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Conserved domains on  [gi|495778639|ref|WP_008503218|]
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MULTISPECIES: LuxR family transcriptional regulator [Enterobacter]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10677008)

helix-turn-helix (HTH) transcriptional regulator containing a LuxR family HTH DNA-binding domain; may act as a transcription activator/repressor, or have a dual role for different sites

Gene Ontology:  GO:0006355|GO:0003677|GO:0003700
PubMed:  15808743|19076237|10473770|8831795

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 168-221 2.35e-23

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


:

Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 88.74  E-value: 2.35e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 495778639   168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKL 221
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
52-228 7.92e-22

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


:

Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 89.04  E-value: 7.92e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639  52 EWFTIYLEKKYQFIDPVIIRALRCVEDFFWESDVVLSDGYNLTRIFDESVQYDIYQGQTFPLHDYLNNLVVLSVISPKHS 131
Cdd:COG2771   12 ALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639 132 GIDIEKYRPHFLRFLVQLHQKTLNLYSQHQQKKNVFLSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLG 211
Cdd:COG2771   92 ALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLG 171

                        170
                 ....*....|....*..
gi 495778639 212 VNNARHAIKLGTELRLL 228
Cdd:COG2771  172 VSSRAELVALALRLGLI 188
 
Name Accession Description Interval E-value
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 168-221 2.35e-23

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 88.74  E-value: 2.35e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 495778639   168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKL 221
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
52-228 7.92e-22

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 89.04  E-value: 7.92e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639  52 EWFTIYLEKKYQFIDPVIIRALRCVEDFFWESDVVLSDGYNLTRIFDESVQYDIYQGQTFPLHDYLNNLVVLSVISPKHS 131
Cdd:COG2771   12 ALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639 132 GIDIEKYRPHFLRFLVQLHQKTLNLYSQHQQKKNVFLSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLG 211
Cdd:COG2771   92 ALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLG 171

                        170
                 ....*....|....*..
gi 495778639 212 VNNARHAIKLGTELRLL 228
Cdd:COG2771  172 VSSRAELVALALRLGLI 188
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 168-229 1.94e-21

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 86.10  E-value: 1.94e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKLGTELRLLE 229
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLLD 131
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 168-221 1.69e-20

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 are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 81.43  E-value: 1.69e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKL 221
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
GerE pfam00196
Bacterial regulatory proteins, luxR family;
168-219 2.50e-20

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 80.71  E-value: 2.50e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 495778639  168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAI 219
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELV 54
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 14-152 6.55e-16

Autoinducer binding domain; This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 427319  Cd Length: 148  Bit Score: 72.01  E-value: 6.55e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639   14 QIQSELDAFFED--FKGIVFAYAIMNKKDPSQMRIINNSP-EWFTIYLEKKYQFIDPVIIRALRCVEDFFWESDVVLSDG 90
Cdd:pfam03472   4 ELFDALARLAAAlgFDHFAYGARAPLGLSAPDVLVLSNYPaEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAEAR 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 495778639   91 YNLTRIFDESVQYDIYQGQTFPLHDYLNNLVVLSVISPKH--SGIDIEKYRPHFLRFLVQLHQK 152
Cdd:pfam03472  84 GAERRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEdlDPAEAIEAAARLQLLAIYAHLR 147
PRK10188 PRK10188
transcriptional regulator SdiA;
51-214 6.56e-13

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 65.58  E-value: 6.56e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639  51 PEWFTIYLEKKYQFIDPVIIRALRCVEDFFWEsDVVLSDGYNLtriFDESVQYDIYQG--QTFPLHDYLNNLVVLSVISP 128
Cdd:PRK10188  65 EAWVSHYQAENYFAIDPVLKPENFSQGHLMWN-DDLFSEAQAL---WDAARAHGLRRGvtQCLMLPNRALGFLSFSRCSA 140

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639 129 KHSGIDIEKYRPHfLRFLVQLHQKTL-NLYSQHQQKKNVFLSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIM 207
Cdd:PRK10188 141 REIPILSDELELR-LQLLVRESLMALmRLEDEMVMTPEMNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQ 219


                 ....*..
gi 495778639 208 KKLGVNN 214
Cdd:PRK10188 220 KKFNAPN 226
PRK15369 PRK15369
two component system response regulator;
168-229 2.39e-10

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 58.17  E-value: 2.39e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKLGTELRLLE 229
Cdd:PRK15369 150 LTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLGLIE 211
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 168-210 2.99e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.94  E-value: 2.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 495778639  168 LSPRERQI--LKWVsAGKTYAEISVILSIAERTVKFHMGNIMKKL 210
Cdd:TIGR02937 111 LPEREREVlvLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 168-221 2.35e-23

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 88.74  E-value: 2.35e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 495778639   168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKL 221
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
52-228 7.92e-22

