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Conserved domains on  [gi|1659001829|gb|TLE39812|]
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helix-turn-helix transcriptional regulator [Clostridioides difficile]

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];
2-63 1.19e-14

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 61.02  E-value: 1.19e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1659001829  2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDTSVEELFFDKE 63
Cdd:COG1476    8 RLKELRKERGLTQEELAELLGVSRQTISAIENGKY-NPSLELALKIARALGVSLEELFSLEE 68
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
2-63 1.19e-14

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 61.02  E-value: 1.19e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1659001829  2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDTSVEELFFDKE 63
Cdd:COG1476    8 RLKELRKERGLTQEELAELLGVSRQTISAIENGKY-NPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
2-58 2.68e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 52.52  E-value: 2.68e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1659001829   2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSKnPSNMLMLKLAQELDTSVEEL 58
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK-PSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 2-58 1.31e-10

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: 50.63  E-value: 1.31e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1659001829  2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDTSVEEL 58
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKR-NPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 3-58 2.54e-09

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: 47.15  E-value: 2.54e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1659001829  3 LKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDTSVEEL 58
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEALGVSLDEL 55
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 9-53 1.89e-05

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 38.97  E-value: 1.89e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1659001829   9 EKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDT 53
Cdd:PRK13890   16 ERHMTKKELSERSGVSISFLSDLTTGKA-NPSLKVMEAIADALET 59
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
2-63 1.19e-14

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 61.02  E-value: 1.19e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1659001829  2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDTSVEELFFDKE 63
Cdd:COG1476    8 RLKELRKERGLTQEELAELLGVSRQTISAIENGKY-NPSLELALKIARALGVSLEELFSLEE 68
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
2-64 2.93e-14

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.40  E-value: 2.93e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1659001829  2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDTSVEELFFDKEE 64
Cdd:COG1396   11 RLRELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKALGVSLDELLGGADE 72
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
2-58 2.68e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 52.52  E-value: 2.68e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1659001829   2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSKnPSNMLMLKLAQELDTSVEEL 58
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK-PSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 2-58 1.31e-10

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: 50.63  E-value: 1.31e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 1659001829  2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDTSVEEL 58
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKR-NPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 3-58 2.54e-09

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: 47.15  E-value: 2.54e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1659001829  3 LKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDTSVEEL 58
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEALGVSLDEL 55
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
2-59 4.92e-09

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 47.06  E-value: 4.92e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1659001829  2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSKNPSNMLMLKLAQELDTSVEELF 59
Cdd:COG3655    5 KLDELLAERGMTKKELAEATGISRATLSRLKNGKAKAVRLDTLEKICKALDCQPGDLL 62
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 2-59 1.69e-07

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: 42.91  E-value: 1.69e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1659001829  2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSKNPSNMLMLKLAQELDTSVEELF 59
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALGCQPGDLL 58
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 3-64 1.86e-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: 43.47  E-value: 1.86e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1659001829  3 LKLKRIEKGIKQYELAEKVGISRYYLSSLERGKsKNPSNMLMLKLAQELDTSVEELFFDKEE 64
Cdd:COG3620   22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGK-RDPTVSTLEKIAEALGKELSAVLVVDDG 82
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 2-57 5.01e-07

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: 41.85  E-value: 5.01e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1659001829  2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDTSVEE 57
Cdd:COG1813   16 RIREAREARGLSQEELAEKLGVSESTIRRIERGEA-TPSLDTLRKLEKALGISLAE 70
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 3-58 3.51e-06

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: 39.43  E-value: 3.51e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1659001829  3 LKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSKNPSNMLMLKLAQELDTSVEEL 58
Cdd:pfam13560  6 LRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVVERLARALGVDGAER 61
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 2-59 1.03e-05

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: 38.42  E-value: 1.03e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1659001829  2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGKSKnPSNMLMLKLAQELDTSVEELF 59
Cdd:pfam12844  3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSV-PPAETLYKIAELLGVPANWLL 59
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 9-53 1.89e-05

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 38.97  E-value: 1.89e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1659001829   9 EKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDT 53
Cdd:PRK13890   16 ERHMTKKELSERSGVSISFLSDLTTGKA-NPSLKVMEAIADALET 59
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 7-58 4.30e-05

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 38.78  E-value: 4.30e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1659001829   7 RIEKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDTSVEEL 58
Cdd:PRK08154   37 RARRGMSRKVLAQASGVSERYLAQLESGQG-NVSILLLRRVARALGCSLADL 87
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 9-56 4.56e-05

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 37.10  E-value: 4.56e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 1659001829  9 EKGIKQYELAEKVGISRYYLSSLERGKSkNPSNMLMLKLAQELDTSVE 56
Cdd:COG3093   20 PLGLSQTELAKALGVSRQRISEILNGKR-AITADTALRLARAFGTSAE 66
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 2-35 2.61e-04

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 34.78  E-value: 2.61e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 1659001829  2 KLKLKRIEKGIKQYELAEKVGISRYYLSSLERGK 35
Cdd:COG1426    9 LLRQAREAKGLSLEDVAERTKISVSYLEAIEEGD 42
 
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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