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Conserved domains on  [gi|1124991290|gb|OKZ59945|]
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transcriptional regulator [Clostridiales bacterium 45_37]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10611674)

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_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 3-65 8.94e-08

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: 45.60  E-value: 8.94e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1124991290   3 FGAFISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRPAPEGAFVERISSFLELDKQEHEML 65
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVVERLARALGVDGAERAEL 64
 
Name Accession Description Interval E-value
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 3-65 8.94e-08

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: 45.60  E-value: 8.94e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1124991290   3 FGAFISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRPAPEGAFVERISSFLELDKQEHEML 65
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVVERLARALGVDGAERAEL 64
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-58 2.50e-07

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 44.99  E-value: 2.50e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1124991290   1 MTFGAFISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRpAPEGAFVERISSFLELD 58
Cdd:COG1396     6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKALGVS 62
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 4.33e-05

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: 38.30  E-value: 4.33e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1124991290   4 GAFISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRPaPEGAFVERISSFLELDKQE 61
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRN-PSLETLEKLAKALGVSLDE 57
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-58 6.51e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 37.88  E-value: 6.51e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1124991290    6 FISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRPaPEGAFVERISSFLELD 58
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK-PSLETLKKLAKALGVS 52
 
Name Accession Description Interval E-value
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 3-65 8.94e-08

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: 45.60  E-value: 8.94e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1124991290   3 FGAFISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRPAPEGAFVERISSFLELDKQEHEML 65
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVVERLARALGVDGAERAEL 64
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-58 2.50e-07

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 44.99  E-value: 2.50e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1124991290   1 MTFGAFISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRpAPEGAFVERISSFLELD 58
Cdd:COG1396     6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKALGVS 62
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 1-61 8.52e-06

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: 40.56  E-value: 8.52e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1124991290   1 MTFGAFISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRPAPEG-----AFVERISSFLELDKQE 61
Cdd:COG1426     4 ETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGpvyvrGFLRSYARALGLDPEE 69
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 4.33e-05

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: 38.30  E-value: 4.33e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1124991290   4 GAFISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRPaPEGAFVERISSFLELDKQE 61
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRN-PSLETLEKLAKALGVSLDE 57
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-58 6.51e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 37.88  E-value: 6.51e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1124991290    6 FISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRPaPEGAFVERISSFLELD 58
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK-PSLETLKKLAKALGVS 52
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-68 6.93e-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: 38.04  E-value: 6.93e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1124991290   4 GAFISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRpAPEGAFVERISSFLELDKQEHEMLLDL 68
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKS-VPPAETLYKIAELLGVPANWLLQGEGE 64
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 2-58 9.49e-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: 38.00  E-value: 9.49e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1124991290   2 TFGAFISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRPaPEGAFVERISSFLELD 58
Cdd:COG1813    12 DYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEAT-PSLDTLRKLEKALGIS 67
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-61 8.43e-04

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 35.21  E-value: 8.43e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1124991290   1 MTFGAFISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRpAPEGAFVERISSFLELDKQE 61
Cdd:COG1476     3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKY-NPSLELALKIARALGVSLEE 62
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 9.62e-04

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: 34.82  E-value: 9.62e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1124991290   7 ISTRRKEAKLNLRDTAKHLGISNGYLCDIEQGRRpAPEGAFVERISSFLELDKQE 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEALGVSLDE 54
 
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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