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Conserved domains on  [gi|750154972|ref|WP_040459047|]
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RNA polymerase sigma factor [Limosilactobacillus antri]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

RNA polymerase sigma factor plays a role in bacterial signal transduction and is regulated by anti-sigma factors. May belong to the ECF-type subfamily. Generally, sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

CATH:  1.10.1740.10
Gene Ontology:  GO:0016987|GO:0006352|GO:0003677
PubMed:  28575802
SCOP:  4003741

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 18-182 1.43e-16

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: 73.49  E-value: 1.43e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  18 EEIFQRYRPLIIKLWQRYYVSGLELADWEQEarpVILRVLE-LYRGDGKDQFSGFLKQSLVNRILDLYRARQAHKRIPAE 96
Cdd:COG1595   20 EELYERYRPRLYRYARRLLGDRADAEDLVQE---TFLRLWRkLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  97 KIGALTPESEEmlqeqpwrqPEELVHGHF---CLRQLIAACSPFERQVLI-SYNQGYSTDEVAERLRCTKRQVQSAMGRS 172
Cdd:COG1595   97 LAEELPDEAAD---------PEEALEAEElleALLAALERLPPRQREVLVlRYLEGLSYAEIAEILGISEGTVKSRLSRA 167

                        170
                 ....*....|
gi 750154972 173 RRKMLEIIQA 182
Cdd:COG1595  168 RKKLREALEE 177
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 18-182 1.43e-16

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: 73.49  E-value: 1.43e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  18 EEIFQRYRPLIIKLWQRYYVSGLELADWEQEarpVILRVLE-LYRGDGKDQFSGFLKQSLVNRILDLYRARQAHKRIPAE 96
Cdd:COG1595   20 EELYERYRPRLYRYARRLLGDRADAEDLVQE---TFLRLWRkLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  97 KIGALTPESEEmlqeqpwrqPEELVHGHF---CLRQLIAACSPFERQVLI-SYNQGYSTDEVAERLRCTKRQVQSAMGRS 172
Cdd:COG1595   97 LAEELPDEAAD---------PEEALEAEElleALLAALERLPPRQREVLVlRYLEGLSYAEIAEILGISEGTVKSRLSRA 167

                        170
                 ....*....|
gi 750154972 173 RRKMLEIIQA 182
Cdd:COG1595  168 RKKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-180 1.51e-16

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: 72.77  E-value: 1.51e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972   18 EEIFQRYRPLIIKLWQRYYVSGLELADWEQEarpVILRVLELY-RGDGKDQFSGFLKQSLVNRILDLYRARQAHKRIPAE 96
Cdd:TIGR02937   4 EELYERYLPLVYRYARRYLGDDADAEDLVQE---AFLKLLEALdRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972   97 kigALTPESEEMLQEQPWRQPEELvhghFCLRQLIAACSPFERQVLI-SYNQGYSTDEVAERLRCTKRQVQSAMGRSRRK 175
Cdd:TIGR02937  81 ---LEELLDSDPSPEEELEQEEER----EALREALEKLPEREREVLVlRYLEGLSYKEIAEILGISVGTVKRRLKRARKK 153


                  ....*
gi 750154972  176 MLEII 180
Cdd:TIGR02937 154 LRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 18-183 9.11e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 49.58  E-value: 9.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  18 EEIFQRYRPLIIKLWQRYYVSGLELADWEQEARPVILRVLELYRGDGKDqfSGFLKQSLVNRILDLYRARQAHKripaEK 97
Cdd:PRK11924  16 SELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSA--RTWLLTIARNVCYDLLRRRRREK----AV 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  98 IGALTPESEEMLQeqpWRQPEELVHGHFCLRQL---IAACSPFERQVLI-SYNQGYSTDEVAERLRCTKRQVQSAMGRSR 173
Cdd:PRK11924  90 LSDDALEPEFAET---AETPEAALLAKDDLARIdrcLDALPVKQREVFLlRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166

                        170
                 ....*....|
gi 750154972 174 RKMLEIIQAS 183
Cdd:PRK11924 167 QLLRECLEAQ 176
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 20-88 9.96e-05

