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Conserved domains on  [gi|489936783|ref|WP_003840090|]
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MULTISPECIES: hypochlorite stress DNA-binding transcriptional regulator HypT [Citrobacter]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10082 super family cl32457
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-291 1.38e-141

hypochlorite stress DNA-binding transcriptional regulator HypT;


The actual alignment was detected with superfamily member PRK10082:

Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 401.35  E-value: 1.38e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783   1 MKNIETKWLYDFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLEC 80
Cdd:PRK10082   8 LHNIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLES 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  81 NLDELSGHNLLGVPNIKIAAAHSLSLTMLPRLVHSMSAwgeEFVYHVEAIDVVQAVNTLREGKSDFIISFRDEDLMQSPF 160
Cdd:PRK10082  88 NLAELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPP---LFTWAIEAIDVDEAVDKLREGQSDCIFSFHDEDLLEAPF 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 161 CGLKVFESELYPVCAADSQGKALFDIYQPQVPILNYTSTSYMGRLVNRHLAEVGSISARTLFMSSMSELLKNMALDGHGI 240
Cdd:PRK10082 165 DHIRLFESQLFPVCASDEHGEALFNLAQPHFPLLNYSRNSYMGRLINRTLTRHSELSFSTFFVSSMSELLKQVALDGCGI 244

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489936783 241 AWLPAWTIVNELRDKRLVCLDTPELMVPIQAYIYRMDTRLNKTAEHFWRIL 291
Cdd:PRK10082 245 AWLPEYAIQQEIRSGQLVVLNRDELVIPIQAYAYRMNTRMNPVAERFWREL 295
 
Name Accession Description Interval E-value
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-291 1.38e-141

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 401.35  E-value: 1.38e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783   1 MKNIETKWLYDFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLEC 80
Cdd:PRK10082   8 LHNIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLES 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  81 NLDELSGHNLLGVPNIKIAAAHSLSLTMLPRLVHSMSAwgeEFVYHVEAIDVVQAVNTLREGKSDFIISFRDEDLMQSPF 160
Cdd:PRK10082  88 NLAELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPP---LFTWAIEAIDVDEAVDKLREGQSDCIFSFHDEDLLEAPF 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 161 CGLKVFESELYPVCAADSQGKALFDIYQPQVPILNYTSTSYMGRLVNRHLAEVGSISARTLFMSSMSELLKNMALDGHGI 240
Cdd:PRK10082 165 DHIRLFESQLFPVCASDEHGEALFNLAQPHFPLLNYSRNSYMGRLINRTLTRHSELSFSTFFVSSMSELLKQVALDGCGI 244

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489936783 241 AWLPAWTIVNELRDKRLVCLDTPELMVPIQAYIYRMDTRLNKTAEHFWRIL 291
Cdd:PRK10082 245 AWLPEYAIQQEIRSGQLVVLNRDELVIPIQAYAYRMNTRMNPVAERFWREL 295
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-297 5.35e-43

DNA-binding transcriptional regulator, LysR family [Transcription];


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 148.09  E-value: 5.35e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783   4 IETKWLYDFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLECNLD 83
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  84 ELSGHNLLGVPNIKIAAAHSLSLTMLPRLVHSMSAWGEEFVYHVEAIDVVQAVNTLREGKSDFIISFRDEDlmQSPFCGL 163
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPP--DPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 164 KVFESELYPVCAADSqgkalfdiyqpqvpilnytstsymgrlvnrHLAEVGSIsartlfmSSMSELLKNMALDGHGIAWL 243
Cdd:COG0583  159 PLGEERLVLVASPDH------------------------------PLARRAPL-------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489936783 244 PAWTIVNELRDKRLVCLDTPELMVPIQAY-IYRMDTRLNKTAEHFWRILYNHMPE 297
Cdd:COG0583  202 PRFLAADELAAGRLVALPLPDPPPPRPLYlVWRRRRHLSPAVRAFLDFLREALAE 256
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-65 1.31e-18

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.81  E-value: 1.31e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 489936783    7 KWLYDFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGK 65
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 2-291 3.80e-17

