108011156 Organic solvent tolerance protein; Region: OstA_C; pfam04453 342108011157 peptidyl-prolyl cis-trans isomerase, EpsD family; Region: cis_trans_EpsD; TIGR02925 342108011158 SurA N-terminal domain; Region: SurA_N; pfam09312 342108011159 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 342108011160 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 342108011161 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK05312 342108011162 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 342108011163 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 342108011164 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108011165 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108011166 dimer interface [polypeptide binding]; other site 342108011167 putative CheW interface [polypeptide binding]; other site 342108011168 Cytidylate kinase-like family; Region: Cytidylate_kin2; pfam13189 342108011169 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 342108011170 Sporulation related domain; Region: SPOR; cl10051 342108011171 PAS fold; Region: PAS; pfam00989 342108011172 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 342108011173 putative active site [active] 342108011174 heme pocket [chemical binding]; other site 342108011175 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 342108011176 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 342108011177 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108011178 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 342108011179 dimer interface [polypeptide binding]; other site 342108011180 phosphorylation site [posttranslational modification] 342108011181 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 342108011182 ATP binding site [chemical binding]; other site 342108011183 Mg2+ binding site [ion binding]; other site 342108011184 G-X-G motif; other site 342108011185 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 342108011186 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 342108011187 aminotransferase; Validated; Region: PRK09148 342108011188 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 342108011189 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108011190 homodimer interface [polypeptide binding]; other site 342108011191 catalytic residue [active] 342108011192 homoserine dehydrogenase; Provisional; Region: PRK06349 342108011193 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 342108011194 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 342108011195 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 342108011196 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 342108011197 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 342108011198 putative active site [active] 342108011199 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 342108011200 DHH family; Region: DHH; pfam01368 342108011201 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 342108011202 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 342108011203 PhnA protein; Region: PhnA; pfam03831 342108011204 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 342108011205 Beta-lactamase; Region: Beta-lactamase; pfam00144 342108011206 Protein of unknown function (DUF3090); Region: DUF3090; cl12832 342108011207 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 342108011208 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 342108011209 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 342108011210 dimer interface [polypeptide binding]; other site 342108011211 phosphorylation site [posttranslational modification] 342108011212 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 342108011213 ATP binding site [chemical binding]; other site 342108011214 Mg2+ binding site [ion binding]; other site 342108011215 G-X-G motif; other site 342108011216 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108011217 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 342108011218 active site 342108011219 phosphorylation site [posttranslational modification] 342108011220 intermolecular recognition site; other site 342108011221 dimerization interface [polypeptide binding]; other site 342108011222 Response regulator receiver domain; Region: Response_reg; pfam00072 342108011223 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 342108011224 active site 342108011225 phosphorylation site [posttranslational modification] 342108011226 intermolecular recognition site; other site 342108011227 dimerization interface [polypeptide binding]; other site 342108011228 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 342108011229 putative binding surface; other site 342108011230 active site 342108011231 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108011232 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 342108011233 ligand binding site [chemical binding]; other site 342108011234 flexible hinge region; other site 342108011235 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cl17320 342108011236 Flp/Fap pilin component; Region: Flp_Fap; pfam04964 342108011237 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 342108011238 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 342108011239 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 342108011240 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 342108011241 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 342108011242 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 342108011243 Pilus biogenesis CpaD protein (pilus_cpaD); Region: Pilus_CpaD; pfam09476 342108011244 Type IV pili component [Cell motility and secretion]; Region: COG5461 342108011245 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 342108011246 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 342108011247 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 342108011248 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 342108011249 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 342108011250 ATP binding site [chemical binding]; other site 342108011251 Walker A motif; other site 342108011252 hexamer interface [polypeptide binding]; other site 342108011253 Walker B motif; other site 342108011254 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 342108011255 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 342108011256 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 342108011257 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 342108011258 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 342108011259 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 342108011260 binding surface 342108011261 TPR motif; other site 342108011262 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 342108011263 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 342108011264 TadE-like protein; Region: TadE; pfam07811 342108011265 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 342108011266 TadE-like protein; Region: TadE; pfam07811 342108011267 Domain of unknown function (DUF955); Region: DUF955; cl01076 342108011268 Transposase; Region: HTH_Tnp_1; pfam01527 342108011269 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108011270 HTH-like domain; Region: HTH_21; pfam13276 342108011271 Integrase core domain; Region: rve; pfam00665 342108011272 Integrase core domain; Region: rve_3; pfam13683 342108011273 Bacterial TniB protein; Region: TniB; pfam05621 342108011274 AAA domain; Region: AAA_22; pfam13401 342108011275 Helix-turn-helix domain; Region: HTH_28; pfam13518 342108011276 Winged helix-turn helix; Region: HTH_29; pfam13551 342108011277 Integrase core domain; Region: rve; pfam00665 342108011278 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 342108011279 TnsA endonuclease C terminal; Region: Tn7_Tnp_TnsA_C; pfam08721 342108011280 TniQ; Region: TniQ; pfam06527 342108011281 SEC-C motif; Region: SEC-C; pfam02810 342108011282 Helix-turn-helix domain; Region: HTH_28; pfam13518 342108011283 Winged helix-turn helix; Region: HTH_29; pfam13551 342108011284 Integrase core domain; Region: rve; pfam00665 342108011285 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 342108011286 TnsA endonuclease C terminal; Region: Tn7_Tnp_TnsA_C; pfam08721 342108011287 TniQ; Region: TniQ; pfam06527 342108011288 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 342108011289 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 342108011290 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 342108011291 active site 342108011292 catalytic residues [active] 342108011293 DNA binding site [nucleotide binding] 342108011294 Int/Topo IB signature motif; other site 342108011295 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 342108011296 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 342108011297 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 342108011298 Surface antigen; Region: Bac_surface_Ag; pfam01103 342108011299 haemagglutination activity domain; Region: Haemagg_act; smart00912 342108011300 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 342108011301 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 342108011302 FliG C-terminal domain; Region: FliG_C; pfam01706 342108011303 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 342108011304 active site 342108011305 catalytic residues [active] 342108011306 DNA binding site [nucleotide binding] 342108011307 Int/Topo IB signature motif; other site 342108011308 exopolyphosphatase; Region: exo_poly_only; TIGR03706 342108011309 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 342108011310 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 342108011311 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 342108011312 S-adenosylmethionine binding site [chemical binding]; other site 342108011313 Protein required for attachment to host cells; Region: Host_attach; pfam10116 342108011314 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 342108011315 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 342108011316 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 342108011317 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 342108011318 active site 342108011319 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 342108011320 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 342108011321 substrate binding pocket [chemical binding]; other site 342108011322 membrane-bound complex binding site; other site 342108011323 hinge residues; other site 342108011324 ribosomal RNA small subunit methyltransferase RsmB; Region: rsmB; TIGR00563 342108011325 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 342108011326 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108011327 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108011328 NAD(P) binding site [chemical binding]; other site 342108011329 active site 342108011330 CDP-tyvelose 2-epimerase, extended (e) SDRs; Region: CDP_TE_SDR_e; cd05258 342108011331 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108011332 NAD binding site [chemical binding]; other site 342108011333 homotetramer interface [polypeptide binding]; other site 342108011334 homodimer interface [polypeptide binding]; other site 342108011335 active site 342108011336 substrate binding site [chemical binding]; other site 342108011337 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 342108011338 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108011339 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 342108011340 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 342108011341 FeS/SAM binding site; other site 342108011342 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 342108011343 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 342108011344 TPR motif; other site 342108011345 binding surface 342108011346 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 342108011347 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 342108011348 binding surface 342108011349 TPR motif; other site 342108011350 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 342108011351 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 342108011352 dimerization interface [polypeptide binding]; other site 342108011353 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108011354 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108011355 dimer interface [polypeptide binding]; other site 342108011356 putative CheW interface [polypeptide binding]; other site 342108011357 Hemerythrin; Region: Hemerythrin; cd12107 342108011358 Fe binding site [ion binding]; other site 342108011359 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 342108011360 MoaE homodimer interface [polypeptide binding]; other site 342108011361 MoaD interaction [polypeptide binding]; other site 342108011362 active site residues [active] 342108011363 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 342108011364 MoaE interaction surface [polypeptide binding]; other site 342108011365 MoeB interaction surface [polypeptide binding]; other site 342108011366 thiocarboxylated glycine; other site 342108011367 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 342108011368 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 342108011369 dimer interface [polypeptide binding]; other site 342108011370 putative functional site; other site 342108011371 putative MPT binding site; other site 342108011372 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 342108011373 Walker A motif; other site 342108011374 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 342108011375 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 342108011376 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 342108011377 GIY-YIG motif/motif A; other site 342108011378 active site 342108011379 catalytic site [active] 342108011380 putative DNA binding site [nucleotide binding]; other site 342108011381 metal binding site [ion binding]; metal-binding site 342108011382 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 342108011383 short chain dehydrogenase; Provisional; Region: PRK09134 342108011384 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 342108011385 NAD(P) binding site [chemical binding]; other site 342108011386 active site 342108011387 Catalytic domain of Protein Kinases; Region: PKc; cd00180 342108011388 Protein kinase domain; Region: Pkinase; pfam00069 342108011389 active site 342108011390 substrate binding site [chemical binding]; other site 342108011391 ATP binding site [chemical binding]; other site 342108011392 activation loop (A-loop); other site 342108011393 excinuclease ABC subunit B; Provisional; Region: PRK05298 342108011394 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 342108011395 ATP binding site [chemical binding]; other site 342108011396 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 342108011397 nucleotide binding region [chemical binding]; other site 342108011398 ATP-binding site [chemical binding]; other site 342108011399 Ultra-violet resistance protein B; Region: UvrB; pfam12344 342108011400 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108011401 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108011402 dimer interface [polypeptide binding]; other site 342108011403 putative CheW interface [polypeptide binding]; other site 342108011404 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 342108011405 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 342108011406 active site 342108011407 SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat; Region: GT2_SpsF; cd02518 342108011408 ligand binding site; other site 342108011409 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 342108011410 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 342108011411 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 342108011412 inhibitor-cofactor binding pocket; inhibition site 342108011413 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108011414 catalytic residue [active] 342108011415 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 342108011416 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 342108011417 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 342108011418 TPR motif; other site 342108011419 binding surface 342108011420 Flagellar protein FlaF; Region: FlaF; pfam07309 342108011421 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 342108011422 catalytic residue [active] 342108011423 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 342108011424 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 342108011425 acyl-activating enzyme (AAE) consensus motif; other site 342108011426 AMP binding site [chemical binding]; other site 342108011427 active site 342108011428 CoA binding site [chemical binding]; other site 342108011429 TM1410 hypothetical-related protein; Region: DUF297; cl00997 342108011430 hydroxyglutarate oxidase; Provisional; Region: PRK11728 342108011431 Predicted dehydrogenase [General function prediction only]; Region: COG0579 342108011432 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 342108011433 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members...; Region: MopB_3; cd02766 342108011434 putative [4Fe-4S] binding site [ion binding]; other site 342108011435 putative molybdopterin cofactor binding site [chemical binding]; other site 342108011436 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the...; Region: MopB_CT_3; cd02786 342108011437 putative molybdopterin cofactor binding site; other site 342108011438 ATPase MipZ; Region: MipZ; pfam09140 342108011439 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 342108011440 P-loop; other site 342108011441 Magnesium ion binding site [ion binding]; other site 342108011442 Predicted membrane protein [Function unknown]; Region: COG2510 342108011443 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 342108011444 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108011445 putative CheW interface [polypeptide binding]; other site 342108011446 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 342108011447 flagellar assembly regulator FliX; Reviewed; Region: fliX; PRK12787 342108011448 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 342108011449 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 342108011450 Rod binding protein; Region: Rod-binding; cl01626 342108011451 FlgN protein; Region: FlgN; pfam05130 342108011452 flagellar hook-associated protein FlgK; Region: flgK_ends; TIGR02492 342108011453 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 342108011454 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 342108011455 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 342108011456 Flagellar protein FlbT; Region: FlbT; pfam07378 342108011457 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 342108011458 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 342108011459 putative catalytic residue [active] 342108011460 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 342108011461 short chain dehydrogenase; Provisional; Region: PRK12747 342108011462 NADP binding site [chemical binding]; other site 342108011463 homodimer interface [polypeptide binding]; other site 342108011464 active site 342108011465 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_6; cd06154 342108011466 homotrimer interaction site [polypeptide binding]; other site 342108011467 putative active site [active] 342108011468 Ion transport protein; Region: Ion_trans; pfam00520 342108011469 Ion channel; Region: Ion_trans_2; pfam07885 342108011470 