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Conserved domains on  [gi|1468707888|ref|WP_117579796|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Bacillota]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11495650)

sigma-70 family RNA polymerase sigma factor is a general transcription factor that reversibly binds RNA polymerase and mediates transcription.

Gene Ontology:  GO:0003677|GO:0016987|GO:0006352
PubMed:  28117604

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 6-136 5.30e-12

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: 59.67  E-value: 5.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1468707888   6 RNDYGERCQFDAYCKLVLYHEAIDYLREMQRRRDRELSFSDIPQMemdklcvvDHYPSDRFtfsshgyDLHIENELVADA 85
Cdd:TIGR02937  43 LDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLDS--------DPSPEEEL-------EQEEEREALREA 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1468707888  86 FAGLSVQEQSILILHFVLDLPDQEVGRLVGMSRSAVQRRRAKSLTELRIKL 136
Cdd:TIGR02937 108 LEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 6-136 5.30e-12

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: 59.67  E-value: 5.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1468707888   6 RNDYGERCQFDAYCKLVLYHEAIDYLREMQRRRDRELSFSDIPQMemdklcvvDHYPSDRFtfsshgyDLHIENELVADA 85
Cdd:TIGR02937  43 LDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLDS--------DPSPEEEL-------EQEEEREALREA 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1468707888  86 FAGLSVQEQSILILHFVLDLPDQEVGRLVGMSRSAVQRRRAKSLTELRIKL 136
Cdd:TIGR02937 108 LEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 6-141 5.50e-10

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: 54.62  E-value: 5.50e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1468707888   6 RNDYGERCQFDAYCKLVLYHEAIDYLRemQRRRDRELSFSDIPQMEMDKLCVVDHYPSDRFTfsshgydlhienELVADA 85
Cdd:COG1595    59 LDSFRGRGSFRAWLYRIARNLAIDHLR--KRRRRRELLDELAEELPDEAADPEEALEAEELL------------EALLAA 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1468707888  86 FAGLSVQEQSILILHFVLDLPDQEVGRLVGMSRSAVQRRRAKSLTELRIKLAALMP 141
Cdd:COG1595   125 LERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGA 180
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 79-133 6.32e-07

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: 43.63  E-value: 6.32e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1468707888  79 NELVADAFAGLSVQEQSILILHFVLDLPDQEVGRLVGMSRSAVQRRRAKSLTELR 133
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 81-137 2.04e-03

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 36.97  E-value: 2.04e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1468707888  81 LVADAFAGLSVQEQSILILHFVLDLPDQEVGRLVGMSRSAVQRRRAKSLTELRIKLA 137
Cdd:PRK06288  205 VIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLA 261
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 6-136 5.30e-12

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: 59.67  E-value: 5.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1468707888   6 RNDYGERCQFDAYCKLVLYHEAIDYLREMQRRRDRELSFSDIPQMemdklcvvDHYPSDRFtfsshgyDLHIENELVADA 85
Cdd:TIGR02937  43 LDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLDS--------DPSPEEEL-------EQEEEREALREA 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1468707888  86 FAGLSVQEQSILILHFVLDLPDQEVGRLVGMSRSAVQRRRAKSLTELRIKL 136
Cdd:TIGR02937 108 LEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 6-141 5.50e-10

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: 54.62  E-value: 5.50e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1468707888   6 RNDYGERCQFDAYCKLVLYHEAIDYLRemQRRRDRELSFSDIPQMEMDKLCVVDHYPSDRFTfsshgydlhienELVADA 85
Cdd:COG1595    59 LDSFRGRGSFRAWLYRIARNLAIDHLR--KRRRRRELLDELAEELPDEAADPEEALEAEELL------------EALLAA 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1468707888  86 FAGLSVQEQSILILHFVLDLPDQEVGRLVGMSRSAVQRRRAKSLTELRIKLAALMP 141
Cdd:COG1595   125 LERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGA 180
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 79-133 6.32e-07

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: 43.63  E-value: 6.32e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1468707888  79 NELVADAFAGLSVQEQSILILHFVLDLPDQEVGRLVGMSRSAVQRRRAKSLTELR 133
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 81-137 2.04e-03

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 36.97  E-value: 2.04e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1468707888  81 LVADAFAGLSVQEQSILILHFVLDLPDQEVGRLVGMSRSAVQRRRAKSLTELRIKLA 137
Cdd:PRK06288  205 VIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLA 261
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 8-137 6.45e-03

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 35.30  E-value: 6.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1468707888   8 DYGERCQFDAYCKLVLYHEAIDYLREmqRRRDRelsfsdipqMEMDKLCVvdhypsDRFTFSSHGYDLHIENELVADAF- 86
Cdd:PRK09640   70 NFEGKSKFKTWLYSITYNECITQYRK--ERRKR---------RLMDALSL------DPLEEASEEKAPKPEERGGLDRWl 132

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1468707888  87 AGLSVQEQSILILHFVLDLPDQEVGRLVGMSRSAVQRRRAKSLTELRIKLA 137
Cdd:PRK09640  133 VHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKFA 183
 
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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