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Conserved domains on  [gi|2052873225|tpg|DAF54194|]
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MAG TPA: ECF sigma factor [Phage sp. ctcqm2]

Protein Classification

sigma-70 RNA polymerase sigma factor region 4 domain-containing protein( domain architecture ID 1001861)

sigma-70 RNA polymerase sigma factor region 4 domain-containing protein which may or may not bind DNA or function as a sigma factor.

Gene Ontology:  GO:0003677|GO:0016987|GO:0006352
PubMed:  1597408

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
sigma70-ECF super family cl37189
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 29-72 2.70e-04

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


The actual alignment was detected with superfamily member TIGR02937:

Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.94  E-value: 2.70e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2052873225  29 LPEDEESCIILCDIRRKSYIQVSNALHVSPESVKRNRRRAFSKI 72
Cdd:TIGR02937 111 LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 29-72 2.70e-04

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.94  E-value: 2.70e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2052873225  29 LPEDEESCIILCDIRRKSYIQVSNALHVSPESVKRNRRRAFSKI 72
Cdd:TIGR02937 111 LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 29-72 6.02e-04

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: 6.02e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 2052873225 29 LPEDEESCIILCDIRRKSYIQVSNALHVSPESVKRNRRRAFSKI 72
Cdd:cd06171   11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 29-77 1.31e-03

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 34.97  E-value: 1.31e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2052873225  29 LPEDEESCIILCDIRRKSYIQVSNALHVSPESVKRNRRRAFSKIVDALT 77
Cdd:COG1595   128 LPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALE 176
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 29-72 2.70e-04

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.94  E-value: 2.70e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2052873225  29 LPEDEESCIILCDIRRKSYIQVSNALHVSPESVKRNRRRAFSKI 72
Cdd:TIGR02937 111 LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 29-72 6.02e-04

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: 6.02e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 2052873225 29 LPEDEESCIILCDIRRKSYIQVSNALHVSPESVKRNRRRAFSKI 72
Cdd:cd06171   11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 29-77 1.31e-03

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 34.97  E-value: 1.31e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2052873225  29 LPEDEESCIILCDIRRKSYIQVSNALHVSPESVKRNRRRAFSKIVDALT 77
Cdd:COG1595   128 LPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALE 176
 
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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