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 39.11  E-value: 9.96e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 750154972   20 IFQRYRPLIIKLWQRYYVSGLELADWEQEARPVILRVLELYRGDGKDQFSGFLKQSLVNRILDLYRARQ 88
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 126-176 6.14e-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: 33.62  E-value: 6.14e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 750154972 126 CLRQLIAACSPFERQVLI-SYNQGYSTDEVAERLRCTKRQVQSAMGRSRRKM 176
Cdd:cd06171    3 RLEEALDKLPEREREVILlRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 18-182 1.43e-16

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: 73.49  E-value: 1.43e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  18 EEIFQRYRPLIIKLWQRYYVSGLELADWEQEarpVILRVLE-LYRGDGKDQFSGFLKQSLVNRILDLYRARQAHKRIPAE 96
Cdd:COG1595   20 EELYERYRPRLYRYARRLLGDRADAEDLVQE---TFLRLWRkLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  97 KIGALTPESEEmlqeqpwrqPEELVHGHF---CLRQLIAACSPFERQVLI-SYNQGYSTDEVAERLRCTKRQVQSAMGRS 172
Cdd:COG1595   97 LAEELPDEAAD---------PEEALEAEElleALLAALERLPPRQREVLVlRYLEGLSYAEIAEILGISEGTVKSRLSRA 167

                        170
                 ....*....|
gi 750154972 173 RRKMLEIIQA 182
Cdd:COG1595  168 RKKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-180 1.51e-16

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: 72.77  E-value: 1.51e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972   18 EEIFQRYRPLIIKLWQRYYVSGLELADWEQEarpVILRVLELY-RGDGKDQFSGFLKQSLVNRILDLYRARQAHKRIPAE 96
Cdd:TIGR02937   4 EELYERYLPLVYRYARRYLGDDADAEDLVQE---AFLKLLEALdRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972   97 kigALTPESEEMLQEQPWRQPEELvhghFCLRQLIAACSPFERQVLI-SYNQGYSTDEVAERLRCTKRQVQSAMGRSRRK 175
Cdd:TIGR02937  81 ---LEELLDSDPSPEEELEQEEER----EALREALEKLPEREREVLVlRYLEGLSYKEIAEILGISVGTVKRRLKRARKK 153


                  ....*
gi 750154972  176 MLEII 180
Cdd:TIGR02937 154 LRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 18-183 9.11e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 49.58  E-value: 9.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  18 EEIFQRYRPLIIKLWQRYYVSGLELADWEQEARPVILRVLELYRGDGKDqfSGFLKQSLVNRILDLYRARQAHKripaEK 97
Cdd:PRK11924  16 SELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSA--RTWLLTIARNVCYDLLRRRRREK----AV 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  98 IGALTPESEEMLQeqpWRQPEELVHGHFCLRQL---IAACSPFERQVLI-SYNQGYSTDEVAERLRCTKRQVQSAMGRSR 173
Cdd:PRK11924  90 LSDDALEPEFAET---AETPEAALLAKDDLARIdrcLDALPVKQREVFLlRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166

                        170
                 ....*....|
gi 750154972 174 RKMLEIIQAS 183
Cdd:PRK11924 167 QLLRECLEAQ 176
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 20-88 9.96e-05

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 39.11  E-value: 9.96e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 750154972   20 IFQRYRPLIIKLWQRYYVSGLELADWEQEARPVILRVLELYRGDGKDQFSGFLKQSLVNRILDLYRARQ 88
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 124-176 2.96e-04

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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 37.05  E-value: 2.96e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 750154972  124 HFCLRQLIAACSPFERQVLI-SYNQGYSTDEVAERLRCTKRQVQSAMGRSRRKM 176
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLlRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 18-179 1.83e-03

