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Conserved domains on  [gi|1102501163|gb|APC49604|]
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hypothetical protein BME96_16015 [Virgibacillus halodenitrificans]

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];
1-77 3.45e-16

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.10  E-value: 3.45e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1102501163   1 MKGLGQRLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYLLRGKEYHSSEELPTD 77
Cdd:COG1396     5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLSE 81
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-77 3.45e-16

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.10  E-value: 3.45e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1102501163   1 MKGLGQRLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYLLRGKEYHSSEELPTD 77
Cdd:COG1396     5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLSE 81
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-62 1.07e-11

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: 56.02  E-value: 1.07e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1102501163   5 GQRLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYL 62
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
7-62 1.48e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 52.91  E-value: 1.48e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1102501163    7 RLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYL 62
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-62 3.42e-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: 49.46  E-value: 3.42e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1102501163   8 LENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYL 62
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 4-89 3.16e-03

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 35.21  E-value: 3.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102501163   4 LGQRLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYLLRGKEYHS-----SEELPTDI 78
Cdd:PRK09706    6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFGDEDKQptppvPLNQPVEL 85

                          90
                  ....*....|..
gi 1102501163  79 L-DLKRLLKIYR 89
Cdd:PRK09706   86 SeDQKELLELFD 97
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-77 3.45e-16

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.10  E-value: 3.45e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1102501163   1 MKGLGQRLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYLLRGKEYHSSEELPTD 77
Cdd:COG1396     5 KKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLSE 81
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-67 3.30e-12

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 57.55  E-value: 3.30e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1102501163   1 MKGLGQRLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYLLRGKE 67
Cdd:COG1476     2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-62 1.07e-11

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: 56.02  E-value: 1.07e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1102501163   5 GQRLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYL 62
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
7-62 1.48e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 52.91  E-value: 1.48e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1102501163    7 RLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYL 62
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-62 3.42e-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: 49.46  E-value: 3.42e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1102501163   8 LENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYL 62
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-61 9.34e-08

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: 46.08  E-value: 9.34e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1102501163   4 LGQRLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDY 61
Cdd:COG1813    13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 4-60 8.43e-06

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: 40.59  E-value: 8.43e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1102501163   4 LGQRLENLRERSDYKQKEISALLGFTTNVYGMYEREERA-PSLDTLVELADFFHVSVD 60
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGrPSPAVVERLARALGVDGA 59
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 5-66 1.93e-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: 39.96  E-value: 1.93e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1102501163   5 GQRLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYLLRGK 66
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGE 62
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 4-63 9.57e-05

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: 38.85  E-value: 9.57e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102501163   4 LGQRLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYLL 63
Cdd:COG3620    18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVL 77
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 4-89 3.16e-03

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 35.21  E-value: 3.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1102501163   4 LGQRLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYLLRGKEYHS-----SEELPTDI 78
Cdd:PRK09706    6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFGDEDKQptppvPLNQPVEL 85

                          90
                  ....*....|..
gi 1102501163  79 L-DLKRLLKIYR 89
Cdd:PRK09706   86 SeDQKELLELFD 97
PHA01976 PHA01976
helix-turn-helix protein
 7-65 6.42e-03

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 33.39  E-value: 6.42e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1102501163   7 RLENLRERSDYKQKEISALLGFTTNVYGMYEREERAPSLDTLVELADFFHVSVDYLLRG 65
Cdd:PHA01976    6 QLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGR 64
 
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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