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Conserved domains on  [gi|503085115|ref|WP_013319981|]
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LuxR family transcriptional regulator [Dickeya dadantii]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10507063)

helix-turn-helix (HTH) transcriptional regulator containing an N-terminal an autoinducer binding domain and a LuxR family HTH DNA-binding domain; may act as an activator or repressor in response to an inducer

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
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 14-158 9.72e-38

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: 129.41  E-value: 9.72e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503085115   14 TIQSYLNRKLKSYGDPKYAY--LIMNKKKPTDVVIISNYPTEWVDIYRNNNYQHIDPVILTAINKISPFSWDDDLVISSK 91
Cdd:pfam03472   4 ELFDALARLAAALGFDHFAYgaRAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAEAR 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503085115   92 LKFSRIFNLSKDYDIVNGYTFVLHDPGNNLAALSFMIEEHRSEELEEIIqnNKDKLQMLLISAHEKL 158
Cdd:pfam03472  84 GAERRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEDLDPAEAIE--AAARLQLLAIYAHLRL 148
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
147-240 5.53e-19

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


:

Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 81.73  E-value: 5.53e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503085115 147 LQMLLISAHEKLTSLYREMSRNRNNSKSQEADLFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLN 226
Cdd:COG2771   95 AALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSS 174

                         90
                 ....*....|....
gi 503085115 227 AKHAIRLGVEMNLI 240
Cdd:COG2771  175 RAELVALALRLGLI 188
 
Name Accession Description Interval E-value
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 14-158 9.72e-38

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: 129.41  E-value: 9.72e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503085115   14 TIQSYLNRKLKSYGDPKYAY--LIMNKKKPTDVVIISNYPTEWVDIYRNNNYQHIDPVILTAINKISPFSWDDDLVISSK 91
Cdd:pfam03472   4 ELFDALARLAAALGFDHFAYgaRAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAEAR 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503085115   92 LKFSRIFNLSKDYDIVNGYTFVLHDPGNNLAALSFMIEEHRSEELEEIIqnNKDKLQMLLISAHEKL 158
Cdd:pfam03472  84 GAERRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEDLDPAEAIE--AAARLQLLAIYAHLRL 148
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
147-240 5.53e-19

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 81.73  E-value: 5.53e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503085115 147 LQMLLISAHEKLTSLYREMSRNRNNSKSQEADLFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLN 226
Cdd:COG2771   95 AALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSS 174

                         90
                 ....*....|....
gi 503085115 227 AKHAIRLGVEMNLI 240
Cdd:COG2771  175 RAELVALALRLGLI 188
PRK10188 PRK10188
transcriptional regulator SdiA;
44-226 6.03e-19

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 82.91  E-value: 6.03e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503085115  44 VVIISNYPTEWVDIYRNNNYQHIDPVILTAINKISPFSWDDDLVISSKlkfsRIFNLSKDYDIVNGYTFVLHDPGNnlaA 123
Cdd:PRK10188  57 VAFYTTYPEAWVSHYQAENYFAIDPVLKPENFSQGHLMWNDDLFSEAQ----ALWDAARAHGLRRGVTQCLMLPNR---A 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503085115 124 LSFMIEEHRSEELEEIIQNNKD-KLQMLlisAHEKLTSLYR---------EMSrnrnnsksqeadlFSQRENEILHWASM 193
Cdd:PRK10188 130 LGFLSFSRCSAREIPILSDELElRLQLL---VRESLMALMRledemvmtpEMN-------------FSKREKEILKWTAE 193

                        170       180       190
                 ....*....|....*....|....*....|...
gi 503085115 194 GKTYQEIALILGITTSTVKFHIGNVVKKLGVLN 226
Cdd:PRK10188 194 GKTSAEIAMILSISENTVNFHQKNMQKKFNAPN 226
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 177-233 1.22e-18

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 76.80  E-value: 1.22e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 503085115   177 ADLFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAIRL 233
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 180-236 1.25e-14

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: 66.40  E-value: 1.25e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 503085115 180 FSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAIRLGVE 236
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
178-233 7.91e-13