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 79.97  E-value: 3.80e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783   2 KNIETkwlydFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLL---QQL 78
Cdd:NF040786   4 KQLEA-----FVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLdlwEKL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  79 ECNLDELSGhnlLGVPNIKIAAAHSLSLTMLPRLVHS-MSAWGEEFVYHVEAiDVVQAVNTLREGKSDFII---SFRDED 154
Cdd:NF040786  79 EEEFDRYGK---ESKGVLRIGASTIPGQYLLPELLKKfKEKYPNVRFKLMIS-DSIKVIELLLEGEVDIGFtgtKLEKKR 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 155 LMQSPFcglkvFESELYPVCAADSqgkALFDIYQPQVPILNYTSTSYMGR--------LVNRHLAEVGsISARTLFMS-S 225
Cdd:NF040786 155 LVYTPF-----YKDRLVLITPNGT---EKYRMLKEEISISELQKEPFIMReegsgtrkEAEKALKSLG-ISLEDLNVVaS 225

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489936783 226 MS--ELLKNMALDGHGIAWLPAWTIVNELRDKRLVCLDTPELMVPIQAYI-YRMDTRLNKTAEHFWRIL 291
Cdd:NF040786 226 LGstEAIKQSVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLvYNKNRQLSPTAEAFLQFV 294
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 4-258 4.06e-11

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 62.45  E-value: 4.06e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783   4 IETKWLYDFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLECNLD 83
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  84 ELSghNLLGVPNIKIAAAHSLSLTMLPRLVHS-MSAWGE----EFVYHVEAidvvQAVNTLREGKSDFIISFRDEDLMQS 158
Cdd:NF041036  81 ELK--SFKGRQRLSICCTPTFGMAHLPGVLNRfMLRNADvvdlKFLFHSPA----QALEGIQNKEFDLAIIEHCADLDLG 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 159 PFCGLKVFESELYPVCAADsqgkalFDIYQPQVPILNYTSTSYMGR--------LVNRHLAEVG-SISA-RTLFMSSMSE 228
Cdd:NF041036 155 RFHTYPLPQDELVFVSAPS------LGLPTPNVTLERLLELCLITRrdgcssrdLLRRNLAEQGrDLDDfRRVVVSDDLR 228

                        250       260       270
                 ....*....|....*....|....*....|
gi 489936783 229 LLKNMALDGHGIAWLPAWTIVNELRDKRLV 258
Cdd:NF041036 229 LTIQTVLDGGGISFVSRSLVCEYLKNGQLR 258
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 96-291 5.23e-09

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 54.91  E-value: 5.23e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  96 IKIAAAHSLSLTMLPRLvhsMSAWGEEF---VYHVEAIDVVQAVNTLREGKSDFIISFRDEDlmQSPFCGLKVFESELYP 172
Cdd:cd05466    2 LRIGASPSIAAYLLPPL---LAAFRQRYpgvELSLVEGGSSELLEALLEGELDLAIVALPVD--DPGLESEPLFEEPLVL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 173 VCAAD---SQGKA--LFDIYQpqVPILNYTSTSYMGRLVNRHLAEVGSISARTLFMSSMsELLKNMALDGHGIAWLPAWt 247
Cdd:cd05466   77 VVPPDhplAKRKSvtLADLAD--EPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSL-EAIKALVAAGLGIALLPES- 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 489936783 248 IVNELRDKRLVC--LDTPELMVPIqAYIYRMDTRLNKTAEHFWRIL 291
Cdd:cd05466  153 AVEELADGGLVVlpLEDPPLSRTI-GLVWRKGRYLSPAARAFLELL 197
 
Name Accession Description Interval E-value
PRK10082 PRK10082
hypochlorite stress DNA-binding transcriptional regulator HypT;
1-291 1.38e-141

hypochlorite stress DNA-binding transcriptional regulator HypT;


Pssm-ID: 182228 [Multi-domain]  Cd Length: 303  Bit Score: 401.35  E-value: 1.38e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783   1 MKNIETKWLYDFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLEC 80
Cdd:PRK10082   8 LHNIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLES 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  81 NLDELSGHNLLGVPNIKIAAAHSLSLTMLPRLVHSMSAwgeEFVYHVEAIDVVQAVNTLREGKSDFIISFRDEDLMQSPF 160
Cdd:PRK10082  88 NLAELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPP---LFTWAIEAIDVDEAVDKLREGQSDCIFSFHDEDLLEAPF 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 161 CGLKVFESELYPVCAADSQGKALFDIYQPQVPILNYTSTSYMGRLVNRHLAEVGSISARTLFMSSMSELLKNMALDGHGI 240
Cdd:PRK10082 165 DHIRLFESQLFPVCASDEHGEALFNLAQPHFPLLNYSRNSYMGRLINRTLTRHSELSFSTFFVSSMSELLKQVALDGCGI 244