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108011471 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 342108011472 ligand binding site [chemical binding]; other site 342108011473 flexible hinge region; other site 342108011474 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 342108011475 putative catalytic site [active] 342108011476 putative metal binding site [ion binding]; other site 342108011477 putative phosphate binding site [ion binding]; other site 342108011478 Hemerythrin; Region: Hemerythrin; cd12107 342108011479 Fe binding site [ion binding]; other site 342108011480 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 342108011481 MraZ protein; Region: MraZ; pfam02381 342108011482 MraW methylase family; Region: Methyltransf_5; cl17771 342108011483 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 342108011484 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 342108011485 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 342108011486 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 342108011487 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 342108011488 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 342108011489 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 342108011490 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 342108011491 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 342108011492 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional; Region: PRK14093 342108011493 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 342108011494 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 342108011495 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 342108011496 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 342108011497 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 342108011498 Mg++ binding site [ion binding]; other site 342108011499 putative catalytic motif [active] 342108011500 putative substrate binding site [chemical binding]; other site 342108011501 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01390 342108011502 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 342108011503 cell division protein FtsW; Region: ftsW; TIGR02614 342108011504 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 342108011505 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 342108011506 active site 342108011507 homodimer interface [polypeptide binding]; other site 342108011508 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 342108011509 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 342108011510 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 342108011511 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 342108011512 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 342108011513 FAD binding domain; Region: FAD_binding_4; pfam01565 342108011514 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 342108011515 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 342108011516 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 342108011517 ATP-grasp domain; Region: ATP-grasp_4; cl17255 342108011518 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 342108011519 Cell division protein FtsQ; Region: FtsQ; pfam03799 342108011520 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 342108011521 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 342108011522 nucleotide binding site [chemical binding]; other site 342108011523 SHS2 domain inserted in FTSA; Region: SHS2_FTSA; pfam02491 342108011524 Cell division protein FtsA; Region: FtsA; pfam14450 342108011525 Cell division GTPase [Cell division and chromosome partitioning]; Region: FtsZ; COG0206 342108011526 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 342108011527 nucleotide binding site [chemical binding]; other site 342108011528 SulA interaction site; other site 342108011529 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 342108011530 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 342108011531 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 342108011532 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 342108011533 binding surface 342108011534 TPR motif; other site 342108011535 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 342108011536 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 342108011537 Walker A/P-loop; other site 342108011538 ATP binding site [chemical binding]; other site 342108011539 Q-loop/lid; other site 342108011540 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 342108011541 ABC transporter signature motif; other site 342108011542 Walker B; other site 342108011543 D-loop; other site 342108011544 H-loop/switch region; other site 342108011545 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 342108011546 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 342108011547 nucleotide binding pocket [chemical binding]; other site 342108011548 K-X-D-G motif; other site 342108011549 catalytic site [active] 342108011550 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 342108011551 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 342108011552 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 342108011553 Dimer interface [polypeptide binding]; other site 342108011554 BRCT sequence motif; other site 342108011555 EAL domain; Region: EAL; pfam00563 342108011556 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 342108011557 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 342108011558 active site 342108011559 phosphorylation site [posttranslational modification] 342108011560 intermolecular recognition site; other site 342108011561 dimerization interface [polypeptide binding]; other site 342108011562 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 342108011563 DNA binding residues [nucleotide binding] 342108011564 dimerization interface [polypeptide binding]; other site 342108011565 GTP-binding protein LepA; Provisional; Region: PRK05433 342108011566 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 342108011567 G1 box; other site 342108011568 putative GEF interaction site [polypeptide binding]; other site 342108011569 GTP/Mg2+ binding site [chemical binding]; other site 342108011570 Switch I region; other site 342108011571 G2 box; other site 342108011572 G3 box; other site 342108011573 Switch II region; other site 342108011574 G4 box; other site 342108011575 G5 box; other site 342108011576 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 342108011577 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 342108011578 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 342108011579 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 342108011580 Protein of unknown function DUF58; Region: DUF58; pfam01882 342108011581 Domain of unknown function (DUF4159); Region: DUF4159; pfam13709 342108011582 Protein of unknown function (DUF1355); Region: DUF1355; cl17712 342108011583 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 342108011584 Peptidase family M23; Region: Peptidase_M23; pfam01551 342108011585 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 342108011586 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 342108011587 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 342108011588 Cl binding site [ion binding]; other site 342108011589 oligomer interface [polypeptide binding]; other site 342108011590 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108011591 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 342108011592 binding surface 342108011593 TPR motif; other site 342108011594 Tetratricopeptide repeat; Region: TPR_16; pfam13432 342108011595 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 342108011596 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 342108011597 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 342108011598 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 342108011599 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 342108011600 trimer interface [polypeptide binding]; other site 342108011601 active site 342108011602 substrate binding site [chemical binding]; other site 342108011603 CoA binding site [chemical binding]; other site 342108011604 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 342108011605 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 342108011606 metal binding site [ion binding]; metal-binding site 342108011607 dimer interface [polypeptide binding]; other site 342108011608 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 342108011609 dimer interface [polypeptide binding]; other site 342108011610 catalytic triad [active] 342108011611 peroxidatic and resolving cysteines [active] 342108011612 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 342108011613 Tropomyosin like; Region: Tropomyosin_1; pfam12718 342108011614 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 342108011615 dimer interface [polypeptide binding]; other site 342108011616 phosphorylation site [posttranslational modification] 342108011617 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 342108011618 ATP binding site [chemical binding]; other site 342108011619 Mg2+ binding site [ion binding]; other site 342108011620 G-X-G motif; other site 342108011621 Response regulator receiver domain; Region: Response_reg; pfam00072 342108011622 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 342108011623 active site 342108011624 phosphorylation site [posttranslational modification] 342108011625 intermolecular recognition site; other site 342108011626 dimerization interface [polypeptide binding]; other site 342108011627 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 342108011628 phosphorylation site [posttranslational modification] 342108011629 intermolecular recognition site; other site 342108011630 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108011631 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 342108011632 active site 342108011633 phosphorylation site [posttranslational modification] 342108011634 intermolecular recognition site; other site 342108011635 dimerization interface [polypeptide binding]; other site 342108011636 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 342108011637 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 342108011638 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 342108011639 CheB methylesterase; Region: CheB_methylest; pfam01339 342108011640 Response regulator receiver domain; Region: Response_reg; pfam00072 342108011641 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 342108011642 active site 342108011643 phosphorylation site [posttranslational modification] 342108011644 intermolecular recognition site; other site 342108011645 dimerization interface [polypeptide binding]; other site 342108011646 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108011647 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 342108011648 putative active site [active] 342108011649 heme pocket [chemical binding]; other site 342108011650 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 342108011651 dimer interface [polypeptide binding]; other site 342108011652 phosphorylation site [posttranslational modification] 342108011653 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 342108011654 ATP binding site [chemical binding]; other site 342108011655 Mg2+ binding site [ion binding]; other site 342108011656 G-X-G motif; other site 342108011657 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 342108011658 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108011659 ligand binding site [chemical binding]; other site 342108011660 flexible hinge region; other site 342108011661 L-aspartate oxidase; Provisional; Region: PRK09077 342108011662 L-aspartate oxidase; Provisional; Region: PRK06175 342108011663 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 342108011664 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 342108011665 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 342108011666 dimerization interface [polypeptide binding]; other site 342108011667 active site 342108011668 quinolinate synthetase; Provisional; Region: PRK09375 342108011669 Response regulator receiver domain; Region: Response_reg; pfam00072 342108011670 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 342108011671 active site 342108011672 phosphorylation site [posttranslational modification] 342108011673 intermolecular recognition site; other site 342108011674 dimerization interface [polypeptide binding]; other site 342108011675 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 342108011676 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 342108011677 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 342108011678 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 342108011679 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 342108011680 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 342108011681 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 342108011682 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 342108011683 active site 342108011684 phosphorylation site [posttranslational modification] 342108011685 intermolecular recognition site; other site 342108011686 dimerization interface [polypeptide binding]; other site 342108011687 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 342108011688 DNA binding residues [nucleotide binding] 342108011689 dimerization interface [polypeptide binding]; other site 342108011690 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 342108011691 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 342108011692 quinone interaction residues [chemical binding]; other site 342108011693 active site 342108011694 catalytic residues [active] 342108011695 FMN binding site [chemical binding]; other site 342108011696 substrate binding site [chemical binding]; other site 342108011697 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 342108011698 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 342108011699 active site 342108011700 motif I; other site 342108011701 motif II; other site 342108011702 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 342108011703 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 342108011704 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 342108011705 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108011706 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 342108011707 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 342108011708 PAS domain; Region: PAS_9; pfam13426 342108011709 putative active site [active] 342108011710 heme pocket [chemical binding]; other site 342108011711 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108011712 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108011713 metal binding site [ion binding]; metal-binding site 342108011714 active site 342108011715 I-site; other site 342108011716 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 342108011717 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 342108011718 motif II; other site 342108011719 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 342108011720 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 342108011721 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 342108011722 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108011723 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108011724 dimer interface [polypeptide binding]; other site 342108011725 putative CheW interface [polypeptide binding]; other site 342108011726 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 342108011727 dimerization interface [polypeptide binding]; other site 342108011728 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108011729 dimer interface [polypeptide binding]; other site 342108011730 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 342108011731 putative CheW interface [polypeptide binding]; other site 342108011732 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 342108011733 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 342108011734 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 342108011735 SEC-C motif; Region: SEC-C; pfam02810 342108011736 Tar ligand binding domain homologue; Region: TarH; pfam02203 342108011737 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 342108011738 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108011739 dimer interface [polypeptide binding]; other site 342108011740 putative CheW interface [polypeptide binding]; other site 342108011741 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK07530 342108011742 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 342108011743 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 342108011744 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 342108011745 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 342108011746 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 342108011747 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 342108011748 Ligand binding site [chemical binding]; other site 342108011749 Electron transfer flavoprotein domain; Region: ETF; pfam01012 342108011750 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 342108011751 Predicted permeases [General function prediction only]; Region: COG0795 342108011752 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 342108011753 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_6; cd03396 342108011754 active site 342108011755 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 342108011756 DNA-binding site [nucleotide binding]; DNA binding site 342108011757 RNA-binding motif; other site 342108011758 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 342108011759 DNA-binding site [nucleotide binding]; DNA binding site 342108011760 RNA-binding motif; other site 342108011761 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 342108011762 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 342108011763 putative NAD(P) binding site [chemical binding]; other site 342108011764 Protein of unknown function (DUF796); Region: DUF796; pfam05638 342108011765 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 342108011766 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 342108011767 HSP70 interaction site [polypeptide binding]; other site 342108011768 Cobaltochelatase CobS subunit N terminal; Region: CobS_N; pfam12556 342108011769 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 342108011770 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 342108011771 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 342108011772 cobaltochelatase, CobT subunit; Region: CobT; TIGR01651 342108011773 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 342108011774 metal ion-dependent adhesion site (MIDAS); other site 342108011775 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 342108011776 Histidine kinase; Region: HisKA_2; pfam07568 342108011777 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 342108011778 Mg2+ binding site [ion binding]; other site 342108011779 G-X-G motif; other site 342108011780 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 342108011781 MPT binding site; other site 342108011782 trimer interface [polypeptide binding]; other site 342108011783 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 342108011784 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 342108011785 PhoH-like protein; Region: PhoH; pfam02562 342108011786 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 