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Conserved domains on  [gi|496265659|ref|WP_008979044|]
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helix-turn-helix transcriptional regulator [Longicatena caecimuris]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10650117)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-58 4.05e-06

Helix-turn-helix XRE-family like proteins;


:

Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 43.66  E-value: 4.05e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 496265659     9 LRYYRMQQNLSQEGLCKGICV-VSYLSKIEQGKVDASEDILQALFARLQIH 58
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVsRSTLSRIENGKRKPSLETLKKLAKALGVS 52
 
Name Accession Description Interval E-value
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-58 4.05e-06

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 43.66  E-value: 4.05e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 496265659     9 LRYYRMQQNLSQEGLCKGICV-VSYLSKIEQGKVDASEDILQALFARLQIH 58
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVsRSTLSRIENGKRKPSLETLKKLAKALGVS 52
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 6-58 4.15e-06

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: 43.70  E-value: 4.15e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 496265659   6 GALLRYYRMQQNLSQEGLCKGICV-VSYLSKIEQGKVDASEDILQALFARLQIH 58
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVsRSTISRIENGKRNPSLETLEKLAKALGVS 54
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-57 5.04e-06

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 44.22  E-value: 5.04e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496265659   1 MEKIS---GALLRYYRMQQNLSQEGLCKGICV-VSYLSKIEQGKVDASEDILQALFARLQI 57
Cdd:COG1396    1 MSTLKkalGERLRELRKARGLTQEELAERLGVsRSTISRIERGRRNPSLETLLKLAKALGV 61
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 9-58 1.75e-05

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: 41.76  E-value: 1.75e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 496265659    9 LRYYRMQQNLSQEGLCKGICV-VSYLSKIEQGKVDASEDILQALFARLQIH 58
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVsRSTISKIENGKREPSLETLKKLAEALGVS 51
 
Name Accession Description Interval E-value
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-58 4.05e-06

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 43.66  E-value: 4.05e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 496265659     9 LRYYRMQQNLSQEGLCKGICV-VSYLSKIEQGKVDASEDILQALFARLQIH 58
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVsRSTLSRIENGKRKPSLETLKKLAKALGVS 52
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 6-58 4.15e-06

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: 43.70  E-value: 4.15e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 496265659   6 GALLRYYRMQQNLSQEGLCKGICV-VSYLSKIEQGKVDASEDILQALFARLQIH 58
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVsRSTISRIENGKRNPSLETLEKLAKALGVS 54
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-57 5.04e-06

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 44.22  E-value: 5.04e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496265659   1 MEKIS---GALLRYYRMQQNLSQEGLCKGICV-VSYLSKIEQGKVDASEDILQALFARLQI 57
Cdd:COG1396    1 MSTLKkalGERLRELRKARGLTQEELAERLGVsRSTISRIERGRRNPSLETLLKLAKALGV 61
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 9-58 1.75e-05

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: 41.76  E-value: 1.75e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 496265659    9 LRYYRMQQNLSQEGLCKGICV-VSYLSKIEQGKVDASEDILQALFARLQIH 58
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVsRSTISKIENGKREPSLETLKKLAEALGVS 51
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-51 2.00e-03

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: 36.35  E-value: 2.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 496265659    6 GALLRYYRMQQNLSQEGLCKGICV-VSYLSKIEQGKVD-ASEDILQAL 51
Cdd:pfam13560   3 GARLRRLRERAGLSQEALARRLGVsRSTLSRLETGRRGrPSPAVVERL 50
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 6-57 2.54e-03

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: 2.54e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 496265659   6 GALLRYYRMQQNLSQEGLCKGICV-VSYLSKIEQGKVDASEDILQALFARLQI 57
Cdd:COG1813   14 GERIREAREARGLSQEELAEKLGVsESTIRRIERGEATPSLDTLRKLEKALGI 66
 
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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