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Conserved domains on  [gi|503994107|ref|WP_014228101|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Klebsiella]

Protein Classification

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

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 130-171 2.21e-10

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


:

Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 53.69  E-value: 2.21e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 503994107   130 TNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:smart00421   5 TPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
23-171 4.30e-09

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


:

Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 53.61  E-value: 4.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994107  23 LAELIIDIDDLIYLSLEKVRREFVFINLSASSLNYFIRRDSEWLAEMKGKQIVLIAARRSEALANYWYYNGAIRGVVYVD 102
Cdd:COG2771   18 LALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLALLAAL 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503994107 103 LAKDIRQELAYVINGRFLRKDI----KKDKITNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:COG2771   98 LARLAALLLALALAALLLAALArllaRAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170
 
Name Accession Description Interval E-value
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 130-171 2.21e-10

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 53.69  E-value: 2.21e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 503994107   130 TNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:smart00421   5 TPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 130-171 5.20e-10

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: 52.54  E-value: 5.20e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 503994107 130 TNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:cd06170    2 TPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43
GerE pfam00196
Bacterial regulatory proteins, luxR family;
130-171 3.92e-09

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 50.28  E-value: 3.92e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 503994107  130 TNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:pfam00196   4 SPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKL 45
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
23-171 4.30e-09

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 53.61  E-value: 4.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994107  23 LAELIIDIDDLIYLSLEKVRREFVFINLSASSLNYFIRRDSEWLAEMKGKQIVLIAARRSEALANYWYYNGAIRGVVYVD 102
Cdd:COG2771   18 LALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLALLAAL 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503994107 103 LAKDIRQELAYVINGRFLRKDI----KKDKITNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:COG2771   98 LARLAALLLALALAALLLAALArllaRAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 130-171 4.03e-07

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: 46.81  E-value: 4.03e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 503994107 130 TNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:COG2197   71 TPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKL 112
PRK10360 PRK10360
transcriptional regulator UhpA;
70-171 4.21e-06

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 44.97  E-value: 4.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994107  70 KGKQIVLIAARRSEALANYWYYNGAiRGVVYVDLAKDirqELAYVIN-----GRFLRKDI-------KKDKITNREMQII 137
Cdd:PRK10360  71 KGMATIMLSVHDSPALVEQALNAGA-RGFLSKRCSPD---ELIAAVHtvatgGCYLTPDIaiklasgRQDPLTKRERQVA 146

                         90       100       110
                 ....*....|....*....|....*....|....
gi 503994107 138 RMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:PRK10360 147 EKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKL 180
PRK15369 PRK15369
two component system response regulator;
129-171 3.95e-04

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 39.68  E-value: 3.95e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 503994107 129 ITNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:PRK15369 150 LTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKL 192
 
Name Accession Description Interval E-value
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 130-171 2.21e-10

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 53.69  E-value: 2.21e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 503994107   130 TNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:smart00421   5 TPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 130-171 5.20e-10

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: 52.54  E-value: 5.20e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 503994107 130 TNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:cd06170    2 TPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43
GerE pfam00196
Bacterial regulatory proteins, luxR family;
130-171 3.92e-09

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 50.28  E-value: 3.92e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 503994107  130 TNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:pfam00196   4 SPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKL 45
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
23-171 4.30e-09

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 53.61  E-value: 4.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994107  23 LAELIIDIDDLIYLSLEKVRREFVFINLSASSLNYFIRRDSEWLAEMKGKQIVLIAARRSEALANYWYYNGAIRGVVYVD 102
Cdd:COG2771   18 LALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLALLAAL 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503994107 103 LAKDIRQELAYVINGRFLRKDI----KKDKITNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:COG2771   98 LARLAALLLALALAALLLAALArllaRAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 130-171 4.03e-07

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: 46.81  E-value: 4.03e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 503994107 130 TNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:COG2197   71 TPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKL 112
PRK10360 PRK10360
transcriptional regulator UhpA;
70-171 4.21e-06

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 44.97  E-value: 4.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994107  70 KGKQIVLIAARRSEALANYWYYNGAiRGVVYVDLAKDirqELAYVIN-----GRFLRKDI-------KKDKITNREMQII 137
Cdd:PRK10360  71 KGMATIMLSVHDSPALVEQALNAGA-RGFLSKRCSPD---ELIAAVHtvatgGCYLTPDIaiklasgRQDPLTKRERQVA 146

                         90       100       110
                 ....*....|....*....|....*....|....
gi 503994107 138 RMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:PRK10360 147 EKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKL 180
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 126-171 7.88e-05

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: 39.56  E-value: 7.88e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 503994107 126 KDKITNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:COG5905   10 PSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKL 55
PRK15369 PRK15369
two component system response regulator;
129-171 3.95e-04

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 39.68  E-value: 3.95e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 503994107 129 ITNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:PRK15369 150 LTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKL 192
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 127-171 7.84e-03

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: 35.46  E-value: 7.84e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 503994107 127 DKITNREMQIIRMTAQGMHPKSIAKIENCSVKTVYTHRRNAEAKL 171
Cdd:COG4566  136 ASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKL 180
 
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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