342108011787 Domain of unknown function DUF21; Region: DUF21; pfam01595 342108011788 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 342108011789 Transporter associated domain; Region: CorC_HlyC; smart01091 342108011790 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 342108011791 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 342108011792 active site 342108011793 dimer interface [polypeptide binding]; other site 342108011794 metal binding site [ion binding]; metal-binding site 342108011795 shikimate kinase; Provisional; Region: PRK13946 342108011796 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 342108011797 ADP binding site [chemical binding]; other site 342108011798 magnesium binding site [ion binding]; other site 342108011799 putative shikimate binding site; other site 342108011800 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 342108011801 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 342108011802 active site 342108011803 DNA binding site [nucleotide binding] 342108011804 Int/Topo IB signature motif; other site 342108011805 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 342108011806 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 342108011807 putative NAD(P) binding site [chemical binding]; other site 342108011808 active site 342108011809 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 342108011810 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 342108011811 catalytic site [active] 342108011812 putative active site [active] 342108011813 putative substrate binding site [chemical binding]; other site 342108011814 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 342108011815 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 342108011816 putative active site [active] 342108011817 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 342108011818 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 342108011819 OstA-like protein; Region: OstA; cl00844 342108011820 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 342108011821 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 342108011822 Walker A/P-loop; other site 342108011823 ATP binding site [chemical binding]; other site 342108011824 Q-loop/lid; other site 342108011825 ABC transporter signature motif; other site 342108011826 Walker B; other site 342108011827 D-loop; other site 342108011828 H-loop/switch region; other site 342108011829 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 342108011830 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 342108011831 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 342108011832 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 342108011833 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 342108011834 active site 342108011835 phosphorylation site [posttranslational modification] 342108011836 Protein of unknown function (DUF1150); Region: DUF1150; pfam06620 342108011837 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 342108011838 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 342108011839 putative dimer interface [polypeptide binding]; other site 342108011840 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 342108011841 nudix motif; other site 342108011842 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 342108011843 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 342108011844 C-terminal domain interface [polypeptide binding]; other site 342108011845 GSH binding site (G-site) [chemical binding]; other site 342108011846 dimer interface [polypeptide binding]; other site 342108011847 Putative catalytic NodB homology domain of uncharacterized BH0857 protein from Bacillus halodurans and its bacterial homologs; Region: CE4_BH0857_like; cd10955 342108011848 NodB motif; other site 342108011849 putative active site [active] 342108011850 putative catalytic site [active] 342108011851 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 342108011852 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 342108011853 Coenzyme A binding pocket [chemical binding]; other site 342108011854 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 342108011855 pyridoxamine kinase; Validated; Region: PRK05756 342108011856 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 342108011857 dimer interface [polypeptide binding]; other site 342108011858 pyridoxal binding site [chemical binding]; other site 342108011859 ATP binding site [chemical binding]; other site 342108011860 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 342108011861 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 342108011862 Iron-sulfur protein interface; other site 342108011863 proximal quinone binding site [chemical binding]; other site 342108011864 SdhD (CybS) interface [polypeptide binding]; other site 342108011865 proximal heme binding site [chemical binding]; other site 342108011866 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 342108011867 putative SdhC subunit interface [polypeptide binding]; other site 342108011868 putative proximal heme binding site [chemical binding]; other site 342108011869 putative Iron-sulfur protein interface [polypeptide binding]; other site 342108011870 putative proximal quinone binding site; other site 342108011871 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 342108011872 L-aspartate oxidase; Provisional; Region: PRK06175 342108011873 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 342108011874 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 342108011875 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 342108011876 catalytic loop [active] 342108011877 iron binding site [ion binding]; other site 342108011878 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 342108011879 Predicted ATPase [General function prediction only]; Region: COG1485 342108011880 malate dehydrogenase; Reviewed; Region: PRK06223 342108011881 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 342108011882 NAD(P) binding site [chemical binding]; other site 342108011883 dimer interface [polypeptide binding]; other site 342108011884 tetramer (dimer of dimers) interface [polypeptide binding]; other site 342108011885 substrate binding site [chemical binding]; other site 342108011886 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 342108011887 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 342108011888 CoA-ligase; Region: Ligase_CoA; pfam00549 342108011889 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 342108011890 CoA binding domain; Region: CoA_binding; pfam02629 342108011891 CoA-ligase; Region: Ligase_CoA; pfam00549 342108011892 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 342108011893 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 342108011894 TPP-binding site [chemical binding]; other site 342108011895 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 342108011896 dimer interface [polypeptide binding]; other site 342108011897 PYR/PP interface [polypeptide binding]; other site 342108011898 TPP binding site [chemical binding]; other site 342108011899 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 342108011900 E3 interaction surface; other site 342108011901 lipoyl attachment site [posttranslational modification]; other site 342108011902 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 342108011903 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 342108011904 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 342108011905 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 342108011906 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 342108011907 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 342108011908 Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; Region: HTH_YyaN; cd01109 342108011909 DNA binding residues [nucleotide binding] 342108011910 putative dimer interface [polypeptide binding]; other site 342108011911 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 342108011912 Hemerythrin; Region: Hemerythrin; cd12107 342108011913 Fe binding site [ion binding]; other site 342108011914 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 342108011915 putative substrate translocation pore; other site 342108011916 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108011917 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 342108011918 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 342108011919 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 342108011920 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 342108011921 HAMP domain; Region: HAMP; pfam00672 342108011922 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108011923 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108011924 dimer interface [polypeptide binding]; other site 342108011925 putative CheW interface [polypeptide binding]; other site 342108011926 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108011927 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 342108011928 S-adenosylmethionine binding site [chemical binding]; other site 342108011929 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 342108011930 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 342108011931 hypothetical protein; Provisional; Region: PRK06034 342108011932 Chorismate mutase type II; Region: CM_2; pfam01817 342108011933 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 342108011934 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 342108011935 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108011936 homodimer interface [polypeptide binding]; other site 342108011937 catalytic residue [active] 342108011938 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 342108011939 prephenate dehydrogenase; Validated; Region: PRK08507 342108011940 Glyoxalase-like domain; Region: Glyoxalase_3; pfam13468 342108011941 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 342108011942 GAF domain; Region: GAF; cl17456 342108011943 GAF domain; Region: GAF_2; pfam13185 342108011944 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 342108011945 putative active site pocket [active] 342108011946 dimerization interface [polypeptide binding]; other site 342108011947 putative catalytic residue [active] 342108011948 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 342108011949 AAA domain; Region: AAA_23; pfam13476 342108011950 Walker A/P-loop; other site 342108011951 ATP binding site [chemical binding]; other site 342108011952 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 342108011953 ABC transporter signature motif; other site 342108011954 Walker B; other site 342108011955 D-loop; other site 342108011956 H-loop/switch region; other site 342108011957 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 342108011958 Thioredoxin; Region: Thioredoxin_4; pfam13462 342108011959 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 342108011960 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 342108011961 minor groove reading motif; other site 342108011962 helix-hairpin-helix signature motif; other site 342108011963 substrate binding pocket [chemical binding]; other site 342108011964 active site 342108011965 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 342108011966 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 342108011967 DNA binding and oxoG recognition site [nucleotide binding] 342108011968 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 342108011969 catalytic residues [active] 342108011970 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 342108011971 DNA methylase; Region: N6_N4_Mtase; pfam01555 342108011972 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 342108011973 RNA/DNA hybrid binding site [nucleotide binding]; other site 342108011974 active site 342108011975 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 342108011976 transporter, monovalent cation:proton antiporter-2 (CPA2) family; Region: 2a37; TIGR00932 342108011977 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 342108011978 dimerization interface [polypeptide binding]; other site 342108011979 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108011980 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108011981 dimer interface [polypeptide binding]; other site 342108011982 putative CheW interface [polypeptide binding]; other site 342108011983 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 342108011984 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 342108011985 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 342108011986 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 342108011987 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 342108011988 F0F1 ATP synthase subunit B; Provisional; Region: PRK14475 342108011989 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 342108011990 Pirin-related protein [General function prediction only]; Region: COG1741 342108011991 Pirin; Region: Pirin; pfam02678 342108011992 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 342108011993 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 342108011994 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108011995 Major Facilitator Superfamily; Region: MFS_1; pfam07690 342108011996 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 342108011997 putative substrate translocation pore; other site 342108011998 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 342108011999 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 342108012000 PAS domain; Region: PAS_9; pfam13426 342108012001 putative active site [active] 342108012002 heme pocket [chemical binding]; other site 342108012003 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108012004 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108012005 metal binding site [ion binding]; metal-binding site 342108012006 active site 342108012007 I-site; other site 342108012008 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 342108012009 active site 342108012010 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 342108012011 active site 342108012012 dimer interface [polypeptide binding]; other site 342108012013 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 342108012014 IHF dimer interface [polypeptide binding]; other site 342108012015 IHF - DNA interface [nucleotide binding]; other site 342108012016 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 342108012017 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 342108012018 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 342108012019 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; pfam09360 342108012020 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; pfam09360 342108012021 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108012022 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108012023 dimer interface [polypeptide binding]; other site 342108012024 putative CheW interface [polypeptide binding]; other site 342108012025 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 342108012026 PAS fold; Region: PAS_3; pfam08447 342108012027 putative active site [active] 342108012028 heme pocket [chemical binding]; other site 342108012029 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 342108012030 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 342108012031 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108012032 catalytic residue [active] 342108012033 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 342108012034 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 342108012035 substrate binding site [chemical binding]; other site 342108012036 active site 342108012037 catalytic residues [active] 342108012038 heterodimer interface [polypeptide binding]; other site 342108012039 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 342108012040 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 342108012041 PAS fold; Region: PAS_4; pfam08448 342108012042 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 342108012043 putative active site [active] 342108012044 heme pocket [chemical binding]; other site 342108012045 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 342108012046 ATP binding site [chemical binding]; other site 342108012047 Mg2+ binding site [ion binding]; other site 342108012048 G-X-G motif; other site 342108012049 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 342108012050 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 342108012051 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 342108012052 dimer interface [polypeptide binding]; other site 342108012053 phosphorylation site [posttranslational modification] 342108012054 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 342108012055 ATP binding site [chemical binding]; other site 342108012056 Mg2+ binding site [ion binding]; other site 342108012057 G-X-G motif; other site 342108012058 Response regulator receiver domain; Region: Response_reg; pfam00072 342108012059 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 342108012060 active site 342108012061 phosphorylation site [posttranslational modification] 342108012062 intermolecular recognition site; other site 342108012063 dimerization interface [polypeptide binding]; other site 342108012064 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 342108012065 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 342108012066 Predicted transcriptional regulator [Transcription]; Region: COG1959 342108012067 Transcriptional regulator; Region: Rrf2; pfam02082 342108012068 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 342108012069 binding surface 342108012070 TPR motif; other site 342108012071 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 342108012072 binding surface 342108012073 TPR motif; other site 342108012074 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 342108012075 binding surface 342108012076 TPR motif; other site 342108012077 Tetratricopeptide repeat; Region: TPR_12; pfam13424 342108012078 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 342108012079 binding surface 342108012080 TPR motif; other site 342108012081 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 342108012082 Methyltransferase domain; Region: Methyltransf_18; pfam12847 342108012083 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 342108012084 dimer interface [polypeptide binding]; other site 342108012085 active site 342108012086 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 342108012087 Ligand Binding Site [chemical binding]; other site 342108012088 Molecular Tunnel; other site 342108012089 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 342108012090 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 342108012091 Ligand Binding Site [chemical binding]; other site 342108012092 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 342108012093 tetramerization interface [polypeptide binding]; other site 342108012094 active site 342108012095 glutamate--cysteine ligase; Region: PLN02611 342108012096 DDE superfamily endonuclease; Region: DDE_3; pfam13358 342108012097 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 342108012098 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 342108012099 Homeodomain-like domain; Region: HTH_32; pfam13565 342108012100 Plasmid encoded RepA protein; Region: RepA_C; pfam04796 342108012101 Nuclease-related domain; Region: NERD; pfam08378 342108012102 hypothetical protein; Provisional; Region: PRK11770 342108012103 Domain of unknown function (DUF307); Region: