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Conserved domains on  [gi|727177890|ref|WP_033641699|]
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MULTISPECIES: LuxR family transcriptional regulator [Serratia]

Protein Classification

LuxR family transcriptional regulator( domain architecture ID 10507072)

LuxR family transcriptional regulator similar to Brucella abortus helix-turn-helix (HTH)-type quorum sensing-dependent transcriptional regulator VjbR, which mediates the effects of the quorum sensing autoinducer C12-HSL (N-dodecanoyl-homoserine lactone)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 15-153 2.47e-25

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: 97.05  E-value: 2.47e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890   15 LEAALGELG--ELLWAYVVLSKKDISCIFGVTNYPTEWVNKYQEQGLQYIDPVVITARNRLTPFAWDEQIMADSGLHFPE 92
Cdd:pfam03472   9 LARLAAALGfdHFAYGARAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAEARGAERR 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 727177890   93 LFEQAREFGVTHGYTFVLHDYNNNLVTLSFAFSAEQkaeIIPALIERKGEISVLLAS-IHES 153
Cdd:pfam03472  89 FLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGED---LDPAEAIEAAARLQLLAIyAHLR 147
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 172-227 4.40e-17

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


:

Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 72.56  E-value: 4.40e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 727177890   172 ARFTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAVRL 227
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
 
Name Accession Description Interval E-value
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 15-153 2.47e-25

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: 97.05  E-value: 2.47e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890   15 LEAALGELG--ELLWAYVVLSKKDISCIFGVTNYPTEWVNKYQEQGLQYIDPVVITARNRLTPFAWDEQIMADSGLHFPE 92
Cdd:pfam03472   9 LARLAAALGfdHFAYGARAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAEARGAERR 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 727177890   93 LFEQAREFGVTHGYTFVLHDYNNNLVTLSFAFSAEQkaeIIPALIERKGEISVLLAS-IHES 153
Cdd:pfam03472  89 FLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGED---LDPAEAIEAAARLQLLAIyAHLR 147
PRK10188 PRK10188
transcriptional regulator SdiA;
44-220 9.11e-21

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 87.53  E-value: 9.11e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890  44 TNYPTEWVNKYQEQGLQYIDPVVITARNRLTPFAWDEQIMADSglhfPELFEQAREFGVTHGYTFVLHDYNNNLVTLSFA 123
Cdd:PRK10188  61 TTYPEAWVSHYQAENYFAIDPVLKPENFSQGHLMWNDDLFSEA----QALWDAARAHGLRRGVTQCLMLPNRALGFLSFS 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890 124 FSAEQKAEIIPALIERKGEISVllasiHESYLALAPPSDKNAAALEgnARFTDRENEILYWASVGKTYQETAMILGIKTG 203
Cdd:PRK10188 137 RCSAREIPILSDELELRLQLLV-----RESLMALMRLEDEMVMTPE--MNFSKREKEILKWTAEGKTSAEIAMILSISEN 209

                        170
                 ....*....|....*..
gi 727177890 204 TIKYHMSNVVKKLGVTN 220
Cdd:PRK10188 210 TVNFHQKNMQKKFNAPN 226
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
59-234 1.30e-17

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 77.87  E-value: 1.30e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890  59 LQYIDPVVITARNRLTPFAWDEQIMADSGLHFPELFEQAREFGVTHGYTFVLHDYNNNLVTLSFAFSAEQKAEIIPALIE 138
Cdd:COG2771   13 LLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLA 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890 139 RKGEISVLLASIHESYLALAPPSDKNAAALEGNARFTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGV 218
Cdd:COG2771   93 LLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGV 172

                        170
                 ....*....|....*.
gi 727177890 219 TNARHAVRLGMELRLI 234
Cdd:COG2771  173 SSRAELVALALRLGLI 188
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 172-227 4.40e-17

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 72.56  E-value: 4.40e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 727177890   172 ARFTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAVRL 227
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 174-227 6.62e-16

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: 69.49  E-value: 6.62e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 727177890 174 FTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAVRL 227
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 174-234 1.15e-13

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: 65.68  E-value: 1.15e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 727177890 174 FTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAVRLGMELRLI 234
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
GerE pfam00196
Bacterial regulatory proteins, luxR family;
174-227 3.70e-13

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 62.22  E-value: 3.70e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 727177890  174 FTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAVRL 227
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
PRK10100 PRK10100
transcriptional regulator CsgD;
171-225 1.03e-04

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 42.17  E-value: 1.03e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 727177890 171 NARFTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAV 225
Cdd:PRK10100 153 SALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAV 207
 
Name Accession Description Interval E-value
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 15-153 2.47e-25

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: 97.05  E-value: 2.47e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890   15 LEAALGELG--ELLWAYVVLSKKDISCIFGVTNYPTEWVNKYQEQGLQYIDPVVITARNRLTPFAWDEQIMADSGLHFPE 92
Cdd:pfam03472   9 LARLAAALGfdHFAYGARAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAEARGAERR 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 727177890   93 LFEQAREFGVTHGYTFVLHDYNNNLVTLSFAFSAEQkaeIIPALIERKGEISVLLAS-IHES 153
Cdd:pfam03472  89 FLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGED---LDPAEAIEAAARLQLLAIyAHLR 147
PRK10188 PRK10188
transcriptional regulator SdiA;
44-220 9.11e-21

