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Conserved domains on  [gi|1267458432|ref|WP_098278409|]
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MULTISPECIES: LuxR C-terminal-related transcriptional regulator [Priestia]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 1000092)

helix-turn-helix domain-containing protein binds DNA and may function as a transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  15808743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CitB super family cl34424
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 5-56 1.78e-09

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


The actual alignment was detected with superfamily member COG2197:

Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 49.12  E-value: 1.78e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1267458432   5 TQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAVK 56
Cdd:COG2197    71 TPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVL 122
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 5-56 1.78e-09

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: 1.78e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1267458432   5 TQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAVK 56
Cdd:COG2197    71 TPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVL 122
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 5-55 2.69e-09

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 47.14  E-value: 2.69e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1267458432   5 TQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAV 55
Cdd:smart00421  5 TPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAV 55
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 5-56 5.82e-06

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: 38.67  E-value: 5.82e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 1267458432  5 TQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAVK 56
Cdd:cd06170    2 TPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVA 53
GerE pfam00196
Bacterial regulatory proteins, luxR family;
5-55 9.83e-06

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 37.95  E-value: 9.83e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1267458432  5 TQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAV 55
Cdd:pfam00196  4 SPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELV 54
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
1-46 1.98e-03

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 33.73  E-value: 1.98e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1267458432   1 MNQITQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKL 46
Cdd:PRK08295  153 EELLSELEKEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKL 198
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 5-56 1.78e-09

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: 1.78e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1267458432   5 TQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAVK 56
Cdd:COG2197    71 TPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVL 122
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 5-55 2.69e-09

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 47.14  E-value: 2.69e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1267458432   5 TQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAV 55
Cdd:smart00421  5 TPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAV 55
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
5-55 3.03e-09

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 49.75  E-value: 3.03e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1267458432   5 TQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAV 55
Cdd:COG2771   129 TPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELV 179
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 4-55 5.98e-08

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: 44.18  E-value: 5.98e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 1267458432  4 ITQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAV 55
Cdd:COG5905   13 LTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAV 64
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 5-56 5.82e-06

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: 38.67  E-value: 5.82e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 1267458432  5 TQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAVK 56
Cdd:cd06170    2 TPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVA 53
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
13-55 8.87e-06

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 40.07  E-value: 8.87e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1267458432  13 ALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAV 55
Cdd:COG2909   132 RLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAV 174
GerE pfam00196
Bacterial regulatory proteins, luxR family;
5-55 9.83e-06

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 37.95  E-value: 9.83e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1267458432  5 TQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAV 55
Cdd:pfam00196  4 SPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELV 54
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 5-56 1.07e-05

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: 39.70  E-value: 1.07e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1267458432   5 TQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKLNTQSMTEAVK 56
Cdd:COG4566   139 TPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVR 190
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-46 1.57e-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: 33.81  E-value: 1.57e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1267458432   1 MNQITQAEQEVFALS-IDGHSISEIQDILHKEECTIKNQRRRILKKL 46
Cdd:COG1595   125 LERLPPRQREVLVLRyLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
1-46 1.98e-03

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 33.73  E-value: 1.98e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1267458432   1 MNQITQAEQEVFALSIDGHSISEIQDILHKEECTIKNQRRRILKKL 46
Cdd:PRK08295  153 EELLSELEKEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKL 198
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 1-46 2.00e-03

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: 32.04  E-value: 2.00e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 1267458432  1 MNQITQAEQEVFALS-IDGHSISEIQDILHKEECTIKNQRRRILKKL 46
Cdd:pfam08281  8 LEELPPRQREVFLLRyLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
 
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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