DUF307; pfam03733 342108012104 Domain of unknown function (DUF307); Region: DUF307; pfam03733 342108012105 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]; Region: COG1525 342108012106 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 342108012107 Predicted ATPase [General function prediction only]; Region: COG3910 342108012108 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 342108012109 Walker A/P-loop; other site 342108012110 ATP binding site [chemical binding]; other site 342108012111 Q-loop/lid; other site 342108012112 ABC transporter signature motif; other site 342108012113 Walker B; other site 342108012114 D-loop; other site 342108012115 H-loop/switch region; other site 342108012116 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 342108012117 Transposase; Region: HTH_Tnp_1; pfam01527 342108012118 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108012119 HTH-like domain; Region: HTH_21; pfam13276 342108012120 Integrase core domain; Region: rve; pfam00665 342108012121 Integrase core domain; Region: rve_3; pfam13683 342108012122 Helix-turn-helix domain; Region: HTH_17; pfam12728 342108012123 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 342108012124 integron integrase; Region: integrase_gron; TIGR02249 342108012125 active site 342108012126 Int/Topo IB signature motif; other site 342108012127 DNA binding site [nucleotide binding] 342108012128 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 342108012129 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 342108012130 catalytic residues [active] 342108012131 catalytic nucleophile [active] 342108012132 Recombinase; Region: Recombinase; pfam07508 342108012133 EMG1/NEP1 methyltransferase; Region: EMG1; cl00764 342108012134 Helix-turn-helix domain; Region: HTH_17; pfam12728 342108012135 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 342108012136 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 342108012137 HlyD family secretion protein; Region: HlyD_3; pfam13437 342108012138 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 342108012139 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108012140 Walker A/P-loop; other site 342108012141 ATP binding site [chemical binding]; other site 342108012142 Q-loop/lid; other site 342108012143 ABC transporter signature motif; other site 342108012144 Walker B; other site 342108012145 D-loop; other site 342108012146 H-loop/switch region; other site 342108012147 Outer membrane efflux protein; Region: OEP; pfam02321 342108012148 Outer membrane efflux protein; Region: OEP; pfam02321 342108012149 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 342108012150 cyclase homology domain; Region: CHD; cd07302 342108012151 nucleotidyl binding site; other site 342108012152 metal binding site [ion binding]; metal-binding site 342108012153 dimer interface [polypeptide binding]; other site 342108012154 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 342108012155 DEAD-like helicases superfamily; Region: DEXDc; smart00487 342108012156 ATP binding site [chemical binding]; other site 342108012157 Mg++ binding site [ion binding]; other site 342108012158 motif III; other site 342108012159 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 342108012160 nucleotide binding region [chemical binding]; other site 342108012161 ATP-binding site [chemical binding]; other site 342108012162 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 342108012163 RNA binding site [nucleotide binding]; other site 342108012164 signal recognition particle protein; Provisional; Region: PRK10867 342108012165 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 342108012166 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 342108012167 Signal peptide binding domain; Region: SRP_SPB; pfam02978 342108012168 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 342108012169 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK13828 342108012170 RimM N-terminal domain; Region: RimM; pfam01782 342108012171 PRC-barrel domain; Region: PRC; pfam05239 342108012172 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 342108012173 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 342108012174 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 342108012175 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 342108012176 substrate binding site [chemical binding]; other site 342108012177 ligand binding site [chemical binding]; other site 342108012178 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 342108012179 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 342108012180 substrate binding site [chemical binding]; other site 342108012181 tartrate dehydrogenase; Region: TTC; TIGR02089 342108012182 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 342108012183 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 342108012184 translation initiation factor IF-2; Region: IF-2; TIGR00487 342108012185 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 342108012186 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 342108012187 G1 box; other site 342108012188 putative GEF interaction site [polypeptide binding]; other site 342108012189 GTP/Mg2+ binding site [chemical binding]; other site 342108012190 Switch I region; other site 342108012191 G2 box; other site 342108012192 G3 box; other site 342108012193 Switch II region; other site 342108012194 G4 box; other site 342108012195 G5 box; other site 342108012196 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 342108012197 Translation-initiation factor 2; Region: IF-2; pfam11987 342108012198 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 342108012199 hypothetical protein; Provisional; Region: PRK09190 342108012200 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 342108012201 putative RNA binding cleft [nucleotide binding]; other site 342108012202 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 342108012203 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 342108012204 NusA N-terminal domain; Region: NusA_N; pfam08529 342108012205 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 342108012206 RNA binding site [nucleotide binding]; other site 342108012207 homodimer interface [polypeptide binding]; other site 342108012208 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 342108012209 G-X-X-G motif; other site 342108012210 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 342108012211 G-X-X-G motif; other site 342108012212 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 342108012213 Sm and related proteins; Region: Sm_like; cl00259 342108012214 ribosome maturation protein RimP; Reviewed; Region: PRK00092 342108012215 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 342108012216 putative oligomer interface [polypeptide binding]; other site 342108012217 putative RNA binding site [nucleotide binding]; other site 342108012218 6-phosphofructokinase; Provisional; Region: PRK14072 342108012219 allosteric effector site; other site 342108012220 dimerization interface [polypeptide binding]; other site 342108012221 active site 342108012222 ADP/pyrophosphate binding site [chemical binding]; other site 342108012223 fructose-1,6-bisphosphate binding site; other site 342108012224 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 342108012225 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 342108012226 dimerization interface [polypeptide binding]; other site 342108012227 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108012228 dimer interface [polypeptide binding]; other site 342108012229 putative CheW interface [polypeptide binding]; other site 342108012230 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 342108012231 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 342108012232 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 342108012233 GTPase CgtA; Reviewed; Region: obgE; PRK12299 342108012234 GTP1/OBG; Region: GTP1_OBG; pfam01018 342108012235 Obg GTPase; Region: Obg; cd01898 342108012236 G1 box; other site 342108012237 GTP/Mg2+ binding site [chemical binding]; other site 342108012238 Switch I region; other site 342108012239 G2 box; other site 342108012240 G3 box; other site 342108012241 Switch II region; other site 342108012242 G4 box; other site 342108012243 G5 box; other site 342108012244 gamma-glutamyl kinase; Provisional; Region: PRK05429 342108012245 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 342108012246 nucleotide binding site [chemical binding]; other site 342108012247 homotetrameric interface [polypeptide binding]; other site 342108012248 putative phosphate binding site [ion binding]; other site 342108012249 putative allosteric binding site; other site 342108012250 PUA domain; Region: PUA; pfam01472 342108012251 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 342108012252 active site 342108012253 metal binding site [ion binding]; metal-binding site 342108012254 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 342108012255 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 342108012256 putative catalytic cysteine [active] 342108012257 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 342108012258 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 342108012259 active site 342108012260 (T/H)XGH motif; other site 342108012261 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 342108012262 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 342108012263 S-adenosylmethionine binding site [chemical binding]; other site 342108012264 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 342108012265 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 342108012266 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 342108012267 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 342108012268 [2Fe-2S] cluster binding site [ion binding]; other site 342108012269 cytochrome b; Provisional; Region: CYTB; MTH00119 342108012270 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 342108012271 Qi binding site; other site 342108012272 intrachain domain interface; other site 342108012273 interchain domain interface [polypeptide binding]; other site 342108012274 heme bH binding site [chemical binding]; other site 342108012275 heme bL binding site [chemical binding]; other site 342108012276 Qo binding site; other site 342108012277 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 342108012278 interchain domain interface [polypeptide binding]; other site 342108012279 intrachain domain interface; other site 342108012280 Qi binding site; other site 342108012281 Qo binding site; other site 342108012282 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 342108012283 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 342108012284 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 342108012285 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 342108012286 Walker A/P-loop; other site 342108012287 ATP binding site [chemical binding]; other site 342108012288 Q-loop/lid; other site 342108012289 ABC transporter signature motif; other site 342108012290 Walker B; other site 342108012291 D-loop; other site 342108012292 H-loop/switch region; other site 342108012293 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 342108012294 putative acyl-acceptor binding pocket; other site 342108012295 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 342108012296 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 342108012297 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 342108012298 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 342108012299 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 342108012300 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 342108012301 putative acyl-acceptor binding pocket; other site 342108012302 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 342108012303 S-adenosylmethionine binding site [chemical binding]; other site 342108012304 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 342108012305 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 342108012306 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 342108012307 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108012308 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 342108012309 active site 342108012310 phosphorylation site [posttranslational modification] 342108012311 intermolecular recognition site; other site 342108012312 dimerization interface [polypeptide binding]; other site 342108012313 PAS fold; Region: PAS_4; pfam08448 342108012314 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 342108012315 putative active site [active] 342108012316 heme pocket [chemical binding]; other site 342108012317 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 342108012318 dimer interface [polypeptide binding]; other site 342108012319 phosphorylation site [posttranslational modification] 342108012320 PAS fold; Region: PAS_4; pfam08448 342108012321 PAS domain S-box; Region: sensory_box; TIGR00229 342108012322 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 342108012323 putative active site [active] 342108012324 heme pocket [chemical binding]; other site 342108012325 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108012326 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108012327 metal binding site [ion binding]; metal-binding site 342108012328 active site 342108012329 I-site; other site 342108012330 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 342108012331 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 342108012332 Response regulator receiver domain; Region: Response_reg; pfam00072 342108012333 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 342108012334 active site 342108012335 phosphorylation site [posttranslational modification] 342108012336 intermolecular recognition site; other site 342108012337 dimerization interface [polypeptide binding]; other site 342108012338 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 342108012339 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 342108012340 DNA polymerase III subunits gamma and tau; Validated; Region: PRK09111 342108012341 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 342108012342 Walker A motif; other site 342108012343 ATP binding site [chemical binding]; other site 342108012344 Walker B motif; other site 342108012345 arginine finger; other site 342108012346 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 342108012347 DNA polymerase III gamma and tau subunits C terminal; Region: DUF3646; pfam12362 342108012348 hypothetical protein; Validated; Region: PRK00153 342108012349 recombination protein RecR; Reviewed; Region: recR; PRK00076 342108012350 RecR protein; Region: RecR; pfam02132 342108012351 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 342108012352 putative active site [active] 342108012353 putative metal-binding site [ion binding]; other site 342108012354 tetramer interface [polypeptide binding]; other site 342108012355 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 342108012356 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 342108012357 putative C-terminal domain interface [polypeptide binding]; other site 342108012358 putative GSH binding site (G-site) [chemical binding]; other site 342108012359 putative dimer interface [polypeptide binding]; other site 342108012360 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 342108012361 putative N-terminal domain interface [polypeptide binding]; other site 342108012362 putative dimer interface [polypeptide binding]; other site 342108012363 putative substrate binding pocket (H-site) [chemical binding]; other site 342108012364 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 342108012365 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 342108012366 interface (dimer of trimers) [polypeptide binding]; other site 342108012367 Substrate-binding/catalytic site; other site 342108012368 Zn-binding sites [ion binding]; other site 342108012369 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 342108012370 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 342108012371 Cation transport protein; Region: TrkH; cl17365 342108012372 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 342108012373 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 342108012374 membrane ATPase/protein kinase; Provisional; Region: PRK09435 342108012375 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 342108012376 Walker A; other site 342108012377 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 342108012378 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 342108012379 active site 342108012380 Zn binding site [ion binding]; other site 342108012381 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional; Region: PRK11780 342108012382 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 342108012383 conserved cys residue [active] 342108012384 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05389 342108012385 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 342108012386 RNA binding site [nucleotide binding]; other site 342108012387 active site 342108012388 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 342108012389 16S/18S rRNA binding site [nucleotide binding]; other site 342108012390 S13e-L30e interaction site [polypeptide binding]; other site 342108012391 25S rRNA binding site [nucleotide binding]; other site 342108012392 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 342108012393 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 342108012394 RNase E interface [polypeptide binding]; other site 342108012395 trimer interface [polypeptide binding]; other site 342108012396 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 342108012397 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 342108012398 RNase E interface [polypeptide binding]; other site 342108012399 trimer interface [polypeptide binding]; other site 342108012400 active site 342108012401 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 342108012402 putative nucleic acid binding region [nucleotide binding]; other site 342108012403 G-X-X-G motif; other site 342108012404 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 342108012405 RNA binding site [nucleotide binding]; other site 342108012406 domain interface; other site 342108012407 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 342108012408 putative active site [active] 342108012409 putative metal binding site [ion binding]; other site 342108012410 methionine sulfoxide reductase B; Provisional; Region: PRK00222 342108012411 SelR domain; Region: SelR; pfam01641 342108012412 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 342108012413 5'-methylthioadenosine phosphorylase; Provisional; Region: PRK08931 342108012414 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 342108012415 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 342108012416 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 342108012417 S-methyl-5-thioribose-1-phosphate isomerase; Region: salvage_mtnA; TIGR00512 342108012418 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 342108012419 RmuC family; Region: RmuC; pfam02646 342108012420 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 342108012421 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 342108012422 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 342108012423 RNA binding surface [nucleotide binding]; other site 342108012424 