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Conserved domains on  [gi|446698813|ref|WP_000776159|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Bacillus]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10787697)

helix-turn-helix (HTH) transcriptional regulator containing a XRE (Xenobiotic Response Element) family HTH domain may act as a transcriptional regulator that controls the expression of genes involved in stress response

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  10473770|2644244
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-64 1.67e-23

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 83.74  E-value: 1.67e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446698813  1 MKLQNRVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEIFTL 64
Cdd:COG1476   3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSL 66
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-64 1.67e-23

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 83.74  E-value: 1.67e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446698813  1 MKLQNRVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEIFTL 64
Cdd:COG1476   3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSL 66
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-61 9.67e-14

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 59.10  E-value: 9.67e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 446698813  5 NRVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEI 61
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 3.52e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 57.53  E-value: 3.52e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 446698813    6 RVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEI 61
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 1.18e-11

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 53.70  E-value: 1.18e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446698813   7 VRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEI 61
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK04140 PRK04140
transcriptional regulator;
5-58 1.35e-07

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 46.39  E-value: 1.35e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446698813   5 NRVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPV 58
Cdd:PRK04140 129 DVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPL 182
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 7-48 6.31e-03

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 32.60  E-value: 6.31e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 446698813    7 VRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSL 48
Cdd:TIGR03830  70 IRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDK 111
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-64 1.67e-23

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 83.74  E-value: 1.67e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446698813  1 MKLQNRVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEIFTL 64
Cdd:COG1476   3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSL 66
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-63 3.81e-15

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 63.09  E-value: 3.81e-15
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446698813  1 MKLQNRVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEIFT 63
Cdd:COG1396   6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLG 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-61 9.67e-14

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 59.10  E-value: 9.67e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 446698813  5 NRVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEI 61
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 3.52e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 57.53  E-value: 3.52e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 446698813    6 RVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEI 61
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 6-60 9.70e-12

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 54.17  E-value: 9.70e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 446698813  6 RVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEE 60
Cdd:COG1813  16 RIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 1.18e-11

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 53.70  E-value: 1.18e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446698813   7 VRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEI 61
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 6-65 3.51e-09

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains.


Pssm-ID: 463728 [Multi-domain]  Cd Length: 64  Bit Score: 47.67  E-value: 3.51e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446698813   6 RVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEIFTLV 65
Cdd:pfam12844  3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGE 62
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
8-58 2.09e-08

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 48.68  E-value: 2.09e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446698813   8 RELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPV 58
Cdd:COG1395  133 RELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLEEILGEPI 183
PRK04140 PRK04140
transcriptional regulator;
5-58 1.35e-07

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 46.39  E-value: 1.35e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446698813   5 NRVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPV 58
Cdd:PRK04140 129 DVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPL 182
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-61 6.76e-07

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 41.74  E-value: 6.76e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446698813   6 RVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYA-PSIVLSLKIAKIFNVPVEEI 61
Cdd:pfam13560  5 RLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGrPSPAVVERLARALGVDGAER 61
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
6-43 1.22e-05

DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 38.38  E-value: 1.22e-05
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 446698813  6 RVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPS 43
Cdd:COG2944  10 EIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPS 47
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 6-65 1.71e-05

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 38.29  E-value: 1.71e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446698813   6 RVRELRAKHRLSQGDLGKAIGSSRQTISLIERGD-YAPSIVLSLKIAKIFNVPVEEIFTLV 65
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKpKRVSLDTLDKICDALGCQPGDLLEYV 61
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 8-59 1.80e-05

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 38.64  E-value: 1.80e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 446698813  8 RELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVE 59
Cdd:COG3093  15 EEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAE 66
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 3-42 8.23e-05

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 37.91  E-value: 8.23e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 446698813   3 LQNRVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAP 42
Cdd:PRK09706   6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEP 45
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 1-61 1.80e-04

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 36.15  E-value: 1.80e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446698813  1 MKLQNRVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEI 61
Cdd:COG3620  16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAV 76
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
6-62 1.86e-04

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 37.08  E-value: 1.86e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446698813   6 RVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEIF 62
Cdd:PRK09943  11 RLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFF 67
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 6-61 2.67e-04

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 36.86  E-value: 2.67e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446698813   6 RVRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSLKIAKIFNVPVEEI 61
Cdd:PRK08154  32 RVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADL 87
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 7-48 6.31e-03

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 32.60  E-value: 6.31e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 446698813    7 VRELRAKHRLSQGDLGKAIGSSRQTISLIERGDYAPSIVLSL 48
Cdd:TIGR03830  70 IRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDK 111
 
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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