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Conserved domains on  [gi|489531200|ref|WP_003435932|]
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helix-turn-helix domain-containing protein [Clostridioides difficile]

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];
1-65 8.22e-17

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 74.65  E-value: 8.22e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489531200   1 MNEL--NIAKTLILKRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDELI 65
Cdd:COG1396    1 MSTLkkALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-65 8.22e-17

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 74.65  E-value: 8.22e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489531200   1 MNEL--NIAKTLILKRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDELI 65
Cdd:COG1396    1 MSTLkkALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-64 2.14e-13

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: 64.11  E-value: 2.14e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489531200   7 AKTLILKRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDEL 64
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-64 2.55e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 60.99  E-value: 2.55e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 489531200    10 LILKRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDEL 64
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 13-64 3.33e-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: 57.94  E-value: 3.33e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 489531200   13 KRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDEL 64
Cdd:pfam01381   4 LREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 1-45 2.67e-07

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 49.08  E-value: 2.67e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489531200   1 MNELNIAKTLILKRKEKGITQDELANYIGVSKASVSKWETGQSYP 45
Cdd:PRK09706   1 MKNLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEP 45
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 14-45 1.53e-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: 38.00  E-value: 1.53e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 489531200   14 RKEKGITQDELANYIGVSKASVSKWETGQSYP 45
Cdd:TIGR03830  74 RKKLGLSQREAAELLGGGVNAFSRYERGEVRP 105
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-65 8.22e-17

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 74.65  E-value: 8.22e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489531200   1 MNEL--NIAKTLILKRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDELI 65
Cdd:COG1396    1 MSTLkkALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-69 2.38e-14

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 67.18  E-value: 2.38e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489531200   1 MNElNIAKTLILKRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDELICYEP 69
Cdd:COG1476    1 MKK-KLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-64 2.14e-13

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: 64.11  E-value: 2.14e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489531200   7 AKTLILKRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDEL 64
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-64 2.55e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 60.99  E-value: 2.55e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 489531200    10 LILKRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDEL 64
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 13-64 3.33e-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: 57.94  E-value: 3.33e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 489531200   13 KRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDEL 64
Cdd:pfam01381   4 LREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 5-63 7.95e-11

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: 57.26  E-value: 7.95e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489531200   5 NIAKTLILKRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDE 63
Cdd:COG1813   12 DYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
14-46 7.48e-08

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 48.78  E-value: 7.48e-08
                         10        20        30
                 ....*....|....*....|....*....|...
gi 489531200  14 RKEKGITQDELANYIGVSKASVSKWETGQSYPD 46
Cdd:COG2944   15 RERLGLSQAEFAALLGVSVSTVRRWEQGRRKPS 47
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 1-45 2.67e-07

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 49.08  E-value: 2.67e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489531200   1 MNELNIAKTLILKRKEKGITQDELANYIGVSKASVSKWETGQSYP 45
Cdd:PRK09706   1 MKNLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEP 45
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 14-65 3.72e-07

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: 46.90  E-value: 3.72e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 489531200   14 RKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDELI 65
Cdd:pfam12844   8 REERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 3-65 1.43e-06

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: 46.17  E-value: 1.43e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489531200   3 ELNIAKTLILKRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDELI 65
Cdd:COG3620   15 DDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVL 77
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
6-69 1.78e-05

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 42.05  E-value: 1.78e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489531200   6 IAKTLILKRKEKGITQDELANYIGVSKASVSKWETGQSYPdITF--LPQLATYFNITVDELICYEP 69
Cdd:COG3655    2 IYVKLDELLAERGMTKKELAEATGISRATLSRLKNGKAKA-VRLdtLEKICKALDCQPGDLLEYVP 66
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 14-64 2.13e-05

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: 2.13e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 489531200   14 RKEKGITQDELANYIGVSKASVSKWETG-QSYPDITFLPQLATYFNITVDEL 64
Cdd:pfam13560  10 RERAGLSQEALARRLGVSRSTLSRLETGrRGRPSPAVVERLARALGVDGAER 61
PHA01976 PHA01976
helix-turn-helix protein
 10-65 1.51e-04

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 39.55  E-value: 1.51e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489531200  10 LILKRKEKGITQDELANYIGVSKASVSKWETGQSYPDITFLPQLATYFNITVDELI 65
Cdd:PHA01976   7 LIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLC 62
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 15-70 1.60e-04

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: 39.45  E-value: 1.60e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 489531200   15 KEKGITQDELANYIGVSKASVSKWETGQS-YPDITFLPQLATYFNITVDELICYEPQ 70
Cdd:pfam13443   7 ADRGISKSDLARATGISRATLSRLRKGKPkRVSLDTLDKICDALGCQPGDLLEYVPD 63
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
2-59 2.15e-04

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 39.58  E-value: 2.15e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489531200   2 NELNIAKTLILKRKEKGITQDELANYIGVSKASVSKWEtgqSYPDITflpQLATYFNI 59
Cdd:PRK09726   9 SPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFE---NNPDNT---TLTTFFKI 60
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 14-45 1.53e-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: 38.00  E-value: 1.53e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 489531200   14 RKEKGITQDELANYIGVSKASVSKWETGQSYP 45
Cdd:TIGR03830  74 RKKLGLSQREAAELLGGGVNAFSRYERGEVRP 105
 
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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