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Conserved domains on  [gi|2526794203|ref|WP_288132834|]
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RNA polymerase sigma factor [Microbulbifer sp.]

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]; ...
 21-163 1.63e-24

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: 93.52  E-value: 1.63e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  21 EIRRYVQRHSPDPTEAADYYQECIAIVLEQSRR-RAIENPVAYAIRTARNLI-----SKHKRPEQLEE--DDAVSPAPSP 92
Cdd:COG1595    29 RLYRYARRLLGDRADAEDLVQETFLRLWRKLDSfRGRGSFRAWLYRIARNLAidhlrKRRRRRELLDElaEELPDEAADP 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2526794203  93 EDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRALVDIQLHLDKQG 163
Cdd:COG1595   109 EEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEG 179
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 21-163 1.63e-24

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: 93.52  E-value: 1.63e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  21 EIRRYVQRHSPDPTEAADYYQECIAIVLEQSRR-RAIENPVAYAIRTARNLI-----SKHKRPEQLEE--DDAVSPAPSP 92
Cdd:COG1595    29 RLYRYARRLLGDRADAEDLVQETFLRLWRKLDSfRGRGSFRAWLYRIARNLAidhlrKRRRRRELLDElaEELPDEAADP 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2526794203  93 EDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRALVDIQLHLDKQG 163
Cdd:COG1595   109 EEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEG 179
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 22-159 5.40e-21

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: 83.55  E-value: 5.40e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  22 IRRYVQRHSPDPTEAADYYQECIAIVLEQSRR-RAIENPVAYAIRTARNLI------SKHKRPEQLEEDDAVSPAPSPED 94
Cdd:TIGR02937  14 VYRYARRYLGDDADAEDLVQEAFLKLLEALDRfDPEGSFKAWLFRIARNLIldylrrKRRLRRELDLLEELLDSDPSPEE 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2526794203  95 CYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRALVDIQLHL 159
Cdd:TIGR02937  94 ELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 20-152 2.21e-20

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 82.13  E-value: 2.21e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  20 TEIRRYVQRHSPDPTEAADYYQECIAIVLEQSRRRAIENPVAYAIRTARNL-ISKHKR-------PEQLEEDDAVSPAPS 91
Cdd:PRK12527    6 RELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLvVDRHRRhrvrqaePLEVLDEEERLHSPS 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2526794203  92 PEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRAL 152
Cdd:PRK12527   86 PQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAM 146
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 102-152 4.34e-10

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: 52.46  E-value: 4.34e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2526794203 102 LAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRAL 152
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRAR 51
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 102-152 3.10e-05

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: 39.78  E-value: 3.10e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2526794203 102 LAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRAL 152
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRAL 51
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 21-163 1.63e-24

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: 93.52  E-value: 1.63e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  21 EIRRYVQRHSPDPTEAADYYQECIAIVLEQSRR-RAIENPVAYAIRTARNLI-----SKHKRPEQLEE--DDAVSPAPSP 92
Cdd:COG1595    29 RLYRYARRLLGDRADAEDLVQETFLRLWRKLDSfRGRGSFRAWLYRIARNLAidhlrKRRRRRELLDElaEELPDEAADP 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2526794203  93 EDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRALVDIQLHLDKQG 163
Cdd:COG1595   109 EEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEG 179
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 22-159 5.40e-21

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: 83.55  E-value: 5.40e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  22 IRRYVQRHSPDPTEAADYYQECIAIVLEQSRR-RAIENPVAYAIRTARNLI------SKHKRPEQLEEDDAVSPAPSPED 94
Cdd:TIGR02937  14 VYRYARRYLGDDADAEDLVQEAFLKLLEALDRfDPEGSFKAWLFRIARNLIldylrrKRRLRRELDLLEELLDSDPSPEE 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2526794203  95 CYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRALVDIQLHL 159
Cdd:TIGR02937  94 ELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 20-152 2.21e-20

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 82.13  E-value: 2.21e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  20 TEIRRYVQRHSPDPTEAADYYQECIAIVLEQSRRRAIENPVAYAIRTARNL-ISKHKR-------PEQLEEDDAVSPAPS 91
Cdd:PRK12527    6 RELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLvVDRHRRhrvrqaePLEVLDEEERLHSPS 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2526794203  92 PEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRAL 152
Cdd:PRK12527   86 PQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAM 146
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 22-159 7.64e-13

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 62.58  E-value: 7.64e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  22 IRRYVQRHSPDPTEAADYYQECIAIVLEQ-SRRRAIENPVAYAIRTARNLISKHKRPEQLEED--DAVSPAPSPEDCYHT 98
Cdd:TIGR02985  14 LCAFARRYVKDEEDAEDIVQDVFLKLWENrETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKyqEELAEIEERELSEAD 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2526794203  99 GQRL-------AQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRALVDIQLHL 159
Cdd:TIGR02985  94 PEEEleakeleEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 55-153 2.89e-10

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 55.46  E-value: 2.89e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  55 AIENPVAYAIRTARNLISKHKRPEQLEED---------DAVSPAPSPEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRV 125
Cdd:PRK07037   44 AVKQPVAYLFRIVRNLAIDHYRRQALENKyhgdeedglDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRL 123

                          90       100
                  ....*....|....*....|....*...
gi 2526794203 126 HGESREQIAESMNISREAVKKHITRALV 153
Cdd:PRK07037  124 HGETQKDIARELGVSPTLVNFMIRDALV 151
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 102-152 4.34e-10

