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Conserved domains on  [gi|2524289987|ref|WP_286476382|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Empedobacter]

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];
4-65 6.57e-11

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 51.77  E-value: 6.57e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2524289987  4 NRLKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQPSLETLVTIATILDIDVKELLYSTK 65
Cdd:COG1476    7 NRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
4-65 6.57e-11

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 51.77  E-value: 6.57e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2524289987  4 NRLKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQPSLETLVTIATILDIDVKELLYSTK 65
Cdd:COG1476    7 NRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 5-61 1.04e-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: 43.68  E-value: 1.04e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 2524289987  5 RLKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQ-PSLETLVTIATILDIDVKELL 61
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKrVSLDTLDKICDALGCQPGDLL 58
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-60 2.75e-07

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: 42.54  E-value: 2.75e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 2524289987  4 NRLKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQPSLETLVTIATILDIDVKEL 60
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-60 8.78e-07

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.96  E-value: 8.78e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2524289987   5 RLKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQPSLETLVTIATILDIDVKEL 60
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
4-65 6.57e-11

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 51.77  E-value: 6.57e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2524289987  4 NRLKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQPSLETLVTIATILDIDVKELLYSTK 65
Cdd:COG1476    7 NRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
1-61 2.39e-09

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 47.83  E-value: 2.39e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2524289987  1 MKINRLKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQ-PSLETLVTIATILDIDVKELL 61
Cdd:COG3655    1 MIYVKLDELLAERGMTKKELAEATGISRATLSRLKNGKAKaVRLDTLEKICKALDCQPGDLL 62
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
4-61 3.31e-09

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 48.07  E-value: 3.31e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 2524289987  4 NRLKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQPSLETLVTIATILDIDVKELL 61
Cdd:COG1396   10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 5-61 1.04e-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: 43.68  E-value: 1.04e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 2524289987  5 RLKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQ-PSLETLVTIATILDIDVKELL 61
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKrVSLDTLDKICDALGCQPGDLL 58
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-60 2.75e-07

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: 42.54  E-value: 2.75e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 2524289987  4 NRLKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQPSLETLVTIATILDIDVKEL 60
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-60 8.78e-07

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.96  E-value: 8.78e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2524289987   5 RLKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQPSLETLVTIATILDIDVKEL 60
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-60 2.07e-06

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: 40.22  E-value: 2.07e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 2524289987  6 LKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQPSLETLVTIATILDIDVKEL 60
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 18-59 1.20e-05

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: 38.77  E-value: 1.20e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 2524289987 18 KWLSFELGKSESTISRWCTNEIQPSLETLVTIATILDIDVKE 59
Cdd:COG1813   29 EELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 5-61 2.49e-03

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: 32.65  E-value: 2.49e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 2524289987  5 RLKIVLAEKDKTSKWLSFELGKSESTISRWCTNEIQPSLETLVTIATILDIDVKELL 61
Cdd:pfam12844  3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
HTH_5 pfam01022
Bacterial regulatory protein, arsR family; Members of this family contains a DNA binding ...
 4-33 6.95e-03

Bacterial regulatory protein, arsR family; Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.


Pssm-ID: 425993 [Multi-domain]  Cd Length: 45  Bit Score: 30.87  E-value: 6.95e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 2524289987  4 NRLKIV--LAEKDKTSKWLSFELGKSESTISR 33
Cdd:pfam01022  3 TRLKILklLAEGELCVCELAEELGLSQSTVSH 34
 
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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