MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Bacteria]
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.
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 ... |
17-134 | 7.47e-06 | |||
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: 43.10 E-value: 7.47e-06
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Name | Accession | Description | Interval | E-value | |||
sigma70-ECF | TIGR02937 | RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
17-134 | 7.47e-06 | |||
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: 43.10 E-value: 7.47e-06
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RpoE | COG1595 | DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
17-135 | 9.40e-06 | |||
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: 43.06 E-value: 9.40e-06
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Sigma70_r4 | cd06171 | Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
77-131 | 1.99e-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: 1.99e-03
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Sigma70_r4 | pfam04545 | Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
83-132 | 3.60e-03 | |||
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives. Pssm-ID: 461347 [Multi-domain] Cd Length: 50 Bit Score: 33.56 E-value: 3.60e-03
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Name | Accession | Description | Interval | E-value | |||
sigma70-ECF | TIGR02937 | RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
17-134 | 7.47e-06 | |||
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: 43.10 E-value: 7.47e-06
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RpoE | COG1595 | DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
17-135 | 9.40e-06 | |||
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: 43.06 E-value: 9.40e-06
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FliA | COG1191 | DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
79-135 | 1.33e-05 | |||
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase Pssm-ID: 440804 [Multi-domain] Cd Length: 236 Bit Score: 42.89 E-value: 1.33e-05
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Sigma70_r4 | cd06171 | Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
77-131 | 1.99e-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: 1.99e-03
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Sigma70_r4 | pfam04545 | Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
83-132 | 3.60e-03 | |||
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives. Pssm-ID: 461347 [Multi-domain] Cd Length: 50 Bit Score: 33.56 E-value: 3.60e-03
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Blast search parameters | ||||
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