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Conserved domains on  [gi|28876251|ref|NP_795440|]
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hypothetical protein SpyM3_0967 [Streptococcus phage 315.2]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10601889)

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_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 4-60 2.03e-09

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: 47.54  E-value: 2.03e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28876251    4 KIEALLIEKKMTKYELSQKAGLNQNCLIDLKKGRKKSLKFDDVVKIADVLGVSLDEF 60
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALGCQPGDL 57
 
Name Accession Description Interval E-value
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 4-60 2.03e-09

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: 47.54  E-value: 2.03e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28876251    4 KIEALLIEKKMTKYELSQKAGLNQNCLIDLKKGRKKSLKFDDVVKIADVLGVSLDEF 60
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALGCQPGDL 57
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
4-59 3.16e-09

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 47.45  E-value: 3.16e-09
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*.
gi 28876251  4 KIEALLIEKKMTKYELSQKAGLNQNCLIDLKKGRKKSLKFDDVVKIADVLGVSLDE 59
Cdd:COG3655  5 KLDELLAERGMTKKELAEATGISRATLSRLKNGKAKAVRLDTLEKICKALDCQPGD 60
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
4-60 1.48e-06

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.19  E-value: 1.48e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 28876251     4 KIEALLIEKKMTKYELSQKAGLNQNCLIDLKKGRKKsLKFDDVVKIADVLGVSLDEF 60
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK-PSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-60 8.75e-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: 38.30  E-value: 8.75e-06
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*..
gi 28876251  4 KIEALLIEKKMTKYELSQKAGLNQNCLIDLKKGrKKSLKFDDVVKIADVLGVSLDEF 60
Cdd:cd00093  3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENG-KRNPSLETLEKLAKALGVSLDEL 58
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 8-57 6.27e-04

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 34.73  E-value: 6.27e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 28876251    8 LLIEKKMTKYELSQKAGLNQNCLIDLKKGRKK-SLKFddVVKIADVLGVSL 57
Cdd:PRK13890  13 LLDERHMTKKELSERSGVSISFLSDLTTGKANpSLKV--MEAIADALETPL 61
 
Name Accession Description Interval E-value
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 4-60 2.03e-09

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: 47.54  E-value: 2.03e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28876251    4 KIEALLIEKKMTKYELSQKAGLNQNCLIDLKKGRKKSLKFDDVVKIADVLGVSLDEF 60
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALGCQPGDL 57
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
4-59 3.16e-09

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 47.45  E-value: 3.16e-09
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*.
gi 28876251  4 KIEALLIEKKMTKYELSQKAGLNQNCLIDLKKGRKKSLKFDDVVKIADVLGVSLDE 59
Cdd:COG3655  5 KLDELLAERGMTKKELAEATGISRATLSRLKNGKAKAVRLDTLEKICKALDCQPGD 60
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
4-60 1.48e-06

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.19  E-value: 1.48e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 28876251     4 KIEALLIEKKMTKYELSQKAGLNQNCLIDLKKGRKKsLKFDDVVKIADVLGVSLDEF 60
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK-PSLETLKKLAKALGVSLDEL 56
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
4-60 3.81e-06

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 39.98  E-value: 3.81e-06
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*..
gi 28876251  4 KIEALLIEKKMTKYELSQKAGLNQNCLIDLKKGRKkSLKFDDVVKIADVLGVSLDEF 60
Cdd:COG1396 11 RLRELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKALGVSLDEL 66
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-60 8.75e-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: 38.30  E-value: 8.75e-06
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*..
gi 28876251  4 KIEALLIEKKMTKYELSQKAGLNQNCLIDLKKGrKKSLKFDDVVKIADVLGVSLDEF 60
Cdd:cd00093  3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENG-KRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 5-60 1.63e-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: 37.52  E-value: 1.63e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 28876251    5 IEALLIEKKMTKYELSQKAGLNQNCLIDLKKGrKKSLKFDDVVKIADVLGVSLDEF 60
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENG-KREPSLETLKKLAEALGVSLDEL 55
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
4-60 2.81e-04

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 34.82  E-value: 2.81e-04
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*..
gi 28876251  4 KIEALLIEKKMTKYELSQKAGLNQNCLIDLKKGrKKSLKFDDVVKIADVLGVSLDEF 60
Cdd:COG1476  8 RLKELRKERGLTQEELAELLGVSRQTISAIENG-KYNPSLELALKIARALGVSLEEL 63
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 8-57 6.27e-04

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 34.73  E-value: 6.27e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 28876251    8 LLIEKKMTKYELSQKAGLNQNCLIDLKKGRKK-SLKFddVVKIADVLGVSL 57
Cdd:PRK13890  13 LLDERHMTKKELSERSGVSISFLSDLTTGKANpSLKV--MEAIADALETPL 61
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-60 4.92e-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: 31.49  E-value: 4.92e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28876251    4 KIEALLIEKKMTKYELSQKAGLNQNCLIDLKKGRKKsLKFDDVVKIADVLGVSLDEF 60
Cdd:pfam12844  3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSV-PPAETLYKIAELLGVPANWL 58
 
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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