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 342108012425 probable active site [active] 342108012426 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 342108012427 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 342108012428 catalytic triad [active] 342108012429 L-lactate permease; Region: Lactate_perm; cl00701 342108012430 glycolate transporter; Provisional; Region: PRK09695 342108012431 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 342108012432 Cysteine-rich domain; Region: CCG; pfam02754 342108012433 Cysteine-rich domain; Region: CCG; pfam02754 342108012434 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 342108012435 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 342108012436 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 342108012437 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 342108012438 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 342108012439 FAD binding domain; Region: FAD_binding_4; pfam01565 342108012440 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 342108012441 enoyl-CoA hydratase; Provisional; Region: PRK06688 342108012442 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 342108012443 substrate binding site [chemical binding]; other site 342108012444 oxyanion hole (OAH) forming residues; other site 342108012445 trimer interface [polypeptide binding]; other site 342108012446 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 342108012447 Hemerythrin; Region: Hemerythrin; cd12107 342108012448 Fe binding site [ion binding]; other site 342108012449 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 342108012450 dinuclear metal binding motif [ion binding]; other site 342108012451 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 342108012452 gamma subunit interface [polypeptide binding]; other site 342108012453 epsilon subunit interface [polypeptide binding]; other site 342108012454 LBP interface [polypeptide binding]; other site 342108012455 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 342108012456 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 342108012457 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 342108012458 alpha subunit interaction interface [polypeptide binding]; other site 342108012459 Walker A motif; other site 342108012460 ATP binding site [chemical binding]; other site 342108012461 Walker B motif; other site 342108012462 inhibitor binding site; inhibition site 342108012463 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 342108012464 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 342108012465 core domain interface [polypeptide binding]; other site 342108012466 delta subunit interface [polypeptide binding]; other site 342108012467 epsilon subunit interface [polypeptide binding]; other site 342108012468 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 342108012469 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 342108012470 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 342108012471 beta subunit interaction interface [polypeptide binding]; other site 342108012472 Walker A motif; other site 342108012473 ATP binding site [chemical binding]; other site 342108012474 Walker B motif; other site 342108012475 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 342108012476 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 342108012477 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 342108012478 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 342108012479 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 342108012480 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 342108012481 active site 342108012482 phosphorylation site [posttranslational modification] 342108012483 intermolecular recognition site; other site 342108012484 dimerization interface [polypeptide binding]; other site 342108012485 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108012486 Zn2+ binding site [ion binding]; other site 342108012487 Mg2+ binding site [ion binding]; other site 342108012488 Response regulator receiver domain; Region: Response_reg; pfam00072 342108012489 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 342108012490 active site 342108012491 phosphorylation site [posttranslational modification] 342108012492 intermolecular recognition site; other site 342108012493 dimerization interface [polypeptide binding]; other site 342108012494 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 342108012495 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 342108012496 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 342108012497 putative active site [active] 342108012498 heme pocket [chemical binding]; other site 342108012499 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 342108012500 dimer interface [polypeptide binding]; other site 342108012501 phosphorylation site [posttranslational modification] 342108012502 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 342108012503 ATP binding site [chemical binding]; other site 342108012504 Mg2+ binding site [ion binding]; other site 342108012505 G-X-G motif; other site 342108012506 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 342108012507 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 342108012508 active site 342108012509 phosphorylation site [posttranslational modification] 342108012510 intermolecular recognition site; other site 342108012511 dimerization interface [polypeptide binding]; other site 342108012512 Response regulator receiver domain; Region: Response_reg; pfam00072 342108012513 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 342108012514 active site 342108012515 phosphorylation site [posttranslational modification] 342108012516 intermolecular recognition site; other site 342108012517 dimerization interface [polypeptide binding]; other site 342108012518 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 342108012519 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 342108012520 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 342108012521 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 342108012522 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 342108012523 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 342108012524 dimerization interface [polypeptide binding]; other site 342108012525 tellurite resistance protein terB; Region: terB; cd07176 342108012526 putative metal binding site [ion binding]; other site 342108012527 Response regulator receiver domain; Region: Response_reg; pfam00072 342108012528 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 342108012529 active site 342108012530 phosphorylation site [posttranslational modification] 342108012531 intermolecular recognition site; other site 342108012532 dimerization interface [polypeptide binding]; other site 342108012533 Chemotaxis phosphatase CheX; Region: CheX; cl15816 342108012534 Chemotaxis phosphatase CheX; Region: CheX; pfam13690 342108012535 PAS domain S-box; Region: sensory_box; TIGR00229 342108012536 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 342108012537 putative active site [active] 342108012538 heme pocket [chemical binding]; other site 342108012539 PAS domain S-box; Region: sensory_box; TIGR00229 342108012540 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 342108012541 putative active site [active] 342108012542 heme pocket [chemical binding]; other site 342108012543 PAS fold; Region: PAS_4; pfam08448 342108012544 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108012545 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108012546 metal binding site [ion binding]; metal-binding site 342108012547 active site 342108012548 I-site; other site 342108012549 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 342108012550 Protein of unknown function (DUF3422); Region: DUF3422; pfam11902 342108012551 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 342108012552 HAMP domain; Region: HAMP; pfam00672 342108012553 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108012554 dimer interface [polypeptide binding]; other site 342108012555 putative CheW interface [polypeptide binding]; other site 342108012556 Hemerythrin; Region: Hemerythrin; cd12107 342108012557 Fe binding site [ion binding]; other site 342108012558 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 342108012559 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 342108012560 active site 342108012561 NTP binding site [chemical binding]; other site 342108012562 metal binding triad [ion binding]; metal-binding site 342108012563 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 342108012564 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 342108012565 putative active site [active] 342108012566 putative CoA binding site [chemical binding]; other site 342108012567 nudix motif; other site 342108012568 metal binding site [ion binding]; metal-binding site 342108012569 Protein of unknown function (DUF1285); Region: DUF1285; pfam06938 342108012570 MoxR-like ATPases [General function prediction only]; Region: COG0714 342108012571 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 342108012572 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 342108012573 Part of AAA domain; Region: AAA_19; pfam13245 342108012574 Family description; Region: UvrD_C_2; pfam13538 342108012575 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 342108012576 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 342108012577 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 342108012578 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 342108012579 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 342108012580 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 342108012581 dimerization interface [polypeptide binding]; other site 342108012582 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108012583 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108012584 dimer interface [polypeptide binding]; other site 342108012585 putative CheW interface [polypeptide binding]; other site 342108012586 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 342108012587 Cytochrome c; Region: Cytochrom_C; pfam00034 342108012588 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 342108012589 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 342108012590 prephenate dehydratase; Provisional; Region: PRK11899 342108012591 Prephenate dehydratase; Region: PDT; pfam00800 342108012592 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 342108012593 putative L-Phe binding site [chemical binding]; other site 342108012594 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 342108012595 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 342108012596 Ligand binding site; other site 342108012597 oligomer interface; other site 342108012598 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 342108012599 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 342108012600 active site 342108012601 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 342108012602 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 342108012603 minor groove reading motif; other site 342108012604 helix-hairpin-helix signature motif; other site 342108012605 substrate binding pocket [chemical binding]; other site 342108012606 active site 342108012607 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 342108012608 Hemerythrin; Region: Hemerythrin; cd12107 342108012609 Fe binding site [ion binding]; other site 342108012610 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 342108012611 Domain of unknown function (DUF4337); Region: DUF4337; pfam14235 342108012612 YciI-like protein; Reviewed; Region: PRK12863 342108012613 EVE domain; Region: EVE; pfam01878 342108012614 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 342108012615 iron-sulfur cluster [ion binding]; other site 342108012616 [2Fe-2S] cluster binding site [ion binding]; other site 342108012617 acetyl-CoA synthetase; Provisional; Region: PRK00174 342108012618 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 342108012619 active site 342108012620 CoA binding site [chemical binding]; other site 342108012621 acyl-activating enzyme (AAE) consensus motif; other site 342108012622 AMP binding site [chemical binding]; other site 342108012623 acetate binding site [chemical binding]; other site 342108012624 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 342108012625 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 342108012626 heme exporter protein CcmB; Region: ccmB; TIGR01190 342108012627 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13539 342108012628 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108012629 Walker A/P-loop; other site 342108012630 ATP binding site [chemical binding]; other site 342108012631 Q-loop/lid; other site 342108012632 ABC transporter signature motif; other site 342108012633 Walker B; other site 342108012634 D-loop; other site 342108012635 H-loop/switch region; other site 342108012636 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 342108012637 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 342108012638 ligand binding site [chemical binding]; other site 342108012639 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 342108012640 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 342108012641 Elongation factor Tu GTP binding domain; Region: GTP_EFTU; pfam00009 342108012642 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 342108012643 G1 box; other site 342108012644 putative GEF interaction site [polypeptide binding]; other site 342108012645 GTP/Mg2+ binding site [chemical binding]; other site 342108012646 Switch I region; other site 342108012647 G2 box; other site 342108012648 G3 box; other site 342108012649 Switch II region; other site 342108012650 G4 box; other site 342108012651 G5 box; other site 342108012652 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 342108012653 Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor.The physiological function of AK is associated with the regulation of extracellular...; Region: adenosine_kinase; cd01168 342108012654 substrate binding site [chemical binding]; other site 342108012655 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 342108012656 ATP binding site [chemical binding]; other site 342108012657 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 342108012658 Transcriptional regulators [Transcription]; Region: GntR; COG1802 342108012659 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 342108012660 DNA-binding site [nucleotide binding]; DNA binding site 342108012661 FCD domain; Region: FCD; pfam07729 342108012662 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 342108012663 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 342108012664 transmembrane helices; other site 342108012665 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 342108012666 4Fe-4S binding domain; Region: Fer4_5; pfam12801 342108012667 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 342108012668 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 342108012669 Response regulator receiver domain; Region: Response_reg; pfam00072 342108012670 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 342108012671 active site 342108012672 phosphorylation site [posttranslational modification] 342108012673 intermolecular recognition site; other site 342108012674 dimerization interface [polypeptide binding]; other site 342108012675 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 342108012676 Methyltransferase domain; Region: Methyltransf_23; pfam13489 342108012677 S-adenosylmethionine binding site [chemical binding]; other site 342108012678 Methyltransferase domain; Region: Methyltransf_11; pfam08241 342108012679 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 342108012680 putative amphipathic alpha helix; other site 342108012681 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 342108012682 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 342108012683 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 342108012684 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 342108012685 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 342108012686 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 342108012687 heme exporter protein CcmC; Region: ccmC; TIGR01191 342108012688 Heme exporter protein D (CcmD); Region: CcmD; cl11475 342108012689 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 342108012690 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 342108012691 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 342108012692 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 342108012693 catalytic residues [active] 342108012694 central insert; other site 342108012695 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 342108012696 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 342108012697 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 342108012698 binding surface 342108012699 TPR motif; other site 342108012700 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 342108012701 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 342108012702 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 342108012703 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 342108012704 Putative Catalytic site; other site 342108012705 DXD motif; other site 342108012706 Uncharacterized conserved protein [Function unknown]; Region: COG0398 342108012707 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 342108012708 BON domain; Region: BON; pfam04972 342108012709 BON domain; Region: BON; pfam04972 342108012710 Uncharacterized conserved protein [Function unknown]; Region: COG5316 342108012711 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 342108012712 DNA polymerase I; Provisional; Region: PRK05755 342108012713 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 342108012714 active site 342108012715 metal binding site 1 [ion binding]; metal-binding site 342108012716 putative 5' ssDNA interaction site; other site 342108012717 metal binding site 3; metal-binding site 342108012718 metal binding site 2 [ion binding]; metal-binding site 342108012719 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 342108012720 putative DNA binding site [nucleotide binding]; other site 342108012721 putative metal binding site [ion binding]; other site 342108012722 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 342108012723 active site 342108012724 catalytic site [active] 342108012725 substrate binding site [chemical binding]; other site 342108012726 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 342108012727 active site 342108012728 DNA binding site [nucleotide binding] 342108012729 catalytic site [active] 342108012730 Zinc-finger domain; Region: zf-CHCC; cl01821 342108012731 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 342108012732 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 342108012733 Walker A/P-loop; other site 342108012734 ATP binding site [chemical binding]; other site 342108012735 Q-loop/lid; other site 342108012736 ABC transporter signature motif; other site 342108012737 Walker B; other site 342108012738 D-loop; other site 342108012739 H-loop/switch region; other site 342108012740 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 342108012741 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 342108012742 Protein of unknown function (DUF1800); Region: DUF1800; pfam08811 342108012743 