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489936783 241 AWLPAWTIVNELRDKRLVCLDTPELMVPIQAYIYRMDTRLNKTAEHFWRIL 291
Cdd:PRK10082 245 AWLPEYAIQQEIRSGQLVVLNRDELVIPIQAYAYRMNTRMNPVAERFWREL 295
LysR COG0583
DNA-binding transcriptional regulator, LysR family [Transcription];
4-297 5.35e-43

DNA-binding transcriptional regulator, LysR family [Transcription];


Pssm-ID: 440348 [Multi-domain]  Cd Length: 256  Bit Score: 148.09  E-value: 5.35e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783   4 IETKWLYDFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLECNLD 83
Cdd:COG0583    1 MDLRQLRAFVAVAEEGSFTAAAERLGVSQPAVSRQIRRLEEELGVPLFERTGRGLRLTEAGERLLERARRILAELEEAEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  84 ELSGHNLLGVPNIKIAAAHSLSLTMLPRLVHSMSAWGEEFVYHVEAIDVVQAVNTLREGKSDFIISFRDEDlmQSPFCGL 163
Cdd:COG0583   81 ELRALRGGPRGTLRIGAPPSLARYLLPPLLARFRARHPGVRLELREGNSDRLVDALLEGELDLAIRLGPPP--DPGLVAR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 164 KVFESELYPVCAADSqgkalfdiyqpqvpilnytstsymgrlvnrHLAEVGSIsartlfmSSMSELLKNMALDGHGIAWL 243
Cdd:COG0583  159 PLGEERLVLVASPDH------------------------------PLARRAPL-------VNSLEALLAAVAAGLGIALL 201

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489936783 244 PAWTIVNELRDKRLVCLDTPELMVPIQAY-IYRMDTRLNKTAEHFWRILYNHMPE 297
Cdd:COG0583  202 PRFLAADELAAGRLVALPLPDPPPPRPLYlVWRRRRHLSPAVRAFLDFLREALAE 256
HTH_1 pfam00126
Bacterial regulatory helix-turn-helix protein, lysR family;
7-65 1.31e-18

Bacterial regulatory helix-turn-helix protein, lysR family;


Pssm-ID: 459683 [Multi-domain]  Cd Length: 60  Bit Score: 77.81  E-value: 1.31e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 489936783    7 KWLYDFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGK 65
Cdd:pfam00126   2 RQLRLFVAVAETGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGVRLTEAGE 60
LysR_substrate pfam03466
LysR substrate binding domain; The structure of this domain is known and is similar to the ...
 96-296 1.02e-17

LysR substrate binding domain; The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 460931 [Multi-domain]  Cd Length: 205  Bit Score: 79.64  E-value: 1.02e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783   96 IKIAAAHSLSLTMLPRLVHSMSAWGEEFVYHVEAIDVVQAVNTLREGKSDFIISFRDEDlmQSPFCGLKVFESELYPVCA 175
Cdd:pfam03466   4 LRIGAPPTLASYLLPPLLARFRERYPDVELELTEGNSEELLDLLLEGELDLAIRRGPPD--DPGLEARPLGEEPLVLVAP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  176 ADSQ--GKALFDIYQ-PQVPILNYTSTSYMGRLVNRHLAEVGsISARTLFMSSMSELLKNMALDGHGIAWLPAWTIVNEL 252
Cdd:pfam03466  82 PDHPlaRGEPVSLEDlADEPLILLPPGSGLRDLLDRALRAAG-LRPRVVLEVNSLEALLQLVAAGLGIALLPRSAVAREL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 489936783  253 RDKRLVCLDTPELMVPIQAY-IYRMDTRLNKTAEHFWRILYNHMP 296
Cdd:pfam03466 161 ADGRLVALPLPEPPLPRELYlVWRKGRPLSPAVRAFIEFLREALA 205
LysR_Sec_metab NF040786
selenium metabolism-associated LysR family transcriptional regulator; LysR family ...
 2-291 3.80e-17

selenium metabolism-associated LysR family transcriptional regulator; LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations.


