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Conserved domains on  [gi|817233755|ref|WP_046543847|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Burkholderia]

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];
1-76 1.04e-16

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 67.33  E-value: 1.04e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 817233755  1 MHSQNQAFGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISLVDMSAAIERELAS 76
Cdd:COG1396   1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPE 76
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-76 1.04e-16

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 67.33  E-value: 1.04e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 817233755  1 MHSQNQAFGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISLVDMSAAIERELAS 76
Cdd:COG1396   1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPE 76
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 9-65 2.79e-12

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: 55.64  E-value: 2.79e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 817233755  9 GKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISLVD 65
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDE 57
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
12-65 4.79e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 52.14  E-value: 4.79e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 817233755   12 LRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISLVD 65
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDE 55
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 12-63 9.82e-10

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: 49.08  E-value: 9.82e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 817233755  12 LRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISL 63
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSL 52
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 8-63 2.19e-08

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 45.73  E-value: 2.19e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 817233755   8 FGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISL 63
Cdd:TIGR03070  3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 4-62 9.05e-05

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 37.91  E-value: 9.05e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 817233755   4 QNQAFGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDIS 62
Cdd:PRK09706   2 KNLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCS 60
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-76 1.04e-16

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 67.33  E-value: 1.04e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 817233755  1 MHSQNQAFGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISLVDMSAAIERELAS 76
Cdd:COG1396   1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPE 76
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
5-66 1.34e-13

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 59.09  E-value: 1.34e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 817233755  5 NQAFGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISLVDM 66
Cdd:COG1476   2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEEL 63
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 9-65 2.79e-12

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: 55.64  E-value: 2.79e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 817233755  9 GKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISLVD 65
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDE 57
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 8-65 6.55e-12

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: 54.94  E-value: 6.55e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 817233755  8 FGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISLVD 65
Cdd:COG1813  13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
12-65 4.79e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 52.14  E-value: 4.79e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 817233755   12 LRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISLVD 65
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDE 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 3-63 6.21e-10

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: 50.40  E-value: 6.21e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 817233755  3 SQNQAFGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISL 63
Cdd:COG3620  13 SPDDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKEL 73
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 12-63 9.82e-10

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: 49.08  E-value: 9.82e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 817233755  12 LRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISL 63
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSL 52
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 9-62 1.48e-09

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: 48.82  E-value: 1.48e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 817233755   9 GKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDIS 62
Cdd:pfam12844  1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVP 54
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 8-63 2.19e-08

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 45.73  E-value: 2.19e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 817233755   8 FGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISL 63
Cdd:TIGR03070  3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 7-68 7.91e-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: 44.44  E-value: 7.91e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 817233755   7 AFGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGE-NSPTLDTLLALCRGLDISLVDMSA 68
Cdd:pfam13560  1 ELGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRrGRPSPAVVERLARALGVDGAERAE 63
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
12-65 2.08e-05

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 38.20  E-value: 2.08e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 817233755 12 LRSLRKARKVTQRDLAIHARLDRSYVSAMELGEN-SPTLDTLLALCRGLDISLVD 65
Cdd:COG3655   6 LDELLAERGMTKKELAEATGISRATLSRLKNGKAkAVRLDTLEKICKALDCQPGD 60
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 3-44 3.41e-05

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: 37.86  E-value: 3.41e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 817233755  3 SQNQAFGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGE 44
Cdd:COG1426   1 EALETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGD 42
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 4-62 9.05e-05

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 37.91  E-value: 9.05e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 817233755   4 QNQAFGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDIS 62
Cdd:PRK09706   2 KNLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCS 60
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
1-63 9.38e-04

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 35.54  E-value: 9.38e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 817233755   1 MHSQNQAFGKALRSLRKARKVTQRDLAIHARLDRSYVSAMELGENSPTLDTLLALCRGLDISL 63
Cdd:PRK09943   1 MSDEGLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSL 63
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 12-65 1.08e-03

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: 33.67  E-value: 1.08e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 817233755  12 LRSLRKARKVTQRDLAIHARLDRSYVSAMELGE-NSPTLDTLLALCRGLDISLVD 65
Cdd:pfam13443  2 LRKLMADRGISKSDLARATGISRATLSRLRKGKpKRVSLDTLDKICDALGCQPGD 56
 
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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