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Conserved domains on  [gi|712915109|ref|YP_009102746|]
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RIIB lysis inhibitor [Escherichia phage ECML-134]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11220974)

helix-turn-helix (HTH) domain-containing protein may function in DNA binding

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_29 pfam13551
Winged helix-turn helix; This helix-turn-helix domain is often found in transferases and is ...
 13-49 4.08e-03

Winged helix-turn helix; This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.


:

Pssm-ID: 433301 [Multi-domain]  Cd Length: 64  Bit Score: 35.04  E-value: 4.08e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 712915109   13 AEIVKLYSSGNYTQQELADWQGVSVDTIRRVLKNAEE 49
Cdd:pfam13551   2 ALALLLLAEGVSTVSQAARLLGLSRRTVYRWLKRFNE 38
 
Name Accession Description Interval E-value
HTH_29 pfam13551
Winged helix-turn helix; This helix-turn-helix domain is often found in transferases and is ...
 13-49 4.08e-03

Winged helix-turn helix; This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.


Pssm-ID: 433301 [Multi-domain]  Cd Length: 64  Bit Score: 35.04  E-value: 4.08e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 712915109   13 AEIVKLYSSGNYTQQELADWQGVSVDTIRRVLKNAEE 49
Cdd:pfam13551   2 ALALLLLAEGVSTVSQAARLLGLSRRTVYRWLKRFNE 38
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 4-49 6.69e-03

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 34.39  E-value: 6.69e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 712915109   4 IKCLTKNEQaEIVKLYSSGNYTQQELADWQGVSVDTIRRVLKNAEE 49
Cdd:cd06171    8 LDKLPERER-EVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52
 
Name Accession Description Interval E-value
HTH_29 pfam13551
Winged helix-turn helix; This helix-turn-helix domain is often found in transferases and is ...
 13-49 4.08e-03

Winged helix-turn helix; This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.


Pssm-ID: 433301 [Multi-domain]  Cd Length: 64  Bit Score: 35.04  E-value: 4.08e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 712915109   13 AEIVKLYSSGNYTQQELADWQGVSVDTIRRVLKNAEE 49
Cdd:pfam13551   2 ALALLLLAEGVSTVSQAARLLGLSRRTVYRWLKRFNE 38
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 4-49 6.69e-03

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 34.39  E-value: 6.69e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 712915109   4 IKCLTKNEQaEIVKLYSSGNYTQQELADWQGVSVDTIRRVLKNAEE 49
Cdd:cd06171    8 LDKLPERER-EVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52
 
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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