Pssm-ID: 468737 [Multi-domain]  Cd Length: 298  Bit Score: 79.97  E-value: 3.80e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783   2 KNIETkwlydFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLL---QQL 78
Cdd:NF040786   4 KQLEA-----FVNVAEYKSFSKAAKKLFLTQPTISAHISSLEKELGVRLFVRNTKEVSLTEDGKLLYEYAKEMLdlwEKL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  79 ECNLDELSGhnlLGVPNIKIAAAHSLSLTMLPRLVHS-MSAWGEEFVYHVEAiDVVQAVNTLREGKSDFII---SFRDED 154
Cdd:NF040786  79 EEEFDRYGK---ESKGVLRIGASTIPGQYLLPELLKKfKEKYPNVRFKLMIS-DSIKVIELLLEGEVDIGFtgtKLEKKR 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 155 LMQSPFcglkvFESELYPVCAADSqgkALFDIYQPQVPILNYTSTSYMGR--------LVNRHLAEVGsISARTLFMS-S 225
Cdd:NF040786 155 LVYTPF-----YKDRLVLITPNGT---EKYRMLKEEISISELQKEPFIMReegsgtrkEAEKALKSLG-ISLEDLNVVaS 225

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489936783 226 MS--ELLKNMALDGHGIAWLPAWTIVNELRDKRLVCLDTPELMVPIQAYI-YRMDTRLNKTAEHFWRIL 291
Cdd:NF040786 226 LGstEAIKQSVEAGLGISVISELAAEKEVERGRVLIFPIPGLPKNRDFYLvYNKNRQLSPTAEAFLQFV 294
PRK09791 PRK09791
LysR family transcriptional regulator;
15-290 1.47e-11

LysR family transcriptional regulator;


Pssm-ID: 182077 [Multi-domain]  Cd Length: 302  Bit Score: 64.01  E-value: 1.47e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  15 LEACRHFSQAAEER--NLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLECNLDELS---GHn 89
Cdd:PRK09791  14 VEVARQGSIRGASRmlNMSQPALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAAQEDIRqrqGQ- 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  90 LLGVPNIKIAAahSLSLTMLPRLVHSMSAWGEEFVYHVEAIDVVQAVNTLREGKSDFIIS----------FRDEDLMQSP 159
Cdd:PRK09791  93 LAGQINIGMGA--SIARSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINtyyqgpydheFTFEKLLEKQ 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 160 FCglkVFESELYPVCAADSQG-----------------KALFDIY--QPQVPILNYTSTSYMGRLvnrhlaevgSISART 220
Cdd:PRK09791 171 FA---VFCRPGHPAIGARSLKqlldyswtmptphgsyyKQLSELLddQAQTPQVGVVCETFSACI---------SLVAKS 238

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 221 LFMSSMSELLKNMALDGHGIAWLPawtiVNELRDKRLVCLdtpelmvpiqayIYRMDTRLNKTAEHFWRI 290
Cdd:PRK09791 239 DFLSILPEEMGCDPLHGQGLVMLP----VSEILPKATYYL------------IQRRDTRQTPLTASLITL 292
decaheme_TF NF041036
multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, ...
 4-258 4.06e-11

multiheme cytochrome-associated LysR family transcriptional regulator; Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome.


Pssm-ID: 468965 [Multi-domain]  Cd Length: 301  Bit Score: 62.45  E-value: 4.06e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783   4 IETKWLYDFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLECNLD 83
Cdd:NF041036   1 METRYLKTLVIVAEEGSFSKAAEKLHLTQSAVSQRIKFLEECYGYQLFDRSGPSLEPTAAGEMVLEKARRILDIEDSLMD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  84 ELSghNLLGVPNIKIAAAHSLSLTMLPRLVHS-MSAWGE----EFVYHVEAidvvQAVNTLREGKSDFIISFRDEDLMQS 158
Cdd:NF041036  81 ELK--SFKGRQRLSICCTPTFGMAHLPGVLNRfMLRNADvvdlKFLFHSPA----QALEGIQNKEFDLAIIEHCADLDLG 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 159 PFCGLKVFESELYPVCAADsqgkalFDIYQPQVPILNYTSTSYMGR--------LVNRHLAEVG-SISA-RTLFMSSMSE 228
Cdd:NF041036 155 RFHTYPLPQDELVFVSAPS------LGLPTPNVTLERLLELCLITRrdgcssrdLLRRNLAEQGrDLDDfRRVVVSDDLR 228

                        250       260       270
                 ....*....|....*....|....*....|
gi 489936783 229 LLKNMALDGHGIAWLPAWTIVNELRDKRLV 258
Cdd:NF041036 229 LTIQTVLDGGGISFVSRSLVCEYLKNGQLR 258
PRK10086 PRK10086
DNA-binding transcriptional regulator DsdC;
9-87 5.83e-11