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4102 342108012744 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 342108012745 homodecamer interface [polypeptide binding]; other site 342108012746 GTP cyclohydrolase I; Provisional; Region: PLN03044 342108012747 active site 342108012748 putative catalytic site residues [active] 342108012749 zinc binding site [ion binding]; other site 342108012750 GTP-CH-I/GFRP interaction surface; other site 342108012751 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 342108012752 O-succinylhomoserine sulfhydrylase; Provisional; Region: PRK07810 342108012753 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 342108012754 homodimer interface [polypeptide binding]; other site 342108012755 substrate-cofactor binding pocket; other site 342108012756 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108012757 catalytic residue [active] 342108012758 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 342108012759 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK07533 342108012760 NAD binding site [chemical binding]; other site 342108012761 homotetramer interface [polypeptide binding]; other site 342108012762 homodimer interface [polypeptide binding]; other site 342108012763 substrate binding site [chemical binding]; other site 342108012764 active site 342108012765 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108012766 Zn2+ binding site [ion binding]; other site 342108012767 Mg2+ binding site [ion binding]; other site 342108012768 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 342108012769 Zn2+ binding site [ion binding]; other site 342108012770 Mg2+ binding site [ion binding]; other site 342108012771 Predicted transcriptional regulator [Transcription]; Region: COG2932 342108012772 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 342108012773 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 342108012774 Catalytic site [active] 342108012775 hypothetical protein; Region: PHA00670 342108012776 Bacteriophage head to tail connecting protein; Region: Head-tail_con; pfam12236 342108012777 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 342108012778 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 342108012779 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 342108012780 B12 binding site [chemical binding]; other site 342108012781 cobalt ligand [ion binding]; other site 342108012782 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 342108012783 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 342108012784 active site 342108012785 substrate binding site [chemical binding]; other site 342108012786 coenzyme B12 binding site [chemical binding]; other site 342108012787 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 342108012788 active site clefts [active] 342108012789 zinc binding site [ion binding]; other site 342108012790 dimer interface [polypeptide binding]; other site 342108012791 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 342108012792 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 342108012793 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 342108012794 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 342108012795 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 342108012796 carboxyltransferase (CT) interaction site; other site 342108012797 biotinylation site [posttranslational modification]; other site 342108012798 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 342108012799 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 342108012800 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 342108012801 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108012802 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 342108012803 non-specific DNA binding site [nucleotide binding]; other site 342108012804 salt bridge; other site 342108012805 sequence-specific DNA binding site [nucleotide binding]; other site 342108012806 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 342108012807 Domain of unknown function (DUF955); Region: DUF955; pfam06114 342108012808 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 342108012809 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 342108012810 ATP binding site [chemical binding]; other site 342108012811 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 342108012812 putative Mg++ binding site [ion binding]; other site 342108012813 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 342108012814 nucleotide binding region [chemical binding]; other site 342108012815 ATP-binding site [chemical binding]; other site 342108012816 MarR family; Region: MarR; pfam01047 342108012817 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 342108012818 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 342108012819 Substrate binding site; other site 342108012820 metal-binding site 342108012821 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 342108012822 Phosphotransferase enzyme family; Region: APH; pfam01636 342108012823 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 342108012824 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 342108012825 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 342108012826 active site 342108012827 DNA binding site [nucleotide binding] 342108012828 Int/Topo IB signature motif; other site 342108012829 Protein of unknown function (DUF805); Region: DUF805; pfam05656 342108012830 Protein of unknown function, DUF484; Region: DUF484; cl17449 342108012831 primosome assembly protein PriA; Validated; Region: PRK05580 342108012832 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 342108012833 ATP binding site [chemical binding]; other site 342108012834 putative Mg++ binding site [ion binding]; other site 342108012835 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 342108012836 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 342108012837 ATP binding site [chemical binding]; other site 342108012838 putative Mg++ binding site [ion binding]; other site 342108012839 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 342108012840 nucleotide binding region [chemical binding]; other site 342108012841 ATP-binding site [chemical binding]; other site 342108012842 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 342108012843 HRDC domain; Region: HRDC; pfam00570 342108012844 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108012845 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 342108012846 ligand binding site [chemical binding]; other site 342108012847 flexible hinge region; other site 342108012848 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 342108012849 putative coenzyme Q binding site [chemical binding]; other site 342108012850 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 342108012851 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 342108012852 RNA binding site [nucleotide binding]; other site 342108012853 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 342108012854 RNA binding site [nucleotide binding]; other site 342108012855 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 342108012856 RNA binding site [nucleotide binding]; other site 342108012857 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec4; cd05689 342108012858 RNA binding site [nucleotide binding]; other site 342108012859 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 342108012860 RNA binding site [nucleotide binding]; other site 342108012861 S1_RPS1_repeat_ec6: 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_ec6; cd05691 342108012862 RNA binding site [nucleotide binding]; other site 342108012863 cytidylate kinase; Region: cmk; TIGR00017 342108012864 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 342108012865 CMP-binding site; other site 342108012866 The sites determining sugar specificity; other site 342108012867 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 342108012868 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 342108012869 hinge; other site 342108012870 active site 342108012871 Protein of unknown function (FYDLN_acid); Region: FYDLN_acid; pfam09538 342108012872 TIGR02300 family protein; Region: FYDLN_acid 342108012873 Hemerythrin; Region: Hemerythrin; cd12107 342108012874 Fe binding site [ion binding]; other site 342108012875 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 342108012876 NAD binding site [chemical binding]; other site 342108012877 hypothetical protein; Region: PHA00662 342108012878 hypothetical protein; Region: PHA00661 342108012879 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 342108012880 SPRY domain-like in bacteria; Region: SPRY_like; cd12886 342108012881 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 342108012882 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 342108012883 diiron binding motif [ion binding]; other site 342108012884 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 342108012885 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 342108012886 catalytic residues [active] 342108012887 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 342108012888 active site 342108012889 catalytic residues [active] 342108012890 DNA binding site [nucleotide binding] 342108012891 Int/Topo IB signature motif; other site 342108012892 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 342108012893 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 342108012894 Walker A motif; other site 342108012895 ATP binding site [chemical binding]; other site 342108012896 Walker B motif; other site 342108012897 arginine finger; other site 342108012898 SpoVG; Region: SpoVG; cl00915 342108012899 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 342108012900 active site 342108012901 catalytic residues [active] 342108012902 DNA binding site [nucleotide binding] 342108012903 Int/Topo IB signature motif; other site 342108012904 Hemerythrin; Region: Hemerythrin; cd12107 342108012905 Fe binding site [ion binding]; other site 342108012906 sensory histidine kinase CreC; Provisional; Region: PRK11100 342108012907 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 342108012908 ATP binding site [chemical binding]; other site 342108012909 Mg2+ binding site [ion binding]; other site 342108012910 G-X-G motif; other site 342108012911 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 342108012912 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 342108012913 active site 342108012914 phosphorylation site [posttranslational modification] 342108012915 intermolecular recognition site; other site 342108012916 dimerization interface [polypeptide binding]; other site 342108012917 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 342108012918 DNA binding site [nucleotide binding] 342108012919 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 342108012920 dimerization interface [polypeptide binding]; other site 342108012921 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 342108012922 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 342108012923 dimer interface [polypeptide binding]; other site 342108012924 putative CheW interface [polypeptide binding]; other site 342108012925 putative chaperone; Provisional; Region: PRK11678 342108012926 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 342108012927 nucleotide binding site [chemical binding]; other site 342108012928 putative NEF/HSP70 interaction site [polypeptide binding]; other site 342108012929 SBD interface [polypeptide binding]; other site 342108012930 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 342108012931 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 342108012932 transmembrane helices; other site 342108012933 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 342108012934 metal binding site 2 [ion binding]; metal-binding site 342108012935 putative DNA binding helix; other site 342108012936 metal binding site 1 [ion binding]; metal-binding site 342108012937 dimer interface [polypeptide binding]; other site 342108012938 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 342108012939 active site 342108012940 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 342108012941 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 342108012942 glutathionine S-transferase; Provisional; Region: PRK10542 342108012943 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 342108012944 C-terminal domain interface [polypeptide binding]; other site 342108012945 GSH binding site (G-site) [chemical binding]; other site 342108012946 dimer interface [polypeptide binding]; other site 342108012947 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 342108012948 N-terminal domain interface [polypeptide binding]; other site 342108012949 dimer interface [polypeptide binding]; other site 342108012950 substrate binding pocket (H-site) [chemical binding]; other site 342108012951 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 342108012952 active site 342108012953 HIGH motif; other site 342108012954 nucleotide binding site [chemical binding]; other site 342108012955 active site 342108012956 KMSKS motif; other site 342108012957 putative hydrolase; Provisional; Region: PRK11460 342108012958 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 342108012959 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 342108012960 active site 342108012961 Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; Region: CE4_DAC_u4_5s; cd10973 342108012962 putative active site [active] 342108012963 putative metal binding site [ion binding]; other site 342108012964 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 342108012965 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 342108012966 active site 342108012967 metal binding site [ion binding]; metal-binding site 342108012968 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 342108012969 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 342108012970 4Fe-4S binding domain; Region: Fer4; pfam00037 342108012971 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 342108012972 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 342108012973 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 342108012974 putative active site [active] 342108012975 PAS fold; Region: PAS_3; pfam08447 342108012976 heme pocket [chemical binding]; other site 342108012977 PAS domain S-box; Region: sensory_box; TIGR00229 342108012978 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 342108012979 putative active site [active] 342108012980 heme pocket [chemical binding]; other site 342108012981 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 342108012982 PAS fold; Region: PAS_3; pfam08447 342108012983 putative active site [active] 342108012984 heme pocket [chemical binding]; other site 342108012985 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108012986 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108012987 metal binding site [ion binding]; metal-binding site 342108012988 active site 342108012989 I-site; other site 342108012990 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 342108012991 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 342108012992 HSP70 interaction site [polypeptide binding]; other site 342108012993 Predicted integral membrane protein (DUF2189); Region: DUF2189; pfam09955 342108012994 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 342108012995 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 342108012996 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 342108012997 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 342108012998 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 342108012999 active site 342108013000 catalytic triad [active] 342108013001 oxyanion hole [active] 342108013002 switch loop; other site 342108013003 FIST N domain; Region: FIST; pfam08495 342108013004 FIST C domain; Region: FIST_C; pfam10442 342108013005 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 342108013006 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 342108013007 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 342108013008 EamA-like transporter family; Region: EamA; pfam00892 342108013009 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 342108013010 EamA-like transporter family; Region: EamA; pfam00892 342108013011 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 342108013012 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 342108013013 Na binding site [ion binding]; other site 342108013014 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 342108013015 cobalt transport protein CbiM; Validated; Region: PRK06265 342108013016 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 342108013017 cobalt ABC transporter, permease protein CbiQ; Region: CbiQ_TIGR; TIGR02454 342108013018 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 342108013019 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 342108013020 Walker A/P-loop; other site 342108013021 ATP binding site [chemical binding]; other site 342108013022 Q-loop/lid; other site 342108013023 ABC transporter signature motif; other site 342108013024 Walker B; other site 342108013025 D-loop; other site 342108013026 H-loop/switch region; other site 342108013027 Transcriptional regulator [Transcription]; Region: LysR; COG0583 342108013028 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 342108013029 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 342108013030 dimerization interface [polypeptide binding]; other site 342108013031 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 342108013032 30S subunit binding site; other site 342108013033 heat shock protein 90; Provisional; Region: PRK05218 342108013034 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 342108013035 ATP binding site [chemical binding]; other site 342108013036 Mg2+ binding site [ion binding]; other site 342108013037 G-X-G motif; other site 342108013038 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108013039 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108013040 metal binding site [ion binding]; metal-binding site 342108013041 active site 342108013042 I-site; other site 342108013043 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]; Region: MenA; cl17224 342108013044 UbiA prenyltransferase family; Region: UbiA; pfam01040 342108013045 GTP-binding protein YchF; Reviewed; Region: PRK09601 342108013046 YchF GTPase; Region: YchF; cd01900 342108013047 G1 box; other site 342108013048 GTP/Mg2+ binding site [chemical binding]; other site 342108013049 Switch I region; other site 342108013050 G2 box; other site 342108013051 Switch II region; other site 342108013052 G3 box; other site 342108013053 G4 box; other site 342108013054 G5 box; other site 342108013055 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 342108013056 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 342108013057 putative active site [active] 342108013058 catalytic residue [active] 342108013059 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 342108013060 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 342108013061 5S rRNA interface [nucleotide binding]; other site 342108013062 CTC domain interface [polypeptide binding]; other site 342108013063 L16 interface [polypeptide binding]; other site 342108013064 H+ Antiporter protein; Region: 2A0121; TIGR00900 342108013065 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 342108013066 putative substrate translocation pore; other site 342108013067 HD domain; Region: HD_3; pfam13023 342108013068 Trans-aconitate methyltransferase [General function prediction only]; Region: Tam; COG4106 342108013069 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 342108013070 S-adenosylmethionine binding site [chemical binding]; other site 342108013071 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 342108013072 Ribonuclease P; Region: Ribonuclease_P; pfam00825 342108013073 Haemolytic domain; Region: Haemolytic; pfam01809 342108013074 membrane protein insertase; Provisional; Region: PRK01318 342108013075 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 342108013076 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 342108013077 G1 box; other site 342108013078 GTP/Mg2+ binding site [chemical binding]; other site 342108013079 Switch I region; other site 342108013080 G2 box; other site 342108013081 G3 box; other site 342108013082 Switch II region; other site 342108013083 G4 box; other site 342108013084 G5 box; other site 342108013085 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 342108013086 feedback inhibition sensing region; other site 342108013087 homohexameric interface [polypeptide binding]; other site 342108013088 nucleotide binding site [chemical binding]; other site 342108013089 N-acetyl-L-glutamate binding site [chemical binding]; other site 342108013090 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 342108013091 HPP family; Region: HPP; pfam04982 342108013092 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108013093 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 342108013094 non-specific DNA binding site [nucleotide binding]; other site 342108013095 salt bridge; other site 342108013096 sequence-specific DNA binding site [nucleotide binding]; other site 342108013097 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 342108013098 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 342108013099 putative RNA binding site [nucleotide binding]; other site 342108013100 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 342108013101 S-adenosylmethionine binding site [chemical binding]; other site 342108013102 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 342108013103 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; pfam02433 342108013104 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 342108013105 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 342108013106 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 342108013107 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 342108013108 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 342108013109 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 342108013110 Predicted integral membrane protein linked to a cation pump [Inorganic ion transport and metabolism]; Region: COG5456 342108013111 FixH; Region: FixH; pfam05751 342108013112 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 342108013113 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 342108013114 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 342108013115 metal-binding site [ion binding] 342108013116 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 342108013117 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 342108013118 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 342108013119 ligand binding site [chemical binding]; other site 342108013120 flexible hinge region; other site 342108013121 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 342108013122 putative switch regulator; other site 342108013123 non-specific DNA interactions [nucleotide binding]; other site 342108013124 DNA binding site [nucleotide binding] 342108013125 sequence specific DNA binding site [nucleotide binding]; other site 342108013126 putative cAMP binding site [chemical binding]; other site 342108013127 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 342108013128 oligomerization interface [polypeptide binding]; other site 342108013129 active site 342108013130 metal binding site [ion binding]; metal-binding site 342108013131 pantoate--beta-alanine ligase; Region: panC; TIGR00018 342108013132 Pantoate-beta-alanine ligase; Region: PanC; cd00560 342108013133 active site 342108013134 ATP-binding site [chemical binding]; other site 342108013135 pantoate-binding site; other site 342108013136 HXXH motif; other site 342108013137 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 342108013138 NnrU protein; Region: NnrU; pfam07298 342108013139 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14188 342108013140 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 342108013141 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 342108013142 homodimer interface [polypeptide binding]; other site 342108013143 NADP binding site [chemical binding]; other site 342108013144 substrate binding site [chemical binding]; other site 342108013145 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 342108013146 YGGT family; Region: YGGT; pfam02325 342108013147 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 342108013148 MarR family; Region: MarR_2; pfam12802 342108013149 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 342108013150 catalytic core [active] 342108013151 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 342108013152 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 342108013153 putative tRNA-binding site [nucleotide binding]; other site 342108013154 B3/4 domain; Region: B3_4; pfam03483 342108013155 tRNA synthetase B5 domain; Region: B5; smart00874 342108013156 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 342108013157 dimer interface [polypeptide binding]; other site 342108013158 motif 1; other site 342108013159 motif 3; other site 342108013160 motif 2; other site 342108013161 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; smart00896 342108013162 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 342108013163 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 342108013164 dimer interface [polypeptide binding]; other site 342108013165 motif 1; other site 342108013166 active site 342108013167 motif 2; other site 342108013168 motif 3; other site 342108013169 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 342108013170 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 342108013171 23S rRNA binding site [nucleotide binding]; other site 342108013172 L21 binding site [polypeptide binding]; other site 342108013173 L13 binding site [polypeptide binding]; other site 342108013174 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 342108013175 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 342108013176 EamA-like transporter family; Region: EamA; pfam00892 342108013177 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 342108013178 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 342108013179 Walker A/P-loop; other site 342108013180 ATP binding site [chemical binding]; other site 342108013181 Q-loop/lid; other site 342108013182 ABC transporter signature motif; other site 342108013183 Walker B; other site 342108013184 D-loop; other site 342108013185 H-loop/switch region; other site 342108013186 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 342108013187 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 342108013188 Walker A/P-loop; other site 342108013189 ATP binding site [chemical binding]; other site 342108013190 Q-loop/lid; other site 342108013191 ABC transporter signature motif; other site 342108013192 Walker B; other site 342108013193 D-loop; other site 342108013194 H-loop/switch region; other site 342108013195 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 342108013196 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 342108013197 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 342108013198 ABC-ATPase subunit interface; other site 342108013199 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 342108013200 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 342108013201 dimer interface [polypeptide binding]; other site 342108013202 conserved gate region; other site 342108013203 putative PBP binding loops; other site 342108013204 ABC-ATPase subunit interface; other site 342108013205 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 342108013206 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 342108013207 FecR protein; Region: FecR; pfam04773 342108013208 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 342108013209 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 342108013210 homotetramer interface [polypeptide binding]; other site 342108013211 ligand binding site [chemical binding]; other site 342108013212 catalytic site [active] 342108013213 NAD binding site [chemical binding]; other site 342108013214 Cupin domain; Region: Cupin_2; pfam07883 342108013215 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 342108013216 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 342108013217 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 342108013218 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 342108013219 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 342108013220 dimerization domain swap beta strand [polypeptide binding]; other site 342108013221 regulatory protein interface [polypeptide binding]; other site 342108013222 active site 342108013223 regulatory phosphorylation site [posttranslational modification]; other site 342108013224 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 342108013225 active pocket/dimerization site; other site 342108013226 active site 342108013227 phosphorylation site [posttranslational modification] 342108013228 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 342108013229 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 342108013230 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 342108013231 N-acetyl-D-glucosamine binding site [chemical binding]; other site 342108013232 catalytic residue [active] 342108013233 Domain of unknown function (DUF1848); Region: DUF1848; pfam08902 342108013234 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 342108013235 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 342108013236 substrate binding site [chemical binding]; other site 342108013237 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 342108013238 substrate binding site [chemical binding]; other site 342108013239 ligand binding site [chemical binding]; other site 342108013240 Hemerythrin; Region: Hemerythrin; cd12107 342108013241 Fe binding site [ion binding]; other site 342108013242 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl17361 342108013243 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 342108013244 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 342108013245 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 342108013246 Ligand Binding Site [chemical binding]; other site 342108013247 Putative transmembrane protein (Alph_Pro_TM); Region: Alph_Pro_TM; pfam09608 342108013248 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 342108013249 Uncharacterized protein conserved in bacteria (DUF2333); Region: DUF2333; cl11978 342108013250 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 342108013251 active site 342108013252 dimer interface [polypeptide binding]; other site 342108013253 KMSKS motif; other site 342108013254 integral membrane protein MviN; Region: mviN; TIGR01695 342108013255 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 342108013256 Histone acetyltransferase HPA2 and related acetyltransferases [Transcription / General function prediction only]; Region: WecD; COG0454 342108013257 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 342108013258 Coenzyme A binding pocket [chemical binding]; other site 342108013259 Fe2+ transport protein; Region: Iron_transport; pfam10634 342108013260 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 342108013261 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 342108013262 4Fe-4S binding domain; Region: Fer4_5; pfam12801 342108013263 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 342108013264 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 342108013265 active site 342108013266 dimer interface [polypeptide binding]; other site 342108013267 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 342108013268 dimer interface [polypeptide binding]; other site 342108013269 active site 342108013270 PAS domain; Region: PAS_9; pfam13426 342108013271 PAS domain S-box; Region: sensory_box; TIGR00229 342108013272 PAS fold; Region: PAS_4; pfam08448 342108013273 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 342108013274 putative active site [active] 342108013275 heme pocket [chemical binding]; other site 342108013276 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108013277 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108013278 metal binding site [ion binding]; metal-binding site 342108013279 active site 342108013280 I-site; other site 342108013281 DNA mismatch repair protein MutL; Region: mutl; TIGR00585 342108013282 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 342108013283 ATP binding site [chemical binding]; other site 342108013284 Mg2+ binding site [ion binding]; other site 342108013285 G-X-G motif; other site 342108013286 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 342108013287 ATP binding site [chemical binding]; other site 342108013288 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 342108013289 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 342108013290 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 342108013291 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 342108013292 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 342108013293 UGMP family protein; Validated; Region: PRK09604 342108013294 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 342108013295 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl17708 342108013296 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 342108013297 active site 342108013298 domain interfaces; other site 342108013299 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 342108013300 active site 342108013301 Mitochondrial inner membrane protein; Region: Mitofilin; pfam09731 342108013302 Uncharacterized membrane-bound protein [Function unknown]; Region: COG3898 342108013303 Cytochrome c; Region: Cytochrom_C; cl11414 342108013304 Cytochrome c; Region: Cytochrom_C; cl11414 342108013305 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 342108013306 homotrimer interface [polypeptide binding]; other site 342108013307 Walker A motif; other site 342108013308 GTP binding site [chemical binding]; other site 342108013309 Walker B motif; other site 342108013310 cobalamin biosynthesis protein CobW; Region: CobW; TIGR02475 342108013311 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 342108013312 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 342108013313 cobaltochelatase subunit CobN; Reviewed; Region: cobN; PRK05989 342108013314 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 342108013315 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 342108013316 Transposase; Region: HTH_Tnp_1; pfam01527 342108013317 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 342108013318 HTH-like domain; Region: HTH_21; pfam13276 342108013319 Integrase core domain; Region: rve; pfam00665 342108013320 Integrase core domain; Region: rve_3; pfam13683 342108013321 Domain of unknown function (DUF955); Region: DUF955; cl01076 342108013322 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 342108013323 active site 342108013324 DNA binding site [nucleotide binding] 342108013325 Int/Topo IB signature motif; other site 342108013326 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14608 342108013327 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 342108013328 binding surface 342108013329 TPR motif; other site 342108013330 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 342108013331 TPR repeat; Region: TPR_11; pfam13414 342108013332 binding surface 342108013333 TPR motif; other site 342108013334 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 342108013335 binding surface 342108013336 TPR motif; other site 342108013337 TPR repeat; Region: TPR_11; pfam13414 342108013338 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 342108013339 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 342108013340 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 342108013341 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 342108013342 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 342108013343 Fe-S cluster binding site [ion binding]; other site 342108013344 active site 342108013345 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 342108013346 dimer interface [polypeptide binding]; other site 342108013347 phosphorylation site [posttranslational modification] 342108013348 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 342108013349 ATP binding site [chemical binding]; other site 342108013350 Mg2+ binding site [ion binding]; other site 342108013351 G-X-G motif; other site 342108013352 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 342108013353 Nucleotide-binding domain of human HSPA9, Escherichia coli DnaK, and similar proteins; Region: HSPA9-like_NBD; cd11733 342108013354 nucleotide binding site [chemical binding]; other site 342108013355 NEF interaction site [polypeptide binding]; other site 342108013356 SBD interface [polypeptide binding]; other site 342108013357 chaperone protein DnaJ; Provisional; Region: PRK10767 342108013358 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 342108013359 HSP70 interaction site [polypeptide binding]; other site 342108013360 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 342108013361 substrate binding site [polypeptide binding]; other site 342108013362 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 342108013363 Zn binding sites [ion binding]; other site 342108013364 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 342108013365 dimer interface [polypeptide binding]; other site 342108013366 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 342108013367 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 342108013368 Walker A/P-loop; other site 342108013369 ATP binding site [chemical binding]; other site 342108013370 Q-loop/lid; other site 342108013371 ABC transporter signature motif; other site 342108013372 Walker B; other site 342108013373 D-loop; other site 342108013374 H-loop/switch region; other site 342108013375 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 342108013376 Uncharacterized conserved protein [Function unknown]; Region: COG1434 342108013377 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 342108013378 putative active site [active] 342108013379 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 342108013380 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 342108013381 putative acyl-acceptor binding pocket; other site 342108013382 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 342108013383 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 342108013384 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 342108013385 active site 342108013386 dimer interface [polypeptide binding]; other site 342108013387 effector binding site; other site 342108013388 TSCPD domain; Region: TSCPD; pfam12637 342108013389 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 342108013390 RNA binding surface [nucleotide binding]; other site 342108013391 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT); Region: AGAT_like; cd06451 342108013392 homodimer interface [polypeptide binding]; other site 342108013393 pyridoxal 5'-phosphate binding site [chemical binding]; other site 342108013394 catalytic residue [active] 342108013395 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4093 342108013396 Uncharacterized protein conserved in bacteria (DUF2125); Region: DUF2125; pfam09898 342108013397 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 342108013398 putative active site pocket [active] 342108013399 dimerization interface [polypeptide binding]; other site 342108013400 putative catalytic residue [active] 342108013401 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 342108013402 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 342108013403 active site 342108013404 tetramer interface; other site 342108013405 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 342108013406 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cl00089 342108013407 active site 342108013408 substrate binding site [chemical binding]; other site 342108013409 Mg2+ binding site [ion binding]; other site 342108013410 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 342108013411 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 342108013412 phosphate binding site [ion binding]; other site 342108013413 D-alanyl-D-alanine dipeptidase; Provisional; Region: PRK10178 342108013414 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 342108013415 Glycoprotease family; Region: Peptidase_M22; pfam00814 342108013416 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 342108013417 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 342108013418 Coenzyme A binding pocket [chemical binding]; other site 342108013419 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 342108013420 CPxP motif; other site 342108013421 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 342108013422 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 342108013423 metal binding site 2 [ion binding]; metal-binding site 342108013424 putative DNA binding helix; other site 342108013425 metal binding site 1 [ion binding]; metal-binding site 342108013426 dimer interface [polypeptide binding]; other site 342108013427 structural Zn2+ binding site [ion binding]; other site 342108013428 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 342108013429 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 342108013430 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 342108013431 putative acyl-acceptor binding pocket; other site 342108013432 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 342108013433 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 342108013434 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 342108013435 FeS/SAM binding site; other site 342108013436 TRAM domain; Region: TRAM; pfam01938 342108013437 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 342108013438 PhoH-like protein; Region: PhoH; pfam02562 342108013439 Uncharacterized protein family UPF0054; Region: UPF0054; pfam02130 342108013440 FOG: CBS domain [General function prediction only]; Region: COG0517 342108013441 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 342108013442 Transporter associated domain; Region: CorC_HlyC; smart01091 342108013443 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 342108013444 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 342108013445 putative active site [active] 342108013446 catalytic triad [active] 342108013447 putative dimer interface [polypeptide binding]; other site 342108013448 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108013449 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 342108013450 non-specific DNA binding site [nucleotide binding]; other site 342108013451 salt bridge; other site 342108013452 sequence-specific DNA binding site [nucleotide binding]; other site 342108013453 S-adenosylmethionine synthetase; Validated; Region: PRK05250 342108013454 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 342108013455 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 342108013456 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 342108013457 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 342108013458 S-adenosylmethionine binding site [chemical binding]; other site 342108013459 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 342108013460 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 342108013461 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 342108013462 PhoU domain; Region: PhoU; pfam01895 342108013463 PhoU domain; Region: PhoU; pfam01895 342108013464 phosphate transporter ATP-binding protein; Provisional; Region: PRK14235 342108013465 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 342108013466 Walker A/P-loop; other site 342108013467 ATP binding site [chemical binding]; other site 342108013468 Q-loop/lid; other site 342108013469 ABC transporter signature motif; other site 342108013470 Walker B; other site 342108013471 D-loop; other site 342108013472 H-loop/switch region; other site 342108013473 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; Region: CobA_CobO_BtuR; cl17276 342108013474 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 342108013475 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 342108013476 homodimer interface [polypeptide binding]; other site 342108013477 ATP binding site [chemical binding]; other site 342108013478 Walker A motif; other site 342108013479 hydroxycobalamin binding site [chemical binding]; other site 342108013480 Walker B motif; other site 342108013481 PII uridylyl-transferase; Provisional; Region: PRK05092 342108013482 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 342108013483 metal binding triad; other site 342108013484 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 342108013485 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 342108013486 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 342108013487 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 342108013488 benzoate transport; Region: 2A0115; TIGR00895 342108013489 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 342108013490 putative substrate translocation pore; other site 342108013491 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 342108013492 putative substrate translocation pore; other site 342108013493 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 342108013494 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 342108013495 putative active site [active] 342108013496 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 342108013497 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 342108013498 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 342108013499 Protein of unknown function (DUF4254); Region: DUF4254; pfam14063 342108013500 CreA protein; Region: CreA; pfam05981 342108013501 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 342108013502 dimer interface [polypeptide binding]; other site 342108013503 substrate binding site [chemical binding]; other site 342108013504 metal binding sites [ion binding]; metal-binding site 342108013505 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 342108013506 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 342108013507 hexamer interface [polypeptide binding]; other site 342108013508 ligand binding site [chemical binding]; other site 342108013509 putative active site [active] 342108013510 NAD(P) binding site [chemical binding]; other site 342108013511 muropeptide transporter; Validated; Region: ampG; cl17669 342108013512 muropeptide transporter; Reviewed; Region: ampG; PRK11902 342108013513 argininosuccinate lyase; Provisional; Region: PRK00855 342108013514 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 342108013515 active sites [active] 342108013516 tetramer interface [polypeptide binding]; other site 342108013517 diaminopimelate decarboxylase; Region: lysA; TIGR01048 342108013518 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 342108013519 active site 342108013520 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 342108013521 substrate binding site [chemical binding]; other site 342108013522 catalytic residues [active] 342108013523 dimer interface [polypeptide binding]; other site 342108013524 Domain of unknown function (DUF4175); Region: DUF4175; pfam13779 342108013525 zinc-ribbon domain; Region: zinc_ribbon_5; pfam13719 342108013526 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 342108013527 PAS domain S-box; Region: sensory_box; TIGR00229 342108013528 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 342108013529 putative active site [active] 342108013530 heme pocket [chemical binding]; other site 342108013531 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 342108013532 PAS domain; Region: PAS_9; pfam13426 342108013533 putative active site [active] 342108013534 heme pocket [chemical binding]; other site 342108013535 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 342108013536 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 342108013537 metal binding site [ion binding]; metal-binding site 342108013538 active site 342108013539 I-site; other site 342108013540 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 342108013541 heat shock protein GrpE; Provisional; Region: PRK14141 342108013542 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 342108013543 dimer interface [polypeptide binding]; other site 342108013544 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 342108013545 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 342108013546 ribonuclease PH; Reviewed; Region: rph; PRK00173 342108013547 Ribonuclease PH; Region: RNase_PH_bact; cd11362 342108013548 hexamer interface [polypeptide binding]; other site 342108013549 active site 342108013550 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 342108013551 active site 342108013552 dimerization interface [polypeptide binding]; other site 342108013553 coproporphyrinogen III oxidase; Provisional; Region: PRK09057 342108013554 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 342108013555 FeS/SAM binding site; other site 342108013556 HemN C-terminal domain; Region: HemN_C; pfam06969 342108013557 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 342108013558 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 342108013559 putative ligand binding site [chemical binding]; other site 342108013560 Predicted methyltransferases [General function prediction only]; Region: COG0313 342108013561 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 342108013562 putative SAM binding site [chemical binding]; other site 342108013563 putative homodimer interface [polypeptide binding]; other site 342108013564 hypothetical protein; Reviewed; Region: PRK12497 342108013565 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 342108013566 BON domain; Region: BON; pfam04972 342108013567 BON domain; Region: BON; pfam04972 342108013568 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 342108013569 Uncharacterized conserved protein [Function unknown]; Region: COG2912 342108013570 glutathione synthetase; Provisional; Region: PRK05246 342108013571 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 342108013572 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 342108013573 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 342108013574 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 342108013575 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 342108013576 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 342108013577 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 342108013578 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 342108013579 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 342108013580 catalytic residues [active] 342108013581 catalytic nucleophile [active] 342108013582 Recombinase; Region: Recombinase; pfam07508 342108013583 PLD-like domain; Region: PLDc_2; pfam13091 342108013584 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 342108013585 putative active site [active] 342108013586 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 342108013587 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 342108013588 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 342108013589 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 342108013590 Mannosyltransferase OCH1 and related enzymes [Cell envelope biogenesis, outer membrane]; Region: OCH1; COG3774 342108013591 Glycosyltransferase sugar-binding region containing DXD motif; Region: Gly_transf_sug; pfam04488 342108013592 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 342108013593 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 342108013594 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 342108013595 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 342108013596 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 342108013597 nucleotide binding site/active site [active] 342108013598 HIT family signature motif; other site 342108013599 catalytic residue [active] 342108013600 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 342108013601 metal binding site [ion binding]; metal-binding site 342108013602 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 342108013603 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 342108013604 substrate binding site [chemical binding]; other site 342108013605 glutamase interaction surface [polypeptide binding]; other site 342108013606 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 342108013607 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 342108013608 catalytic residues [active] 342108013609 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 342108013610 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 342108013611 putative active site [active] 342108013612 oxyanion strand; other site 342108013613 catalytic triad [active] 342108013614 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 342108013615 putative active site pocket [active] 342108013616 4-fold oligomerization interface [polypeptide binding]; other site 342108013617 metal binding residues [ion binding]; metal-binding site 342108013618 3-fold/trimer interface [polypeptide binding]; other site 342108013619 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 342108013620 protein binding site [polypeptide binding]; other site 342108013621 Peptidase family M48; Region: Peptidase_M48; cl12018 342108013622 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 342108013623 active site 342108013624 HslU subunit interaction site [polypeptide binding]; other site 342108013625 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 342108013626 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 342108013627 Walker A motif; other site 342108013628 ATP binding site [chemical binding]; other site 342108013629 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 342108013630 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 342108013631 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 342108013632 global nitrogen regulator NtcA, cyanobacterial; Region: NtcA_cyano; TIGR03697 342108013633 ligand binding site [chemical binding]; other site 342108013634 flexible hinge region; other site 342108013635 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 342108013636 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 342108013637 non-specific DNA binding site [nucleotide binding]; other site 342108013638 salt bridge; other site 342108013639 sequence-specific DNA binding site [nucleotide binding]; other site 342108013640 Smr domain; Region: Smr; pfam01713 342108013641 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 342108013642 MltA specific insert domain; Region: MltA; smart00925 342108013643 3D domain; Region: 3D; pfam06725 342108013644 Tim44-like domain; Region: Tim44; pfam04280 342108013645 preprotein translocase subunit SecB; Validated; Region: PRK05751 342108013646 SecA binding site; other site 342108013647 Preprotein binding site; other site 342108013648 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 342108013649 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 342108013650 active site 342108013651 catalytic site [active] 342108013652 substrate binding site [chemical binding]; other site 342108013653 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 342108013654 dephospho-CoA kinase; Region: TIGR00152 342108013655 CoA-binding site [chemical binding]; other site 342108013656 ATP-binding [chemical binding]; other site 342108013657 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 342108013658 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 342108013659 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 342108013660 shikimate binding site; other site 342108013661 NAD(P) binding site [chemical binding]; other site 342108013662 Maf-like protein; Region: Maf; pfam02545 342108013663 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 342108013664 active site 342108013665 dimer interface [polypeptide binding]; other site 342108013666 PEP synthetase regulatory protein; Provisional; Region: PRK05339 342108013667 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 342108013668 substrate binding site [chemical binding]; other site 342108013669 active site 342108013670 ferrochelatase; Reviewed; Region: hemH; PRK00035 342108013671 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 342108013672 C-terminal domain interface [polypeptide binding]; other site 342108013673 active site 342108013674 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 342108013675 active site 342108013676 N-terminal domain interface [polypeptide binding]; other site 342108013677 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 342108013678 transcription termination factor Rho; Provisional; Region: rho; PRK09376 342108013679 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 342108013680 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 342108013681 RNA binding site [nucleotide binding]; other site 342108013682 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 342108013683 multimer interface [polypeptide binding]; other site 342108013684 Walker A motif; other site 342108013685 ATP binding site [chemical binding]; other site 342108013686 Walker B motif; other site 342108013687 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 342108013688 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 342108013689 NADP binding site [chemical binding]; other site 342108013690 dimer interface [polypeptide binding]; other site 342108013691 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 342108013692 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 342108013693 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 342108013694 DNA binding site [nucleotide binding] 342108013695 active site 342108013696 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 342108013697 TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif. The human/rat protein; Region: SSP411; cd02955 342108013698 catalytic residues [active] 342108013699 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cl00183 342108013700 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 342108013701 dimer interface [polypeptide binding]; other site 342108013702 [2Fe-2S] cluster binding site [ion binding]; other site