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 37.24  E-value: 1.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  18 EEIFQRYRPliiKLWQR--YYVSGLELAdwEQEARPVILRvleLYRGDGKDQFS--GFLKQSLVNRILDLYRARQAHKRI 93
Cdd:PRK09639   6 EDLFEQYYP---DVVQQifYIVKDRTQA--EDLAQEVFLR---LYRSDFKGIENekGWLIKSARNVAYNYLRSEKRRRAR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  94 PAEKI----GALTPESEEMlqeqpWRQPEELVHGHFCLRQliaaCSPFERQVLISYNQGYSTDEVAERLRCTKRQVQSAM 169
Cdd:PRK09639  78 ILGEFqwqeVDNEPSPEEI-----WIRKEEITKVQEVLAK----MTERDRTVLLLRFSGYSYKEIAEALGIKESSVGTTL 148

                        170
                 ....*....|
gi 750154972 170 GRSRRKMLEI 179
Cdd:PRK09639 149 ARAKKKFRKI 158
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
18-176 2.20e-03

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 37.43  E-value: 2.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  18 EEIFQRYRPLIIKLWQRYYVSGLELADWEQEARPVILRVLELYRGDGKDQFSGFLKQSLVNRILDLYRARQAHKRIPAEK 97
Cdd:COG2771   12 ALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALL 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 750154972  98 IGALTPESEEMLQEQPWRQPEELVHGHFCLRQLIAACSPFERQVLISYNQGYSTDEVAERLRCTKRQVQSAMGRSRRKM 176
Cdd:COG2771   92 ALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 18-178 2.40e-03

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 37.00  E-value: 2.40e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  18 EEIFQRYRPliiKLWQ---RYYVSGLELADWEQEARPVILRVLELYRGDGkdQFSGFLKQSLVNRILDLYRARQAHKRIP 94
Cdd:PRK09643  30 GELFRRHHR---RLWAvarRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNACLDRLRRAKARPTVP 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  95 aekigalTPESEEMLQEQPwrQPEELVHGHFCLRQLIAACSPFERQVLISYN-QGYSTDEVAERLRCTKRQVQSAMGRSR 173
Cdd:PRK09643 105 -------LDDVYPVAQLER--DPTARVETALAVQRALMRLPVEQRAALVAVDmQGYSVADAARMLGVAEGTVKSRCARGR 175


                 ....*
gi 750154972 174 RKMLE 178
Cdd:PRK09643 176 ARLAE 180
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 57-179 2.68e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 36.96  E-value: 2.68e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  57 LELYRGDGKDQFSGFLKQSLV----NRILDLYRARQAHKRiPAEKIGaltpesEEMLQEQPWRQPEELVHGHFC---LRQ 129
Cdd:PRK12519  65 LSLWRKSSYDPKRGSLSSYLLtltrSRAIDRLRSRRSRQR-LLERWQ------QELLGEASEDTPLEQASLAERsqrVQT 137

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 750154972 130 LIAACSPFERQVL-ISYNQGYSTDEVAERLRCTKRQVQSamgRSRRKMLEI 179
Cdd:PRK12519 138 ALAQLPESQRQVLeLAYYEGLSQSEIAKRLGIPLGTVKA---RARQGLLKL 185
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 78-178 3.13e-03

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 36.89  E-value: 3.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750154972  78 NRILDLYRARQAHKRIPAEKIGALTPESEEMLQeqpwrqpeELVHghfCLRQLIAACSPFERQVLISYN-QGYSTDEVAE 156
Cdd:PRK09637  62 NTIIDFYRKKNRSEELPDDLLFEDEEREENAKK--------ELAP---CLRPFIDALPEKYAEALRLTElEGLSQKEIAE 130

                         90       100
                 ....*....|....*....|....*
gi 750154972 157 RLRCTKRQVQSAMGRSR---RKMLE 178
Cdd:PRK09637 131 KLGLSLSGAKSRVQRGRvklKELLE 155
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 126-176 6.14e-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: 33.62  E-value: 6.14e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 750154972 126 CLRQLIAACSPFERQVLI-SYNQGYSTDEVAERLRCTKRQVQSAMGRSRRKM 176
Cdd:cd06171    3 RLEEALDKLPEREREVILlRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
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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