DNA-binding transcriptional regulator DsdC;


Pssm-ID: 182231 [Multi-domain]  Cd Length: 311  Bit Score: 61.94  E-value: 5.83e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783   9 LYDFLTleACRH--FSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGK-LFHSQTRSL--LQQ--LECN 81
Cdd:PRK10086  19 LHTFEV--AARHqsFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKrVFWALKSSLdtLNQeiLDIK 96


                 ....*.
gi 489936783  82 LDELSG 87
Cdd:PRK10086  97 NQELSG 102
PRK09986 PRK09986
LysR family transcriptional regulator;
4-79 7.27e-11

LysR family transcriptional regulator;


Pssm-ID: 182183 [Multi-domain]  Cd Length: 294  Bit Score: 61.66  E-value: 7.27e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489936783   4 IETKWLYDFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLE 79
Cdd:PRK09986   7 IDLKLLRYFLAVAEELHFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEESRRLLDNAE 82
PRK11242 PRK11242
DNA-binding transcriptional regulator CynR; Provisional
 12-79 1.01e-10

DNA-binding transcriptional regulator CynR; Provisional


Pssm-ID: 183051 [Multi-domain]  Cd Length: 296  Bit Score: 61.13  E-value: 1.01e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489936783  12 FLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLE 79
Cdd:PRK11242   9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLE 76
PRK11139 PRK11139
DNA-binding transcriptional activator GcvA; Provisional
 17-78 7.62e-10

DNA-binding transcriptional activator GcvA; Provisional


Pssm-ID: 182990 [Multi-domain]  Cd Length: 297  Bit Score: 58.70  E-value: 7.62e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489936783  17 ACRH--FSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQL 78
Cdd:PRK11139  17 AARHlsFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREIFDQL 80
PRK09906 PRK09906
DNA-binding transcriptional regulator HcaR; Provisional
 4-79 2.46e-09

DNA-binding transcriptional regulator HcaR; Provisional


Pssm-ID: 182137 [Multi-domain]  Cd Length: 296  Bit Score: 57.09  E-value: 2.46e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489936783   4 IETKWLYDFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLE 79
Cdd:PRK09906   1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARAILEQAE 76
PRK10094 PRK10094
HTH-type transcriptional activator AllS;
12-85 4.69e-09

HTH-type transcriptional activator AllS;


Pssm-ID: 182237 [Multi-domain]  Cd Length: 308  Bit Score: 56.35  E-value: 4.69e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489936783  12 FLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLECNLDEL 85
Cdd:PRK10094  10 FIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPSEL 83
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 96-291 5.23e-09

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 54.91  E-value: 5.23e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  96 IKIAAAHSLSLTMLPRLvhsMSAWGEEF---VYHVEAIDVVQAVNTLREGKSDFIISFRDEDlmQSPFCGLKVFESELYP 172
Cdd:cd05466    2 LRIGASPSIAAYLLPPL---LAAFRQRYpgvELSLVEGGSSELLEALLEGELDLAIVALPVD--DPGLESEPLFEEPLVL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 173 VCAAD---SQGKA--LFDIYQpqVPILNYTSTSYMGRLVNRHLAEVGSISARTLFMSSMsELLKNMALDGHGIAWLPAWt 247
Cdd:cd05466   77 VVPPDhplAKRKSvtLADLAD--EPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSL-EAIKALVAAGLGIALLPES- 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 489936783 248 IVNELRDKRLVC--LDTPELMVPIqAYIYRMDTRLNKTAEHFWRIL 291
Cdd:cd05466  153 AVEELADGGLVVlpLEDPPLSRTI-GLVWRKGRYLSPAARAFLELL 197
PRK10341 PRK10341
transcriptional regulator TdcA;
24-169 7.63e-09

transcriptional regulator TdcA;


Pssm-ID: 182391 [Multi-domain]  Cd Length: 312  Bit Score: 55.64  E-value: 7.63e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  24 AAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLECNLDELSGHNLLGVPNIKIAAAHS 103
Cdd:PRK10341  27 AAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNEINGMSSEAVVDVSFGFPSL 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489936783 104 LSLTMLPRLVHSMSawgEEF------VYHVEAIDVVQAvntLREGKSDFII-SFRDEDLMQSPFCGLkVFESE 169
Cdd:PRK10341 107 IGFTFMSDMINKFK---EVFpkaqvsMYEAQLSSFLPA---IRDGRLDFAIgTLSNEMKLQDLHVEP-LFESE 172
rbcR CHL00180
LysR transcriptional regulator; Provisional
 21-67 2.36e-08

