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Conserved domains on  [gi|491640586|ref|WP_005498115|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Vibrio]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10648172)

helix-turn-helix domain-containing protein with a LuxR family HTH DNA-binding domain; functions in DNA binding; HTH domains are often found in transcriptional regulators

CATH:  1.10.10.10
Gene Ontology:  GO:0006355|GO:0003677|GO:0003700
PubMed:  15808743|19076237|10473770|8831795
SCOP:  4000720

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
 203-259 3.87e-17

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


:

Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 73.33  E-value: 3.87e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 491640586   203 ESLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLF 259
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
 
Name Accession Description Interval E-value
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 203-259 3.87e-17

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 73.33  E-value: 3.87e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 491640586   203 ESLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLF 259
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 205-262 8.25e-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: 74.54  E-value: 8.25e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 491640586 205 LTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLFLNH 262
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRL 127
GerE pfam00196
Bacterial regulatory proteins, luxR family;
203-259 7.49e-14

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 64.53  E-value: 7.49e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 491640586  203 ESLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLF 259
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 205-261 4.68e-12

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: 59.47  E-value: 4.68e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 491640586 205 LTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLFLN 261
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
PRK10360 PRK10360
transcriptional regulator UhpA;
193-255 9.83e-08

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 51.13  E-value: 9.83e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491640586 193 IEQALSSFGIESLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSEL 255
Cdd:PRK10360 126 IAIKLASGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 202-247 4.49e-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: 36.94  E-value: 4.49e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 491640586  202 IESLTRREQEVASLLA-QGFDTKEISAHLHLVQGTVKNHRKRIYSQL 247
Cdd:TIGR02937 108 LEKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 203-259 3.87e-17

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 73.33  E-value: 3.87e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 491640586   203 ESLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLF 259
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 205-262 8.25e-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: 74.54  E-value: 8.25e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 491640586 205 LTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLFLNH 262
Cdd:COG2197   70 LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRL 127
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 195-260 4.64e-15

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: 68.45  E-value: 4.64e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 491640586 195 QALSSFGIESLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLFL 260
Cdd:COG5905    3 PSSSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWAL 68
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
204-265 6.61e-15

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 71.33  E-value: 6.61e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 491640586 204 SLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLFLNHLIM 265
Cdd:COG2771  127 GLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALALRLGLI 188
GerE pfam00196
Bacterial regulatory proteins, luxR family;
203-259 7.49e-14

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 64.53  E-value: 7.49e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 491640586  203 ESLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLF 259
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 202-260 1.79e-13

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: 67.05  E-value: 1.79e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 491640586 202 IESLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLFL 260
Cdd:COG4566  135 LASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRLAL 193
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 205-261 4.68e-12

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: 59.47  E-value: 4.68e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 491640586 205 LTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLFLN 261
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
208-258 4.58e-09

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 54.71  E-value: 4.58e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 491640586 208 REQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQL 258
Cdd:COG2909  126 LAALRRRLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVAR 176
PRK10360 PRK10360
transcriptional regulator UhpA;
193-255 9.83e-08

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 51.13  E-value: 9.83e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491640586 193 IEQALSSFGIESLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSEL 255
Cdd:PRK10360 126 IAIKLASGRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 198-254 6.71e-07

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 48.87  E-value: 6.71e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 491640586 198 SSFGIESLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSE 254
Cdd:PRK10651 149 TERDVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE 205
PRK09483 PRK09483
response regulator; Provisional
 191-262 1.43e-05

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 45.10  E-value: 1.43e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491640586 191 VAIEQALSSFG------IESLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLFLNH 262
Cdd:PRK09483 129 IAQQMALSQIEpatenpFASLSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRH 206
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
190-262 1.87e-05

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 44.46  E-value: 1.87e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491640586 190 KVAIEQALSSFGIesLTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLFLNH 262
Cdd:PRK10403 141 REMFGAEEDPFSV--LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQ 211
PRK15369 PRK15369
two component system response regulator;
205-257 2.66e-05

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 43.91  E-value: 2.66e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 491640586 205 LTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQ 257
Cdd:PRK15369 150 LTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLN 202
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
205-265 1.03e-04

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 43.39  E-value: 1.03e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491640586 205 LTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSELFQLFLNHLIM 265
Cdd:PRK04841 839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHAQDLLKM 899
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
205-255 2.02e-04

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 41.40  E-value: 2.02e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 491640586 205 LTRREQEVASLLAQGFDTKEISAHLHLVQGTVKNHRKRIYSQLNVSSLSEL 255
Cdd:PRK09935 150 LSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVEL 200
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 202-247 4.49e-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: 36.94  E-value: 4.49e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 491640586  202 IESLTRREQEVASLLA-QGFDTKEISAHLHLVQGTVKNHRKRIYSQL 247
Cdd:TIGR02937 108 LEKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
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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