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 89.04  E-value: 7.92e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639  52 EWFTIYLEKKYQFIDPVIIRALRCVEDFFWESDVVLSDGYNLTRIFDESVQYDIYQGQTFPLHDYLNNLVVLSVISPKHS 131
Cdd:COG2771   12 ALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639 132 GIDIEKYRPHFLRFLVQLHQKTLNLYSQHQQKKNVFLSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLG 211
Cdd:COG2771   92 ALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLG 171

                        170
                 ....*....|....*..
gi 495778639 212 VNNARHAIKLGTELRLL 228
Cdd:COG2771  172 VSSRAELVALALRLGLI 188
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 168-229 1.94e-21

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 86.10  E-value: 1.94e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKLGTELRLLE 229
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLLD 131
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 168-221 1.69e-20

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 are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 81.43  E-value: 1.69e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKL 221
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
GerE pfam00196
Bacterial regulatory proteins, luxR family;
168-219 2.50e-20

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 80.71  E-value: 2.50e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 495778639  168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAI 219
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELV 54
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 168-229 1.16e-19

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 79.62  E-value: 1.16e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKLGTELRLLE 229
Cdd:COG5905   13 LTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGLLS 74
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 14-152 6.55e-16

Autoinducer binding domain; This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 427319  Cd Length: 148  Bit Score: 72.01  E-value: 6.55e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639   14 QIQSELDAFFED--FKGIVFAYAIMNKKDPSQMRIINNSP-EWFTIYLEKKYQFIDPVIIRALRCVEDFFWESDVVLSDG 90
Cdd:pfam03472   4 ELFDALARLAAAlgFDHFAYGARAPLGLSAPDVLVLSNYPaEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAEAR 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 495778639   91 YNLTRIFDESVQYDIYQGQTFPLHDYLNNLVVLSVISPKH--SGIDIEKYRPHFLRFLVQLHQK 152
Cdd:pfam03472  84 GAERRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEdlDPAEAIEAAARLQLLAIYAHLR 147
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 168-222 4.31e-15

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 70.90  E-value: 4.31e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNA----RHAIKLG 222
Cdd:COG4566  138 LTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLaelvRLALALG 196
PRK10188 PRK10188
transcriptional regulator SdiA;
51-214 6.56e-13

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 65.58  E-value: 6.56e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639  51 PEWFTIYLEKKYQFIDPVIIRALRCVEDFFWEsDVVLSDGYNLtriFDESVQYDIYQG--QTFPLHDYLNNLVVLSVISP 128
Cdd:PRK10188  65 EAWVSHYQAENYFAIDPVLKPENFSQGHLMWN-DDLFSEAQAL---WDAARAHGLRRGvtQCLMLPNRALGFLSFSRCSA 140

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639 129 KHSGIDIEKYRPHfLRFLVQLHQKTL-NLYSQHQQKKNVFLSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIM 207
Cdd:PRK10188 141 REIPILSDELELR-LQLLVRESLMALmRLEDEMVMTPEMNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQ 219


                 ....*..
gi 495778639 208 KKLGVNN 214
Cdd:PRK10188 220 KKFNAPN 226
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
178-229 1.21e-12

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 63.95  E-value: 1.21e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 495778639 178 WVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKLGTELRLLE 229
Cdd:COG2909  133 LLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELGLLA 184
PRK13870 PRK13870
transcriptional regulator TraR; Provisional
 33-228 4.22e-11

transcriptional regulator TraR; Provisional


Pssm-ID: 172390 [Multi-domain]  Cd Length: 234  Bit Score: 60.78  E-value: 4.22e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639  33 YAIMNKKDPSQMRIINNSPEWFTIYLEKKYQFIDPVIIRALRCVEDFFWESDvvlSDGYNLTR----IFDESVQYDIYQG 108
Cdd:PRK13870  37 YAYLHIQHRHITAVTNYHREWQSVYFDKKFDALDPVVKRARSRKHIFTWSGE---QERPRLSKderaFYAHAADFGIRSG 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639 109 QTFPLHDYLNNLVVLSVISPKhSGIDIEKYRPHFLR--FLVQLHQKTLNLYSQHQQKKNVFLSPRERQILKWVSAGKTYA 186
Cdd:PRK13870 114 ITIPIKTANGSMSMFTLASEK-PVIDLDREIDAVAAaaTIGQIHARISFLRTTPTAEDAAWLDPKEATYLRWIAVGKTME 192

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 495778639 187 EISVILSIAERTVKFHMGNIMKKLGVNNARHAIKLGTELRLL 228
Cdd:PRK13870 193 EIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
PRK15369 PRK15369
two component system response regulator;
168-229 2.39e-10

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 58.17  E-value: 2.39e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKLGTELRLLE 229
Cdd:PRK15369 150 LTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLGLIE 211
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 127-213 8.68e-08