LysR transcriptional regulator; Provisional


Pssm-ID: 177082 [Multi-domain]  Cd Length: 305  Bit Score: 54.26  E-value: 2.36e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 489936783  21 FSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLF 67
Cdd:CHL00180  22 FKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTEAGELL 68
PRK13348 PRK13348
HTH-type transcriptional regulator ArgP;
19-76 1.17e-07

HTH-type transcriptional regulator ArgP;


Pssm-ID: 237357 [Multi-domain]  Cd Length: 294  Bit Score: 52.28  E-value: 1.17e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  19 RHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRtTSPLQLTEEGK--LFHSQTRSLLQ 76
Cdd:PRK13348  17 GSFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GRPCRPTPAGQrlLRHLRQVALLE 75
PRK11151 PRK11151
DNA-binding transcriptional regulator OxyR; Provisional
 19-77 6.36e-07

DNA-binding transcriptional regulator OxyR; Provisional


Pssm-ID: 182999 [Multi-domain]  Cd Length: 305  Bit Score: 50.03  E-value: 6.36e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489936783  19 RHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQ 77
Cdd:PRK11151  16 RHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQARTVLRE 74
PBP2_LTTR_like_5 cd08426
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 96-291 1.86e-06

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176117 [Multi-domain]  Cd Length: 199  Bit Score: 47.69  E-value: 1.86e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  96 IKIAAAHSLSLTMLPRLVHSMSAWGEEFVYHVEAIDVVQAVNTLREGKSDFIISFrdeDLMQSPfcGLKVFESELYPVCA 175
Cdd:cd08426    2 VRVATGEGLAAELLPSLIARFRQRYPGVFFTVDVASTADVLEAVLSGEADIGLAF---SPPPEP--GIRVHSRQPAPIGA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 176 ADSQGKALfdIYQPQV--------PILNYTSTSYMGRLVNRHLAEVGsISARTLFMSSMSELLKNMALDGHGIAWLPAWT 247
Cdd:cd08426   77 VVPPGHPL--ARQPSVtlaqlagyPLALPPPSFSLRQILDAAFARAG-VQLEPVLISNSIETLKQLVAAGGGISLLTELA 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 489936783 248 IVNELRDKRLVC--LDTPElMVPIQAYIY-RMDTRLNKTAEHFWRIL 291
Cdd:cd08426  154 VRREIRRGQLVAvpLADPH-MNHRQLELQtRAGRQLPAAASAFLQLL 199
PRK03601 PRK03601
HTH-type transcriptional regulator HdfR;
4-64 2.64e-06

HTH-type transcriptional regulator HdfR;


Pssm-ID: 235137 [Multi-domain]  Cd Length: 275  Bit Score: 47.70  E-value: 2.64e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489936783   4 IETKWLYDFLTLEACRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEG 64
Cdd:PRK03601   1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAG 61
PRK03635 PRK03635
ArgP/LysG family DNA-binding transcriptional regulator;
21-88 3.42e-06

ArgP/LysG family DNA-binding transcriptional regulator;


Pssm-ID: 235144 [Multi-domain]  Cd Length: 294  Bit Score: 47.46  E-value: 3.42e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489936783  21 FSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTsPLQLTEEGKL---FHSQTRSLLQQLECNLDELSGH 88
Cdd:PRK03635  19 FERAAQKLHITQSAVSQRIKALEERVGQVLLVRTQ-PCRPTEAGQRllrHARQVRLLEAELLGELPALDGT 88
PBP2_CysL_like cd08420
C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which ...
 208-291 4.95e-06

C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176112 [Multi-domain]  Cd Length: 201  Bit Score: 46.33  E-value: 4.95e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 208 RHLAEVGSISArtlfmssmselLKNMALDGHGIAWLPAWTIVNELRDKRLVCLDTPELMVPIQAY-IYRMDTRLNKTAEH 286
Cdd:cd08420  128 NIVMELGSTEA-----------IKEAVEAGLGISILSRLAVRKELELGRLVALPVEGLRLTRPFSlIYHKDKYLSPAAEA 196


                 ....*
gi 489936783 287 FWRIL 291
Cdd:cd08420  197 FLEFL 201
PBP2_CrgA_like cd08422
The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its ...
 192-258 1.97e-05

The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176114 [Multi-domain]  Cd Length: 197  Bit Score: 44.35  E-value: 1.97e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489936783 192 PILNYTSTSYMGRLVNRHLAEVGSISARTLFMSSMSELLKNMALDGHGIAWLPAWTIVNELRDKRLV 258
Cdd:cd08422   97 RCLGYRLPGRPLRWRFRRGGGEVEVRVRGRLVVNDGEALRAAALAGLGIALLPDFLVAEDLASGRLV 163
PRK11074 PRK11074
putative DNA-binding transcriptional regulator; Provisional
 21-79 2.07e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182948 [Multi-domain]  Cd Length: 300  Bit Score: 45.32  E-value: 2.07e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489936783  21 FSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLE 79
Cdd:PRK11074  19 FSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFVKEARSVIKKMQ 77
PRK10837 PRK10837
putative DNA-binding transcriptional regulator; Provisional
 22-113 3.04e-05

putative DNA-binding transcriptional regulator; Provisional


Pssm-ID: 182768 [Multi-domain]  Cd Length: 290  Bit Score: 44.68  E-value: 3.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  22 SQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQlECNLDELSGHNLLGvpnIKIAAA 101
Cdd:PRK10837  21 TQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQ-AVEIEQLFREDNGA---LRIYAS 96

                         90
                 ....*....|..
gi 489936783 102 HSLSLTMLPRLV 113
Cdd:PRK10837  97 STIGNYILPAMI 108
PRK11233 PRK11233
nitrogen assimilation transcriptional regulator; Provisional
 22-109 5.27e-05

nitrogen assimilation transcriptional regulator; Provisional


Pssm-ID: 183045 [Multi-domain]  Cd Length: 305  Bit Score: 43.90  E-value: 5.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  22 SQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQleCNLDEL----SGHNLLGVPNIK 97
Cdd:PRK11233  19 TQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQ--CEQAQLavhnVGQALSGQVSIG 96

                         90
                 ....*....|....*
gi 489936783  98 IA---AAHSLSLTML 109
Cdd:PRK11233  97 LApgtAASSLTMPLL 111
PRK14997 PRK14997
LysR family transcriptional regulator; Provisional
 24-79 6.04e-05

LysR family transcriptional regulator; Provisional


Pssm-ID: 184959 [Multi-domain]  Cd Length: 301  Bit Score: 43.83  E-value: 6.04e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489936783  24 AAEERNLSQPA--FSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLE 79
Cdd:PRK14997  20 AAAGRALDEPKskLSRRIAQLEERLGVRLIQRTTRQFNVTEVGQTFYEHCKAMLVEAQ 77
PRK12683 PRK12683
transcriptional regulator CysB-like protein; Reviewed
 16-265 8.07e-05

transcriptional regulator CysB-like protein; Reviewed


Pssm-ID: 237172 [Multi-domain]  Cd Length: 309  Bit Score: 43.49  E-value: 8.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  16 EACR---HFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQ-LTEEGKLFHSQTRSLLQQLEcNLDEL------ 85
Cdd:PRK12683  11 EAVRqnfNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTgLTEPGKELLQIVERMLLDAE-NLRRLaeqfad 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  86 --SGHnllgvpnIKIAAAHSLSLTMLPRLVhsmSAWGEEFVyHVEAI----DVVQAVNTLREGKSDFIISfrDEDLMQSP 159
Cdd:PRK12683  90 rdSGH-------LTVATTHTQARYALPKVV---RQFKEVFP-KVHLAlrqgSPQEIAEMLLNGEADIGIA--TEALDREP 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 160 fcGLKVFESELYPVCAADSQGKALFDIYQP------QVPILNYtSTSYMGRL-VNRHLAEVGSISarTLFMSSM-SELLK 231
Cdd:PRK12683 157 --DLVSFPYYSWHHVVVVPKGHPLTGRENLtleaiaEYPIITY-DQGFTGRSrIDQAFAEAGLVP--DIVLTALdADVIK 231

                        250       260       270
                 ....*....|....*....|....*....|....
gi 489936783 232 NMALDGHGIAWLPAWTiVNELRDKRLVCLDTPEL 265
Cdd:PRK12683 232 TYVELGMGVGIVAAMA-YDPQRDTGLVALDTDHL 264
PRK10632 PRK10632
HTH-type transcriptional activator AaeR;
18-118 1.45e-04

