NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1608039465|gb|QBX11395|]
View 

hypothetical protein JavanS568_0004 [Streptococcus satellite phage Javan568]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10475648)

helix-turn-helix (HTH) transcriptional regulator containing a XRE (Xenobiotic Response Element) family HTH domain; similar to Bacillus subtilis uncharacterized HTH-type transcriptional regulator YqaE

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743
SCOP:  4000362

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
XRE super family cl43426
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
8-45 1.11e-03

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


The actual alignment was detected with superfamily member COG1476:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 33.28  E-value: 1.11e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1608039465  8 ARKVRRKRADLMLTKKATAEKLGIKPQTLTKVEQGNYD 45
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYN 43
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
8-45 1.11e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 33.28  E-value: 1.11e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1608039465  8 ARKVRRKRADLMLTKKATAEKLGIKPQTLTKVEQGNYD 45
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYN 43
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 11-42 1.86e-03

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: 32.51  E-value: 1.86e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 1608039465 11 VRRKRADLMLTKKATAEKLGIKPQTLTKVEQG 42
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENG 32
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-45 4.33e-03

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: 31.37  E-value: 4.33e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1608039465  8 ARKVRRKRADLMLTKKATAEKLGIKPQTLTKVEQGNYD 45
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRN 38
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-45 4.37e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 31.33  E-value: 4.37e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1608039465  10 KVRRKRADLMLTKKATAEKLGIKPQTLTKVEQGNYD 45
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK 36
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
8-45 1.11e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 33.28  E-value: 1.11e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1608039465  8 ARKVRRKRADLMLTKKATAEKLGIKPQTLTKVEQGNYD 45
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYN 43
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 11-42 1.86e-03

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: 32.51  E-value: 1.86e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 1608039465 11 VRRKRADLMLTKKATAEKLGIKPQTLTKVEQG 42
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENG 32
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 3-42 2.47e-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: 32.22  E-value: 2.47e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 1608039465  3 LTEDHARKVRRKRADLMLTKKATAEKLGIKPQTLTKVEQG 42
Cdd:COG1813    9 LVEDYGERIREAREARGLSQEELAEKLGVSESTIRRIERG 48
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-45 4.33e-03

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: 31.37  E-value: 4.33e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1608039465  8 ARKVRRKRADLMLTKKATAEKLGIKPQTLTKVEQGNYD 45
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRN 38
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-45 4.37e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 31.33  E-value: 4.37e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1608039465  10 KVRRKRADLMLTKKATAEKLGIKPQTLTKVEQGNYD 45
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK 36
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
8-42 4.52e-03

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 31.89  E-value: 4.52e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 1608039465  8 ARKVRRKRADLMLTKKATAEKLGIKPQTLTKVEQG 42
Cdd:COG1396    9 GERLRELRKARGLTQEELAERLGVSRSTISRIERG 43
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH