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Conserved domains on  [gi|495256283|ref|WP_007981038|]
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autoinducer binding domain-containing protein [Pseudomonas sp. GM33]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 12044921)

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
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 177-237 1.15e-20

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: 84.17  E-value: 1.15e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495256283 177 LSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAANRSGAI 237
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 17-158 1.19e-15

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: 71.24  E-value: 1.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495256283   17 DINTAYRISLNFVRNLGYKFCAFSTISTNSRTDCCPVNLNNYPHDWNTQYEQSNASEIDPVAAYCNHSMLPVLWSKELFC 96
Cdd:pfam03472   1 SEEELFDALARLAAALGFDHFAYGARAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFA 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495256283   97 ATPWLWQLLQQQGLAH----GWSQAIHDeESGLRSILSLARSHCPISAYELYENLGFSVFISRHLH 158
Cdd:pfam03472  81 EARGAERRFLDEARDFglrdGYTVPVHG-PGGRLGALSFAGPGEDLDPAEAIEAAARLQLLAIYAH 145
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 177-237 1.15e-20

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: 84.17  E-value: 1.15e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495256283 177 LSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAANRSGAI 237
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 174-231 1.40e-19

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 79.11  E-value: 1.40e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 495256283   174 APSLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAA 231
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 177-233 7.23e-18

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: 74.49  E-value: 7.23e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495256283 177 LSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAANR 233
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
176-231 1.87e-16

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 71.08  E-value: 1.87e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 495256283  176 SLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAA 231
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 17-158 1.19e-15

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: 71.24  E-value: 1.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495256283   17 DINTAYRISLNFVRNLGYKFCAFSTISTNSRTDCCPVNLNNYPHDWNTQYEQSNASEIDPVAAYCNHSMLPVLWSKELFC 96
Cdd:pfam03472   1 SEEELFDALARLAAALGFDHFAYGARAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFA 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495256283   97 ATPWLWQLLQQQGLAH----GWSQAIHDeESGLRSILSLARSHCPISAYELYENLGFSVFISRHLH 158
Cdd:pfam03472  81 EARGAERRFLDEARDFglrdGYTVPVHG-PGGRLGALSFAGPGEDLDPAEAIEAAARLQLLAIYAH 145
PRK10188 PRK10188
transcriptional regulator SdiA;
57-237 2.00e-15

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 72.90  E-value: 2.00e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495256283  57 NYPHDWNTQYEQSNASEIDPVAAYCNHSMLPVLWSKELFCATPWLWQLLQQQGLAHGWSQAIH--DEESGLRSILSLARS 134
Cdd:PRK10188  62 TYPEAWVSHYQAENYFAIDPVLKPENFSQGHLMWNDDLFSEAQALWDAARAHGLRRGVTQCLMlpNRALGFLSFSRCSAR 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495256283 135 HCPISAYELyeNLGFSVFISRHLHALA-----IGMQPKKpvctnapSLSRREIEVLKLSADGKTAYEIARILNLSERTIN 209
Cdd:PRK10188 142 EIPILSDEL--ELRLQLLVRESLMALMrledeMVMTPEM-------NFSKREKEILKWTAEGKTSAEIAMILSISENTVN 212

                        170       180
                 ....*....|....*....|....*...
gi 495256283 210 FHVHRAIEKLGVNNKMAAVMAANRSGAI 237
Cdd:PRK10188 213 FHQKNMQKKFNAPNKTQIACYAAATGLI 240
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 158-236 1.34e-06

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 47.72  E-value: 1.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495256283 158 HALAIGM-QPKKPVCTNAPSLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKM-AAVMAANRSG 235
Cdd:PRK10651 136 PVLAASLrANRATTERDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVeAAVWVHQERI 215


                 .
gi 495256283 236 A 236
Cdd:PRK10651 216 F 216
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 176-219 8.90e-06

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: 44.26  E-value: 8.90e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 495256283  176 SLSRREIEVLKLSA-DGKTAYEIARILNLSERTINFHVHRAIEKL 219
Cdd:TIGR02937 110 KLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
transpos_IS630 NF033545
IS630 family transposase;
180-217 6.10e-03

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 37.23  E-value: 6.10e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 495256283 180 REIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIE 217
Cdd:NF033545   1 RRARILLLAAEGLSITEIAERLGVSRSTVYRWLKRFNE 38
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 177-237 1.15e-20

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: 84.17  E-value: 1.15e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495256283 177 LSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAANRSGAI 237
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 174-231 1.40e-19

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 79.11  E-value: 1.40e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 495256283   174 APSLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAA 231
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 175-237 3.05e-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: 78.85  E-value: 3.05e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495256283 175 PSLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAANRSGAI 237
Cdd:COG5905   11 SLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGLL 73
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
156-237 7.90e-19

