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Conserved domains on  [gi|16129898|ref|NP_416461|]
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DNA-binding transcriptional activator RcsA [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 11487779)

helix-turn-helix (HTH) transcriptional regulator similar to MalT, which positively regulates the transcription of the maltose regulon, and transcriptional regulatory protein RcsA, which is involved in regulating K30 capsular polysaccharide synthesis

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rcsA PRK15411
transcriptional regulator RcsA;
1-207 1.99e-144

transcriptional regulator RcsA;


:

Pssm-ID: 185309 [Multi-domain]  Cd Length: 207  Bit Score: 400.28  E-value: 1.99e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129898    1 MSTIIMDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIACDSQRPSVVFINEDCFIHDASNSQRIKLIINQHPNTLF 80
Cdd:PRK15411   1 MSTIIMDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIACDSLRPSVVFINEDCFIHDASNSQRIKQIINQHPNTLF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129898   81 IVFMAIANVHFDEYLLVRKNLLISSKSIKPESLDDILGDILKKETTITSFLNMPTLSLSRTESSMLRMWMAGQGTIQISD 160
Cdd:PRK15411  81 IVFMAIANIHFDEYLLVRKNLLISSKSIKPESLDDLLGDILKKETTITSFLNLPTLSLSRTESSMLRMWMAGQGTIQISD 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 16129898  161 QMNIKAKTVSSHKGNIKRKIKTHNKQVIYHVVRLTDNVTNGIFVNMR 207
Cdd:PRK15411 161 QMNIKAKTVSSHKGNIKRKIKTHNKQVIYHVVRLTDNVTNGIFVNMR 207
 
Name Accession Description Interval E-value
rcsA PRK15411
transcriptional regulator RcsA;
1-207 1.99e-144

transcriptional regulator RcsA;


Pssm-ID: 185309 [Multi-domain]  Cd Length: 207  Bit Score: 400.28  E-value: 1.99e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129898    1 MSTIIMDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIACDSQRPSVVFINEDCFIHDASNSQRIKLIINQHPNTLF 80
Cdd:PRK15411   1 MSTIIMDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIACDSLRPSVVFINEDCFIHDASNSQRIKQIINQHPNTLF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129898   81 IVFMAIANVHFDEYLLVRKNLLISSKSIKPESLDDILGDILKKETTITSFLNMPTLSLSRTESSMLRMWMAGQGTIQISD 160
Cdd:PRK15411  81 IVFMAIANIHFDEYLLVRKNLLISSKSIKPESLDDLLGDILKKETTITSFLNLPTLSLSRTESSMLRMWMAGQGTIQISD 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 16129898  161 QMNIKAKTVSSHKGNIKRKIKTHNKQVIYHVVRLTDNVTNGIFVNMR 207
Cdd:PRK15411 161 QMNIKAKTVSSHKGNIKRKIKTHNKQVIYHVVRLTDNVTNGIFVNMR 207
GerE pfam00196
Bacterial regulatory proteins, luxR family;
137-192 1.67e-17

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 73.00  E-value: 1.67e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 16129898   137 SLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQVIYHVV 192
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 138-194 8.79e-13

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: 60.63  E-value: 8.79e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 16129898 138 LSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQVIYHVVRL 194
Cdd:cd06170   1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 137-190 1.93e-12

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 59.85  E-value: 1.93e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 16129898    137 SLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQVIYH 190
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVR 56
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
13-194 3.05e-10

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 57.07  E-value: 3.05e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129898  13 RLGLTGYLLSRGVKKREINDIETVDDLAIACDSQRPSVVFINEDCFIHDASNSQRIKLIINQHPNTLFIVFMAIANVHFD 92
Cdd:COG2771   3 LLALALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLL 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129898  93 EYLLVRKNLLISSKSIKPESLDDILGDILKKETTITSFLNMPTLSLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSH 172
Cdd:COG2771  83 ALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTH 162