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 87.53  E-value: 9.11e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890  44 TNYPTEWVNKYQEQGLQYIDPVVITARNRLTPFAWDEQIMADSglhfPELFEQAREFGVTHGYTFVLHDYNNNLVTLSFA 123
Cdd:PRK10188  61 TTYPEAWVSHYQAENYFAIDPVLKPENFSQGHLMWNDDLFSEA----QALWDAARAHGLRRGVTQCLMLPNRALGFLSFS 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890 124 FSAEQKAEIIPALIERKGEISVllasiHESYLALAPPSDKNAAALEgnARFTDRENEILYWASVGKTYQETAMILGIKTG 203
Cdd:PRK10188 137 RCSAREIPILSDELELRLQLLV-----RESLMALMRLEDEMVMTPE--MNFSKREKEILKWTAEGKTSAEIAMILSISEN 209

                        170
                 ....*....|....*..
gi 727177890 204 TIKYHMSNVVKKLGVTN 220
Cdd:PRK10188 210 TVNFHQKNMQKKFNAPN 226
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
59-234 1.30e-17

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 77.87  E-value: 1.30e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890  59 LQYIDPVVITARNRLTPFAWDEQIMADSGLHFPELFEQAREFGVTHGYTFVLHDYNNNLVTLSFAFSAEQKAEIIPALIE 138
Cdd:COG2771   13 LLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLA 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890 139 RKGEISVLLASIHESYLALAPPSDKNAAALEGNARFTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGV 218
Cdd:COG2771   93 LLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGV 172

                        170
                 ....*....|....*.
gi 727177890 219 TNARHAVRLGMELRLI 234
Cdd:COG2771  173 SSRAELVALALRLGLI 188
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 172-227 4.40e-17

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 72.56  E-value: 4.40e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 727177890   172 ARFTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAVRL 227
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 174-227 6.62e-16

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: 69.49  E-value: 6.62e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 727177890 174 FTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAVRL 227
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
PRK13870 PRK13870
transcriptional regulator TraR; Provisional
 27-234 2.55e-14

transcriptional regulator TraR; Provisional


Pssm-ID: 172390 [Multi-domain]  Cd Length: 234  Bit Score: 69.64  E-value: 2.55e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890  27 WAYVVLSKKDIScifGVTNYPTEWVNKYQEQGLQYIDPVVITARNRLTPFAWD-EQIMADSGLHFPELFEQAREFGVTHG 105
Cdd:PRK13870  37 YAYLHIQHRHIT---AVTNYHREWQSVYFDKKFDALDPVVKRARSRKHIFTWSgEQERPRLSKDERAFYAHAADFGIRSG 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890 106 YTFVLHDYNNNLVTlsFAFSAEQKAeiipalIERKGEISVLLAS-----IHE--SYLALAPPSDkNAAALEgnarftDRE 178
Cdd:PRK13870 114 ITIPIKTANGSMSM--FTLASEKPV------IDLDREIDAVAAAatigqIHAriSFLRTTPTAE-DAAWLD------PKE 178

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 727177890 179 NEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAVRLGMELRLI 234
Cdd:PRK13870 179 ATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 174-234 1.15e-13

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: 65.68  E-value: 1.15e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 727177890 174 FTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAVRLGMELRLI 234
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
GerE pfam00196
Bacterial regulatory proteins, luxR family;
174-227 3.70e-13

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 62.22  E-value: 3.70e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 727177890  174 FTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAVRL 227
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 172-236 2.21e-12

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: 60.74  E-value: 2.21e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 727177890 172 ARFTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAVRLGMELRLIKP 236
Cdd:COG5905   11 SLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGLLSL 75
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
188-234 5.15e-09

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 53.94  E-value: 5.15e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 727177890 188 GKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAVRLGMELRLI 234
Cdd:COG2909  137 GLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELGLL 183
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 145-232 2.45e-06

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: 46.63  E-value: 2.45e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890 145 VLLASIHEsylALA------PPSDKNAAALEGNARFTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGV 218
Cdd:COG4566  106 ALLDAVRR---ALArdrarrAERARRAELRARLASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGA 182

                         90
                 ....*....|....
gi 727177890 219 TNARHAVRLGMELR 232
Cdd:COG4566  183 RSLAELVRLALALG 196
PRK10100 PRK10100
transcriptional regulator CsgD;
171-225 1.03e-04

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 42.17  E-value: 1.03e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 727177890 171 NARFTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLGVTNARHAV 225
Cdd:PRK10100 153 SALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAV 207
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 145-217 6.49e-04

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 39.63  E-value: 6.49e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 727177890 145 VLLASIHESylalAPPSDKNAAALegnarfTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNVVKKLG 217
Cdd:PRK10651 137 VLAASLRAN----RATTERDVNQL------TPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 175-216 2.68e-03

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 plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 35.16  E-value: 2.68e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 727177890 175 TDRENEILYWASV-GKTYQETAMILGIKTGTIKYHMSNVVKKL 216
Cdd:cd06171   12 PEREREVILLRFGeGLSYEEIAEILGISRSTVRQRLHRALKKL 54
fixJ PRK09390
response regulator FixJ; Provisional
 137-229 4.37e-03

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 37.29  E-value: 4.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 727177890 137 IERKGEISVLLASIhESYLALAPPSDKN----AAALEGNARFTDRENEILYWASVGKTYQETAMILGIKTGTIKYHMSNV 212
Cdd:PRK09390 102 IEKPFEDERLIGAI-ERALAQAPEAAKSeavaADIRARIASLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANV 180

                         90
                 ....*....|....*..
gi 727177890 213 VKKLGVTNARHAVRLGM 229
Cdd:PRK09390 181 MTKMQAGSLSELVRMAL 197
 
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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