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 80.96  E-value: 7.90e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495256283 156 HLHALAIGMQPKKPVCTNAPSLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAANRSG 235
Cdd:COG2771  107 ALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALALRLG 186


                 ..
gi 495256283 236 AI 237
Cdd:COG2771  187 LI 188
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 177-233 7.23e-18

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: 74.49  E-value: 7.23e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495256283 177 LSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAANR 233
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
176-231 1.87e-16

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 71.08  E-value: 1.87e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 495256283  176 SLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAA 231
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
Autoind_bind pfam03472
Autoinducer binding domain; This domain is found a a large family of transcriptional ...
 17-158 1.19e-15

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: 71.24  E-value: 1.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495256283   17 DINTAYRISLNFVRNLGYKFCAFSTISTNSRTDCCPVNLNNYPHDWNTQYEQSNASEIDPVAAYCNHSMLPVLWSKELFC 96
Cdd:pfam03472   1 SEEELFDALARLAAALGFDHFAYGARAPLGLSAPDVLVLSNYPAEWLDRYDEANYFAIDPVVRHARRSSSPFSWSDVLFA 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495256283   97 ATPWLWQLLQQQGLAH----GWSQAIHDeESGLRSILSLARSHCPISAYELYENLGFSVFISRHLH 158
Cdd:pfam03472  81 EARGAERRFLDEARDFglrdGYTVPVHG-PGGRLGALSFAGPGEDLDPAEAIEAAARLQLLAIYAH 145
PRK10188 PRK10188
transcriptional regulator SdiA;
57-237 2.00e-15

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 72.90  E-value: 2.00e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495256283  57 NYPHDWNTQYEQSNASEIDPVAAYCNHSMLPVLWSKELFCATPWLWQLLQQQGLAHGWSQAIH--DEESGLRSILSLARS 134
Cdd:PRK10188  62 TYPEAWVSHYQAENYFAIDPVLKPENFSQGHLMWNDDLFSEAQALWDAARAHGLRRGVTQCLMlpNRALGFLSFSRCSAR 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495256283 135 HCPISAYELyeNLGFSVFISRHLHALA-----IGMQPKKpvctnapSLSRREIEVLKLSADGKTAYEIARILNLSERTIN 209
Cdd:PRK10188 142 EIPILSDEL--ELRLQLLVRESLMALMrledeMVMTPEM-------NFSKREKEILKWTAEGKTSAEIAMILSISENTVN 212

                        170       180
                 ....*....|....*....|....*...
gi 495256283 210 FHVHRAIEKLGVNNKMAAVMAANRSGAI 237
Cdd:PRK10188 213 FHQKNMQKKFNAPNKTQIACYAAATGLI 240
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 176-223 5.91e-11

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: 59.73  E-value: 5.91e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 495256283 176 SLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNN 223
Cdd:COG4566  137 SLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARS 184
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
187-237 9.33e-11

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 58.95  E-value: 9.33e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495256283 187 LSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAANRSGAI 237
Cdd:COG2909  133 LLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELGLL 183
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 158-236 1.34e-06

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 47.72  E-value: 1.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495256283 158 HALAIGM-QPKKPVCTNAPSLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKM-AAVMAANRSG 235
Cdd:PRK10651 136 PVLAASLrANRATTERDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVeAAVWVHQERI 215


                 .
gi 495256283 236 A 236
Cdd:PRK10651 216 F 216
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 176-226 1.89e-06

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 47.14  E-value: 1.89e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495256283 176 SLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMA 226
Cdd:PRK10840 150 RLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIA 200
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 176-219 3.13e-06

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: 43.21  E-value: 3.13e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 495256283  176 SLSRREIEVLKLSA-DGKTAYEIARILNLSERTINFHVHRAIEKL 219
Cdd:pfam08281  10 ELPPRQREVFLLRYlEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 176-219 8.90e-06

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: 44.26  E-value: 8.90e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 495256283  176 SLSRREIEVLKLSA-DGKTAYEIARILNLSERTINFHVHRAIEKL 219
Cdd:TIGR02937 110 KLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
PRK10360 PRK10360
transcriptional regulator UhpA;
168-223 1.92e-05

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 44.20  E-value: 1.92e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 495256283 168 KPVCTNAPSLSRREIEVLKLSADGKTAYEIARILNLSERTInfHVHRA--IEKLGVNN 223
Cdd:PRK10360 129 KLASGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTV--HVHRAnlMEKLGVSN 184
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
177-227 1.99e-05