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 50.90  E-value: 8.68e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639 127 SPKHSGIDIEKYRPHFLRFLVQL----HQKTLNLYSQHQQKKNVFLSPRERQILKWVSAGKTYAEISVILSIAERTVKFH 202
Cdd:PRK11475  90 SPLDGVLSKASTLEILQQELFLSlngvRQATDRLNNQWYINQSRMLSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAH 169

                         90
                 ....*....|.
gi 495778639 203 MGNIMKKLGVN 213
Cdd:PRK11475 170 KFNVMSKLGVS 180
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 168-211 3.27e-07

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 49.26  E-value: 3.27e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLG 211
Cdd:PRK10651 156 LTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199
fixJ PRK09390
response regulator FixJ; Provisional
 168-221 3.32e-06

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 46.15  E-value: 3.32e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKL 221
Cdd:PRK09390 142 LSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVRM 195
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 168-210 1.21e-05

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 41.67  E-value: 1.21e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 495778639  168 LSPRERQILKWVSA-GKTYAEISVILSIAERTVKFHMGNIMKKL 210
Cdd:pfam08281  11 LPPRQREVFLLRYLeGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK10100 PRK10100
transcriptional regulator CsgD;
164-219 3.02e-05

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 43.71  E-value: 3.02e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 495778639 164 KNVFLSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAI 219
Cdd:PRK10100 152 ESALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAV 207
PRK10360 PRK10360
transcriptional regulator UhpA;
168-214 3.37e-05

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 43.43  E-value: 3.37e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNN 214
Cdd:PRK10360 138 LTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSN 184
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
168-212 3.05e-04

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 40.61  E-value: 3.05e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGV 212
Cdd:PRK10403 154 LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 168-210 3.54e-04

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 39.98  E-value: 3.54e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 495778639 168 LSPRERQILKWVS-AGKTYAEISVILSIAERTVKFHMGNIMKKL 210
Cdd:COG1595  128 LPPRQREVLVLRYlEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
PRK15201 PRK15201
fimbriae biosynthesis transcriptional regulator FimW;
168-220 5.16e-04

fimbriae biosynthesis transcriptional regulator FimW;


Pssm-ID: 185123  Cd Length: 198  Bit Score: 39.64  E-value: 5.16e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 495778639 168 LSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIK 220
Cdd:PRK15201 134 FSVTERHLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTEQQFLK 186
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 168-210 5.25e-04

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 37.02  E-value: 5.25e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 495778639  168 LSPRERQILKWV-SAGKTYAEISVILSIAERTVKFHMGNIMKKL 210
Cdd:pfam04545   5 LPPRERQVLVLRyGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
141-225 1.58e-03

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 39.16  E-value: 1.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639 141 HFLRFLVQLH----------QKTLNLYSQHQQKKNVF-----------------------LSPRERQILKWVSAGKTYAE 187
Cdd:PRK04841 779 QQLRQLIQLNtlpeleqhraQRILREINQHHRHKFAHfdeafvekllnhpdvpelirtspLTQREWQVLGLIYSGYSNEQ 858

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 495778639 188 ISVILSIAERTVKFHMGNIMKKLGVNNARHAIKLGTEL 225
Cdd:PRK04841 859 IAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHAQDL 896
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
152-228 2.39e-03

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 37.93  E-value: 2.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639 152 KTLNLYSQHQQKKN----VFLSPRERQILKWVSAGKTYAEISVILSIAERTVKFHMGNIMKKLGVNNARHAIKLGTELRL 227
Cdd:PRK09935 130 ETLNYIKSNKCSTNsstdTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAKLHEL 209


                 .
gi 495778639 228 L 228
Cdd:PRK09935 210 L 210
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 168-210 2.99e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.94  E-value: 2.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 495778639  168 LSPRERQI--LKWVsAGKTYAEISVILSIAERTVKFHMGNIMKKL 210
Cdd:TIGR02937 111 LPEREREVlvLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKL 154
PRK08624 PRK08624
hypothetical protein; Provisional
 105-212 9.42e-03

hypothetical protein; Provisional


Pssm-ID: 236314 [Multi-domain]  Cd Length: 373  Bit Score: 36.45  E-value: 9.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495778639 105 IYQGQTFPLHDYLNNLVVLSVISPKHSGIDIEKYRPHFLRFLVQLHQKTLNLYSQHQ------QKKNVFLSPRERQILKw 178
Cdd:PRK08624 180 ISQRIIIPHRDESGELIGIRGRLLDKELVDKNKYFPIYVNDTGYNHPKGKILYGLWQnkkyikEKKKVIIVESEKSVLF- 258

                         90       100       110
                 ....*....|....*....|....*....|....
gi 495778639 179 vsAGKTYAEISVILSIAERTVKFHMGNIMKKLGV 212
Cdd:PRK08624 259 --SDKFYGEGNFVVAICGSNISEVQAEKLLRLGV 290
 
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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