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 61.45  E-value: 7.91e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 503085115  178 DLFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAIRL 233
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 169-223 2.92e-06

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 46.95  E-value: 2.92e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 503085115 169 RNNSKSQEADL--FSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLG 223
Cdd:PRK10651 143 RANRATTERDVnqLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 178-222 1.43e-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: 38.10  E-value: 1.43e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 503085115  178 DLFSQRENEIL-HWASMGKTYQEIALILGITTSTVKFHIGNVVKKL 222
Cdd:TIGR02937 109 EKLPEREREVLvLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 14-158 9.72e-38

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: 129.41  E-value: 9.72e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503085115   14 TIQSYLNRKLKSYGDPKYAY--LIMNKKKPTDVVIISNYPTEWVDIYRNNNYQHIDPVILTAINKISPFSWDDDLVISSK 91
Cdd:pfam03472   4 ELFDALARLAAALGFDHFAYgaRAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFAEAR 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503085115   92 LKFSRIFNLSKDYDIVNGYTFVLHDPGNNLAALSFMIEEHRSEELEEIIqnNKDKLQMLLISAHEKL 158
Cdd:pfam03472  84 GAERRFLDEARDFGLRDGYTVPVHGPGGRLGALSFAGPGEDLDPAEAIE--AAARLQLLAIYAHLRL 148
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
147-240 5.53e-19

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 81.73  E-value: 5.53e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503085115 147 LQMLLISAHEKLTSLYREMSRNRNNSKSQEADLFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLN 226
Cdd:COG2771   95 AALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSS 174

                         90
                 ....*....|....
gi 503085115 227 AKHAIRLGVEMNLI 240
Cdd:COG2771  175 RAELVALALRLGLI 188
PRK10188 PRK10188
transcriptional regulator SdiA;
44-226 6.03e-19

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 82.91  E-value: 6.03e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503085115  44 VVIISNYPTEWVDIYRNNNYQHIDPVILTAINKISPFSWDDDLVISSKlkfsRIFNLSKDYDIVNGYTFVLHDPGNnlaA 123
Cdd:PRK10188  57 VAFYTTYPEAWVSHYQAENYFAIDPVLKPENFSQGHLMWNDDLFSEAQ----ALWDAARAHGLRRGVTQCLMLPNR---A 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503085115 124 LSFMIEEHRSEELEEIIQNNKD-KLQMLlisAHEKLTSLYR---------EMSrnrnnsksqeadlFSQRENEILHWASM 193
Cdd:PRK10188 130 LGFLSFSRCSAREIPILSDELElRLQLL---VRESLMALMRledemvmtpEMN-------------FSKREKEILKWTAE 193

                        170       180       190
                 ....*....|....*....|....*....|...
gi 503085115 194 GKTYQEIALILGITTSTVKFHIGNVVKKLGVLN 226
Cdd:PRK10188 194 GKTSAEIAMILSISENTVNFHQKNMQKKFNAPN 226
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 177-233 1.22e-18

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 76.80  E-value: 1.22e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 503085115   177 ADLFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAIRL 233
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 179-240 1.00e-17

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: 76.85  E-value: 1.00e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503085115 179 LFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAIRLGVEMNLI 240
Cdd:COG2197   69 LLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 172-242 2.03e-16

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: 71.53  E-value: 2.03e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503085115 172 SKSQEADLFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAIRLGVEMNLIKP 242
Cdd:COG5905    5 SSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGLLSL 75
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 180-236 1.25e-14

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: 66.40  E-value: 1.25e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 503085115 180 FSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAIRLGVE 236
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
178-233 7.91e-13

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 61.45  E-value: 7.91e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 503085115  178 DLFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAIRL 233
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
189-240 1.80e-10

