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Conserved domains on  [gi|877058764|gb|AKQ07652|]
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repressor [Mycobacterium phage Smeadley]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 1015842)

sigma-70 family RNA polymerase sigma factor is an initiation factor that promotes the attachment of RNA polymerase to specific initiation sites and is then released

Gene Ontology:  GO:0016987|GO:0003677|GO:0006352

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HipB super family cl34252
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
18-51 1.35e-03

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


The actual alignment was detected with superfamily member COG1396:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 36.13  E-value: 1.35e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 877058764  18 KAKGFTQTEIAEMYGVTRQYVSWIKKtygGRLTP 51
Cdd:COG1396   17 KARGLTQEELAERLGVSRSTISRIER---GRRNP 47
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
18-51 1.35e-03

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 36.13  E-value: 1.35e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 877058764  18 KAKGFTQTEIAEMYGVTRQYVSWIKKtygGRLTP 51
Cdd:COG1396   17 KARGLTQEELAERLGVSRSTISRIER---GRRNP 47
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 13-52 5.59e-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: 33.68  E-value: 5.59e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 877058764  13 IVEDLKAKGFTQTEIAEMYGVTRQYVSWIKKtygGRLTPK 52
Cdd:cd00093    4 LKELRKEKGLTQEELAEKLGVSRSTISRIEN---GKRNPS 40
tfx TIGR00721
DNA-binding protein, Tfx family; PSI-BLAST starting with one member of this family converges ...
 14-43 6.69e-03

DNA-binding protein, Tfx family; PSI-BLAST starting with one member of this family converges with significant hits only to other members of the family, which is restricted to the Archaea. Homology is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter. [Regulatory functions, DNA interactions]


Pssm-ID: 129804 [Multi-domain]  Cd Length: 137  Bit Score: 35.24  E-value: 6.69e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 877058764   14 VEDLKAKGFTQTEIAEMYGVTRQYVSWIKK 43
Cdd:TIGR00721  14 VLELREKGLSQKEIAKELKTTRANVSAIEK 43
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 13-39 9.71e-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: 32.90  E-value: 9.71e-03
                          10        20
                  ....*....|....*....|....*..
gi 877058764   13 IVEDLKAKGFTQTEIAEMYGVTRQYVS 39
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTIS 27
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
18-51 1.35e-03

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 36.13  E-value: 1.35e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 877058764  18 KAKGFTQTEIAEMYGVTRQYVSWIKKtygGRLTP 51
Cdd:COG1396   17 KARGLTQEELAERLGVSRSTISRIER---GRRNP 47
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
13-39 4.69e-03

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 34.80  E-value: 4.69e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 877058764  13 IVEDLKAKGFTQTEIAEMYGVTR----QYVS 39
Cdd:COG2522   20 LAKELVERGLSQSEIAKLLGITQaavsQYLS 50
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 13-52 5.59e-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: 33.68  E-value: 5.59e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 877058764  13 IVEDLKAKGFTQTEIAEMYGVTRQYVSWIKKtygGRLTPK 52
Cdd:cd00093    4 LKELRKEKGLTQEELAEKLGVSRSTISRIEN---GKRNPS 40
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
18-51 5.68e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 34.05  E-value: 5.68e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 877058764  18 KAKGFTQTEIAEMYGVTRQYVSWIKKtygGRLTP 51
Cdd:COG1476   14 KERGLTQEELAELLGVSRQTISAIEN---GKYNP 44
tfx TIGR00721
DNA-binding protein, Tfx family; PSI-BLAST starting with one member of this family converges ...
 14-43 6.69e-03

DNA-binding protein, Tfx family; PSI-BLAST starting with one member of this family converges with significant hits only to other members of the family, which is restricted to the Archaea. Homology is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter. [Regulatory functions, DNA interactions]


Pssm-ID: 129804 [Multi-domain]  Cd Length: 137  Bit Score: 35.24  E-value: 6.69e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 877058764   14 VEDLKAKGFTQTEIAEMYGVTRQYVSWIKK 43
Cdd:TIGR00721  14 VLELREKGLSQKEIAKELKTTRANVSAIEK 43
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 13-39 9.71e-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: 32.90  E-value: 9.71e-03
                          10        20
                  ....*....|....*....|....*..
gi 877058764   13 IVEDLKAKGFTQTEIAEMYGVTRQYVS 39
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTIS 27
HTH_23 pfam13384
Homeodomain-like domain;
17-42 9.88e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 32.63  E-value: 9.88e-03
                          10        20
                  ....*....|....*....|....*..
gi 877058764   17 LKAKGFTQTEIAEMYGVTRQYVS-WIK 42
Cdd:pfam13384  13 LLAEGLSVKEIAELLGVSRRTVYrWLK 39
 
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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