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Conserved domains on  [gi|2275944995|dbj|GKJ86766|]
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transcriptional regulator [Klebsiella variicola]

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];
1-68 8.01e-10

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 49.46  E-value: 8.01e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2275944995  1 MNNIASERQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALNklgaeCSLDSVFPTDK 68
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALG-----VSLEELFSLEE 68
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-68 8.01e-10

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 49.46  E-value: 8.01e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2275944995  1 MNNIASERQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALNklgaeCSLDSVFPTDK 68
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALG-----VSLEELFSLEE 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
3-53 2.40e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 47.90  E-value: 2.40e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2275944995   3 NIASERQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALNK 53
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGV 51
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 1-52 2.56e-09

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: 47.93  E-value: 2.56e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 2275944995  1 MNNIASERQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALN 52
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALG 52
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 4-53 5.47e-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: 46.76  E-value: 5.47e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2275944995  4 IASERQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALNK 53
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGV 50
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 8-33 1.27e-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: 34.53  E-value: 1.27e-03
                          10        20
                  ....*....|....*....|....*.
gi 2275944995   8 RQKLGISQAQLAKTLNWGRSRLSNYE 33
Cdd:TIGR03830  74 RKKLGLSQREAAELLGGGVNAFSRYE 99
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-68 8.01e-10

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 49.46  E-value: 8.01e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2275944995  1 MNNIASERQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALNklgaeCSLDSVFPTDK 68
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALG-----VSLEELFSLEE 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
3-53 2.40e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 47.90  E-value: 2.40e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2275944995   3 NIASERQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALNK 53
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGV 51
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 1-52 2.56e-09

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: 47.93  E-value: 2.56e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 2275944995  1 MNNIASERQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALN 52
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALG 52
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 4-53 5.47e-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: 46.76  E-value: 5.47e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2275944995  4 IASERQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALNK 53
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGV 50
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
2-52 9.36e-08

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 44.60  E-value: 9.36e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 2275944995  2 NNIASERQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALN 52
Cdd:COG1396   10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALG 60
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 8-69 5.19e-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: 40.39  E-value: 5.19e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2275944995  8 RQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALNKlgaecSLDSVFPTDKE 69
Cdd:COG3620   26 RKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGK-----ELSAVLVVDDG 82
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
4-39 9.20e-06

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 38.76  E-value: 9.20e-06
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 2275944995  4 IASERQKLGISQAQLAKTLNWGRSRLSNYEANLREP 39
Cdd:COG2944   11 IRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKP 46
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-52 1.16e-04

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: 36.45  E-value: 1.16e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 2275944995  4 IASERQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALN 52
Cdd:COG1813   17 IREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALG 65
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 8-33 1.27e-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: 34.53  E-value: 1.27e-03
                          10        20
                  ....*....|....*....|....*.
gi 2275944995   8 RQKLGISQAQLAKTLNWGRSRLSNYE 33
Cdd:TIGR03830  74 RKKLGLSQREAAELLGGGVNAFSRYE 99
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 8-52 1.50e-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: 33.42  E-value: 1.50e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 2275944995  8 RQKLGISQAQLAKTLNWGRSRLSNYEANLREPGLTECRSIVDALN 52
Cdd:pfam12844  8 REERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLG 52
COG1709 COG1709
Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];
8-51 2.16e-03

Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];


Pssm-ID: 441315  Cd Length: 234  Bit Score: 34.38  E-value: 2.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2275944995   8 RQKLGISQAQLAKTLNWGRSRLSNYEANLRE-PGLTECRSIVDAL 51
Cdd:COG1709    31 REDFGISQTELARELGVSPSVISDYESGRRKsPGIAFVKKFVEAL 75
 
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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