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 44.07  E-value: 1.99e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495256283 177 LSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAA 227
Cdd:PRK10403 154 LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAA 204
PRK10100 PRK10100
transcriptional regulator CsgD;
171-232 9.63e-05

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 42.17  E-value: 9.63e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495256283 171 CTNAPsLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNNKMAAVMAAN 232
Cdd:PRK10100 151 TESAL-LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWAN 211
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 176-219 9.70e-05

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: 39.01  E-value: 9.70e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 495256283 176 SLSRREIEVLKLS-ADGKTAYEIARILNLSERTINFHVHRAIEKL 219
Cdd:cd06171   10 KLPEREREVILLRfGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 176-219 1.06e-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: 41.52  E-value: 1.06e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 495256283 176 SLSRREIEVLKLSA-DGKTAYEIARILNLSERTINFHVHRAIEKL 219
Cdd:COG1595  127 RLPPRQREVLVLRYlEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
PRK09483 PRK09483
response regulator; Provisional
 176-223 1.97e-04

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 41.24  E-value: 1.97e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 495256283 176 SLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNN 223
Cdd:PRK09483 148 SLSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISG 195
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 176-219 2.30e-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: 37.79  E-value: 2.30e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 495256283  176 SLSRREIEVLKLS-ADGKTAYEIARILNLSERTINFHVHRAIEKL 219
Cdd:pfam04545   4 SLPPRERQVLVLRyGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
HTH_23 pfam13384
Homeodomain-like domain;
179-208 3.35e-04

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 37.63  E-value: 3.35e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 495256283  179 RREIEVLKLSADGKTAYEIARILNLSERTI 208
Cdd:pfam13384   5 RRRARALLLLAEGLSVKEIAELLGVSRRTV 34
PRK15369 PRK15369
two component system response regulator;
172-223 7.64e-04

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 39.29  E-value: 7.64e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 495256283 172 TNAPSLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNN 223
Cdd:PRK15369 145 TNPPLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHK 196
InsA COG3677
Transposase InsA [Mobilome: prophages, transposons];
182-219 2.11e-03

Transposase InsA [Mobilome: prophages, transposons];


Pssm-ID: 442893 [Multi-domain]  Cd Length: 241  Bit Score: 38.31  E-value: 2.11e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 495256283 182 IEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKL 219
Cdd:COG3677   66 LQAIRLLLNGISLRQIARVLGVSYKTVWRWLHRIREAL 103
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 179-214 2.19e-03

Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.


Pssm-ID: 433591 [Multi-domain]  Cd Length: 44  Bit Score: 35.18  E-value: 2.19e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 495256283  179 RREIEVLKlsADGKTAYEIARILNLSERTINFHVHR 214
Cdd:pfam13936  10 REEIARLL--AEGLSLREIARRLGRSPSTISRELRR 43
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
148-223 2.77e-03

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 37.93  E-value: 2.77e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495256283 148 GFSVFISRHLHALAiGMQPKKPVCTNAPsLSRREIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIEKLGVNN 223
Cdd:PRK09935 123 GYTFFPSETLNYIK-SNKCSTNSSTDTV-LSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHS 196
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 172-217 5.22e-03

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 37.52  E-value: 5.22e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 495256283 172 TNAPSLSRReIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIE 217
Cdd:COG3415   20 TKDAREARR-LRAVLLLAEGLSVREIAERLGVSRSTVYRWLKRYRE 64
fixJ PRK09390
response regulator FixJ; Provisional
 176-237 5.43e-03

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 36.90  E-value: 5.43e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 495256283 176 SLSRREIEVLKLSADGKTAYEIARILNLSERTInfHVHRA--IEKLGVNNKMAAVMAANRSGAI 237
Cdd:PRK09390 141 SLSERERQVMDGLVAGLSNKVIARDLDISPRTV--EVYRAnvMTKMQAGSLSELVRMALRAGRG 202
transpos_IS630 NF033545
IS630 family transposase;
180-217 6.10e-03

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 37.23  E-value: 6.10e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 495256283 180 REIEVLKLSADGKTAYEIARILNLSERTINFHVHRAIE 217
Cdd:NF033545   1 RRARILLLAAEGLSITEIAERLGVSRSTVYRWLKRFNE 38
COG1356 COG1356
Transcriptional regulator [Transcription];
177-218 6.86e-03

Transcriptional regulator [Transcription];


Pssm-ID: 440967 [Multi-domain]  Cd Length: 139  Bit Score: 35.98  E-value: 6.86e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 495256283 177 LSRREIEVLKLSADGKTAYEIARILNLSERTINfhvhrAIEK 218
Cdd:COG1356    9 LTRRQAEVLALRERGLTQQEIADILGTSRANVS-----SIEK 45
 
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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