HTH-type transcriptional activator AaeR;


Pssm-ID: 182601 [Multi-domain]  Cd Length: 309  Bit Score: 42.83  E-value: 1.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  18 CRHFSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQQLECNLDELSGHNLLGVPNIK 97
Cdd:PRK10632  16 FGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVHEQLYAFNNTPIGTLR 95

                         90       100
                 ....*....|....*....|.
gi 489936783  98 IAAahslSLTMLPRLVHSMSA 118
Cdd:PRK10632  96 IGC----SSTMAQNVLAGLTA 112
PBP2_CrgA_like_6 cd08475
The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional ...
 228-258 2.16e-03

The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176164 [Multi-domain]  Cd Length: 199  Bit Score: 38.31  E-value: 2.16e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 489936783 228 ELLKNMALDGHGIAWLPAWTIVNELRDKRLV 258
Cdd:cd08475  135 EAIADAALAGLGIAQLPTWLVADHLQRGELV 165
PRK15092 PRK15092
DNA-binding transcriptional repressor LrhA; Provisional
 21-193 2.51e-03

DNA-binding transcriptional repressor LrhA; Provisional


Pssm-ID: 237907 [Multi-domain]  Cd Length: 310  Bit Score: 38.86  E-value: 2.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  21 FSQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEGKLFHSQTRSLLQqleCNlDE----LSGHNLLGVpnI 96
Cdd:PRK15092  28 FAAAAAAVCRTQSAVSQQMQRLEQLVGKELFARHGRNKLLTEHGIQLLGYARKILR---FN-DEacssLMYSNLQGV--L 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  97 KIAAAHSLSLTMLPRLVHSMSAwgeefVYHVEAIDVVQAVNT-----LREGKSDFIISfrDEDLMQSPFCGLKVFESELY 171
Cdd:PRK15092 102 TIGASDDTADTILPFLLNRVSS-----VYPKLALDVRVKRNAfmmemLESQEVDLAVT--THRPSSFPALNLRTSPTLWY 174

                        170       180
                 ....*....|....*....|..
gi 489936783 172 pvCAADSQgkalfdiYQPQVPI 193
Cdd:PRK15092 175 --CAAEYV-------LQKGEPI 187
PBP2_CbbR_RubisCO_like cd08419
The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO ...
 204-291 2.96e-03

The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 176111  Cd Length: 197  Bit Score: 37.87  E-value: 2.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783 204 RLVNRHLAEVGSISARTLFMSSmSELLKNMALDGHGIAWLPAWTIVNELRDKRLVCLDTPELMVPIQAYI-YRMDTRLNK 282
Cdd:cd08419  110 LAMERFFAEHGVTLRVRMELGS-NEAIKQAVMAGLGLSVLSLHTLALELATGRLAVLDVEGFPIRRQWYVvHRKGKRLSP 188


                 ....*....
gi 489936783 283 TAEHFWRIL 291
Cdd:cd08419  189 AAQAFLDFL 197
PRK11716 PRK11716
HTH-type transcriptional activator IlvY;
29-87 3.46e-03

HTH-type transcriptional activator IlvY;


Pssm-ID: 236961 [Multi-domain]  Cd Length: 269  Bit Score: 38.26  E-value: 3.46e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489936783  29 NLSQPAFSRRIKALESAVGVLLFDRTTSPLQLTEEG---KLFHSQTRSLLQQLECNL----DELSG 87
Cdd:PRK11716   2 HVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGeelRPFAQQTLLQWQQLRHTLdqqgPSLSG 67
PRK12684 PRK12684
CysB family HTH-type transcriptional regulator;
22-113 6.29e-03

CysB family HTH-type transcriptional regulator;


Pssm-ID: 237173 [Multi-domain]  Cd Length: 313  Bit Score: 37.65  E-value: 6.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489936783  22 SQAAEERNLSQPAFSRRIKALESAVGVLLFDRTTSPLQ-LTEEGKLFHSQTRSLLQQLEcNL----DELSGHNllgVPNI 96
Cdd:PRK12684  20 TEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRgLTEPGRIILASVERILQEVE-NLkrvgKEFAAQD---QGNL 95

                         90
                 ....*....|....*..
gi 489936783  97 KIAAAHSLSLTMLPRLV 113
Cdd:PRK12684  96 TIATTHTQARYALPAAI 112
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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