                       170       180
                ....*....|....*....|...
gi 16129898 173 KGNIKRKIKTHNK-QVIYHVVRL 194
Cdd:COG2771 163 LKRIYRKLGVSSRaELVALALRL 185
 
Name Accession Description Interval E-value
rcsA PRK15411
transcriptional regulator RcsA;
1-207 1.99e-144

transcriptional regulator RcsA;


Pssm-ID: 185309 [Multi-domain]  Cd Length: 207  Bit Score: 400.28  E-value: 1.99e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129898    1 MSTIIMDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIACDSQRPSVVFINEDCFIHDASNSQRIKLIINQHPNTLF 80
Cdd:PRK15411   1 MSTIIMDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIACDSLRPSVVFINEDCFIHDASNSQRIKQIINQHPNTLF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129898   81 IVFMAIANVHFDEYLLVRKNLLISSKSIKPESLDDILGDILKKETTITSFLNMPTLSLSRTESSMLRMWMAGQGTIQISD 160
Cdd:PRK15411  81 IVFMAIANIHFDEYLLVRKNLLISSKSIKPESLDDLLGDILKKETTITSFLNLPTLSLSRTESSMLRMWMAGQGTIQISD 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 16129898  161 QMNIKAKTVSSHKGNIKRKIKTHNKQVIYHVVRLTDNVTNGIFVNMR 207
Cdd:PRK15411 161 QMNIKAKTVSSHKGNIKRKIKTHNKQVIYHVVRLTDNVTNGIFVNMR 207
GerE pfam00196
Bacterial regulatory proteins, luxR family;
137-192 1.67e-17

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 73.00  E-value: 1.67e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 16129898   137 SLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQVIYHVV 192
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 138-194 8.79e-13

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: 60.63  E-value: 8.79e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 16129898 138 LSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQVIYHVVRL 194
Cdd:cd06170   1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 137-190 1.93e-12

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 59.85  E-value: 1.93e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 16129898    137 SLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQVIYH 190
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVR 56
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
13-194 3.05e-10

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 57.07  E-value: 3.05e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129898  13 RLGLTGYLLSRGVKKREINDIETVDDLAIACDSQRPSVVFINEDCFIHDASNSQRIKLIINQHPNTLFIVFMAIANVHFD 92
Cdd:COG2771   3 LLALALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLL 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129898  93 EYLLVRKNLLISSKSIKPESLDDILGDILKKETTITSFLNMPTLSLSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSH 172
Cdd:COG2771  83 ALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTH 162

                       170       180
                ....*....|....*....|...
gi 16129898 173 KGNIKRKIKTHNK-QVIYHVVRL 194
Cdd:COG2771 163 LKRIYRKLGVSSRaELVALALRL 185
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 131-185 8.54e-08

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: 49.12  E-value: 8.54e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16129898 131 LNMPTLS--------LSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNK 185
Cdd:COG2197  55 IRMPGMDglealrrlLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNR 117
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
1-180 6.45e-03

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 36.41  E-value: 6.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129898    1 MSTIIMDLCSYTRLGLTGYLLSRGVKKreINDIETVDDLAIACDSQRPSVVFINEDcfIHDASNSQRI-KLIINQHPNTL 79
Cdd:PRK09958   1 MNAIIIDDHPLAIAAIRNLLIKNDIEI--LAELTEGGSAVQRVETLKPDIVIIDVD--IPGVNGIQVLeTLRKRQYSGII 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129898   80 FIVfmAIANVHF--DEYLLVRKNLLISSKsikpESLDDILGDILKKETTITSF---LNMPTL----------SLSRTESS 144
Cdd:PRK09958  77 IIV--SAKNDHFygKHCADAGANGFVSKK----EGMNNIIAAIEAAKNGYCYFpfsLNRFVGsltsdqqkldSLSKQEIS 150

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 16129898  145 MLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKI 180
Cdd:PRK09958 151 VMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKL 186
 
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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