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Conserved domains on  [gi|1732943983|gb|TYS20799|]
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helix-turn-helix transcriptional regulator [Bacillus subtilis]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11443570)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  37972151

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
7-64 1.11e-17

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 69.64  E-value: 1.11e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1732943983  7 GRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADEL 64
Cdd:COG1396    9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDEL 66
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
7-64 1.11e-17

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 69.64  E-value: 1.11e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1732943983  7 GRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADEL 64
Cdd:COG1396    9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDEL 66
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-64 1.28e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 60.99  E-value: 1.28e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1732943983   9 RIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADEL 64
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-64 2.58e-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: 60.26  E-value: 2.58e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1732943983  7 GRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADEL 64
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-64 7.49e-13

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: 56.39  E-value: 7.49e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 1732943983 10 IRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADEL 64
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 1-61 1.03e-05

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 40.22  E-value: 1.03e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1732943983   1 MEAEIWGRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISA 61
Cdd:PRK09706    1 MKNLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSP 61
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 10-59 1.11e-03

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 33.40  E-value: 1.11e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 1732943983 10 IRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNI 59
Cdd:TIGR03070  7 VRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGL 56
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
7-64 1.11e-17

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 69.64  E-value: 1.11e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1732943983  7 GRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADEL 64
Cdd:COG1396    9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDEL 66
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-69 4.42e-15

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 62.56  E-value: 4.42e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1732943983  1 MEAEIwGRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADELAPPEK 69
Cdd:COG1476    1 MKKKL-GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-64 1.28e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 60.99  E-value: 1.28e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1732943983   9 RIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADEL 64
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-64 2.58e-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: 60.26  E-value: 2.58e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1732943983  7 GRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADEL 64
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 1-63 3.36e-13

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: 58.03  E-value: 3.36e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1732943983  1 MEAEIWGRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADE 63
Cdd:COG1813    8 ELVEDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-64 7.49e-13

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: 56.39  E-value: 7.49e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 1732943983 10 IRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADEL 64
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 7-65 1.05e-08

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: 46.37  E-value: 1.05e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732943983  7 GRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNR-LPSAAIIQGVADVLNISADELA 65
Cdd:pfam13560  3 GARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRgRPSPAVVERLARALGVDGAERA 62
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 7-68 2.88e-08

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: 45.36  E-value: 2.88e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1732943983  7 GRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADELAPPE 68
Cdd:pfam12844  1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGE 62
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
4-48 2.26e-07

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 43.00  E-value: 2.26e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 1732943983  4 EIWGRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAA 48
Cdd:COG2944    5 PLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGA 49
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 7-69 6.45e-07

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: 42.70  E-value: 6.45e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1732943983  7 GRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADELAPPEK 69
Cdd:COG3620   19 GEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDD 81
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 1-61 1.03e-05

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 40.22  E-value: 1.03e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1732943983   1 MEAEIWGRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISA 61
Cdd:PRK09706    1 MKNLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSP 61
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 7-62 3.34e-04

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 35.17  E-value: 3.34e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1732943983  7 GRRIRA-FRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISAD 62
Cdd:COG3093   10 GEILREeFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAE 66
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 7-68 7.44e-04

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 35.70  E-value: 7.44e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1732943983   7 GRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADELAPPE 68
Cdd:PRK08154   30 GERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLGDV 91
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 10-59 1.11e-03

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 33.40  E-value: 1.11e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 1732943983 10 IRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNI 59
Cdd:TIGR03070  7 VRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGL 56
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 7-64 4.76e-03

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 33.56  E-value: 4.76e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1732943983   7 GRRIRAFRKLKGYTQEGFAKALG-----ISVSILGEIERGNRLPSAAIIQGVADVLNISADEL 64
Cdd:PRK13355    5 AERLKQAMKARGLKQEDLVHAAEargvkLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWL 67
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 10-51 5.34e-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: 5.34e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1732943983  10 IRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQ 51
Cdd:TIGR03830  70 IRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDK 111
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
7-69 7.11e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 32.84  E-value: 7.11e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1732943983   7 GRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADE-LAPPEK 69
Cdd:PRK09943    9 GKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEfFSEPEK 72
PHA01976 PHA01976
helix-turn-helix protein
 8-64 7.67e-03

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 31.46  E-value: 7.67e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1732943983  8 RRIRAfRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQGVADVLNISADEL 64
Cdd:PHA01976   6 QLIKA-RNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWL 61
 
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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