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 58.18  E-value: 1.80e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 503085115 189 HWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAIRLGVEMNLI 240
Cdd:COG2909  132 RLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELGLL 183
PRK13870 PRK13870
transcriptional regulator TraR; Provisional
 26-240 2.26e-10

transcriptional regulator TraR; Provisional


Pssm-ID: 172390 [Multi-domain]  Cd Length: 234  Bit Score: 58.85  E-value: 2.26e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503085115  26 YGDPKYAYLIMNKKKPTDVviiSNYPTEWVDIYRNNNYQHIDPVILTAINKISPFSWDDDLVISSKLKFSRIF-NLSKDY 104
Cdd:PRK13870  32 FGFTGYAYLHIQHRHITAV---TNYHREWQSVYFDKKFDALDPVVKRARSRKHIFTWSGEQERPRLSKDERAFyAHAADF 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503085115 105 DIVNGYTFVLHDPGNNLAALSFmieehrsEELEEIIQNNKdklQMLLISAHEKLTSLYREMSRNRNNSKSQEADLFSQRE 184
Cdd:PRK13870 109 GIRSGITIPIKTANGSMSMFTL-------ASEKPVIDLDR---EIDAVAAAATIGQIHARISFLRTTPTAEDAAWLDPKE 178

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 503085115 185 NEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAIRLGVEMNLI 240
Cdd:PRK13870 179 ATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 181-233 1.38e-07

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: 50.48  E-value: 1.38e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 503085115 181 SQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAIRL 233
Cdd:COG4566  139 TPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRL 191
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 169-223 2.92e-06

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 46.95  E-value: 2.92e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 503085115 169 RNNSKSQEADL--FSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLG 223
Cdd:PRK10651 143 RANRATTERDVnqLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199
PRK10100 PRK10100
transcriptional regulator CsgD;
174-231 2.74e-05

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 44.09  E-value: 2.74e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 503085115 174 SQEADLFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNAKHAI 231
Cdd:PRK10100 150 STESALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAV 207
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
163-224 6.70e-05

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 42.92  E-value: 6.70e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503085115 163 REMSRNRNNSKSQEA--DLFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGV 224
Cdd:PRK10403 135 NQYLREREMFGAEEDpfSVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 194-222 5.85e-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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 37.05  E-value: 5.85e-04
                          10        20
                  ....*....|....*....|....*....
gi 503085115  194 GKTYQEIALILGITTSTVKFHIGNVVKKL 222
Cdd:pfam08281  26 GLSYAEIAELLGISEGTVKSRLSRARKKL 54
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 178-222 1.43e-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: 38.10  E-value: 1.43e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 503085115  178 DLFSQRENEIL-HWASMGKTYQEIALILGITTSTVKFHIGNVVKKL 222
Cdd:TIGR02937 109 EKLPEREREVLvLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 183-212 1.84e-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: 35.54  E-value: 1.84e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 503085115 183 RENEILHWAS-MGKTYQEIALILGITTSTVK 212
Cdd:cd06171   14 REREVILLRFgEGLSYEEIAEILGISRSTVR 44
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 194-222 2.02e-03

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 37.93  E-value: 2.02e-03
                          10        20
                  ....*....|....*....|....*....
gi 503085115  194 GKTYQEIALILGITTSTVKFHIGNVVKKL 222
Cdd:TIGR02985 129 GLSNKEIAEELGISVKTVEYHITKALKFL 157
PRK10360 PRK10360
transcriptional regulator UhpA;
178-226 3.42e-03

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 37.65  E-value: 3.42e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 503085115 178 DLFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLN 226
Cdd:PRK10360 136 DPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSN 184
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 194-222 7.13e-03

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: 36.51  E-value: 7.13e-03
                         10        20
                 ....*....|....*....|....*....
gi 503085115 194 GKTYQEIALILGITTSTVKFHIGNVVKKL 222
Cdd:COG1595  143 GLSYAEIAEILGISEGTVKSRLSRARKKL 171
PRK15369 PRK15369
two component system response regulator;
179-235 9.33e-03

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 36.21  E-value: 9.33e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503085115 179 LFSQRENEILHWASMGKTYQEIALILGITTSTVKFHIGNVVKKLGVLNA----KHAIRLGV 235
Cdd:PRK15369 149 LLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVaellNWARRLGL 209
 
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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