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: 52.46  E-value: 4.34e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2526794203 102 LAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRAL 152
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRAR 51
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 21-152 2.83e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 53.05  E-value: 2.83e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  21 EIRRYVQRHSPDPTEAADYYQECIAIVL---EQSRRRAIENPVAYAI--RTARNLISKHKRPEQLEEDDAVSP-----AP 90
Cdd:PRK11924   25 DLLRYARRQLGDRALAEDAVQEAFLRAWrkaDLFNGKGSARTWLLTIarNVCYDLLRRRRREKAVLSDDALEPefaetAE 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2526794203  91 SPEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRAL 152
Cdd:PRK11924  105 TPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 33-151 1.08e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 51.38  E-value: 1.08e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  33 PTEAADYYQECIAIVLEQSRRRAIENPVAYAIRTARNLISKHKRPEQLE----EDDAVSP---APSPEDCYHTGQRLAQI 105
Cdd:PRK12528   28 PQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLEraylEALAQLPervAPSEEERAIILETLVEL 107

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2526794203 106 ARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRA 151
Cdd:PRK12528  108 DQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKA 153
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 24-159 1.55e-08

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 51.35  E-value: 1.55e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  24 RYVQRHSPDPTEAADYYQECIAIV---LEQSRRRAieNPVAYAIRTARNL----ISKHKRP-----------EQLEEDDA 85
Cdd:PRK09652   25 RLLSRLTRDPADAEDLVQETFIKAyraLHSFRGGA--AFYTWLYRIARNTainyLRKQGRRppasdvdaeeaEDFDLADA 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2526794203  86 VSPAPSPEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRALVDIQLHL 159
Cdd:PRK09652  103 LRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 32-152 1.47e-07

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 48.41  E-value: 1.47e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  32 DPTEAADYYQECIAIVLeQSRRRAIENPVAYAIRTARNL----ISKHKRPEQLEED----DAVSPAPSPEDCYHTGQRLA 103
Cdd:PRK09639   26 DRTQAEDLAQEVFLRLY-RSDFKGIENEKGWLIKSARNVaynyLRSEKRRRARILGefqwQEVDNEPSPEEIWIRKEEIT 104

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2526794203 104 QIARVLEDMPPLRRQVFIrRRVHGESREQIAESMNISREAVKKHITRAL 152
Cdd:PRK09639  105 KVQEVLAKMTERDRTVLL-LRFSGYSYKEIAEALGIKESSVGTTLARAK 152
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 51-153 1.48e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 45.70  E-value: 1.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  51 SRRRAIENPVAYAIRTARNLISKHKRPEQLE----EDDAVSPA---PSPEDCYHTGQRLAQIARVLEDMPPLRRQVFIRR 123
Cdd:PRK12529   60 GQREAIRQPRAYLARIANCVLVSWRRRQSLElawlEALATLPEplhPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMA 139

                          90       100       110
                  ....*....|....*....|....*....|
gi 2526794203 124 RVHGESREQIAESMNISREAVKKHITRALV 153
Cdd:PRK12529  140 TLDGMKQKDIAQALDIALPTVKKYIHQAYV 169
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 108-152 7.62e-06

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: 41.26  E-value: 7.62e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2526794203 108 VLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRAL 152
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRAL 45
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 22-151 1.13e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 43.49  E-value: 1.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  22 IRRYVQRHSP-----------DPTEAADYYQECIAIVLEQSR--RRAIENPVAYAIRTARNLISKH--KRPEQLEED--D 84
Cdd:PRK05602   22 FRVLVARKLPrllalatrmlgDPAEAEDVAQETFLRIWKQAPswRPGEARFDTWLHRVVLNLCYDRlrRRREVPVEDapD 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2526794203  85 AVSPAPSPEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRA 151
Cdd:PRK05602  102 VPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARG 168
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 34-151 2.02e-05

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 43.37  E-value: 2.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  34 TEAADYYQECIaIVLEQSRRRAIENPVAYAIRTARNLI------SKHKR--------PEQL--EEDDAVSPAPSPEDCyh 97
Cdd:PRK09636   29 ADAEDIVQEAW-LRWNNADRAQIRDPRAWLTRVVTRLCldrlrsARHRRetyvgpwlPEPVveELDDPLEAVVAAEDL-- 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2526794203  98 tgqRLAQIaRVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRA 151
Cdd:PRK09636  106 ---SLALM-LALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRA 155
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 102-152 3.10e-05

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: 39.78  E-value: 3.10e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2526794203 102 LAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRAL 152
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRAL 51
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 25-152 3.11e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 42.15  E-value: 3.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  25 YVQRHSPDPTEAADYYQECIAIVLEQSRRRAIENPVAYAIRTARNLISKHKRPEQLE----EDDAVSPA---PSPEDCYH 97
Cdd:PRK12523   26 WLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREPRAFLAAVAKGLMFDHFRRAALEqaylAELALVPEaeqPSPEEQHL 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2526794203  98 TGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRAL 152
Cdd:PRK12523  106 ILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGL 160
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 105-150 7.02e-05

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 41.08  E-value: 7.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2526794203 105 IARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITR 150
Cdd:PRK06811  125 ILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSR 170
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 63-151 1.19e-04

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 40.56  E-value: 1.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  63 AIRTARN-LISKHKRP----------EQLEEDDAVSPAPSPEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESRE 131
Cdd:PRK11923   79 AINTAKNhLVSRGRRPpdsdvssedaEFYDGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYE 158

                          90       100
                  ....*....|....*....|
gi 2526794203 132 QIAESMNISREAVKKHITRA 151
Cdd:PRK11923  159 DIASVMQCPVGTVRSRIFRA 178
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 26-152 3.79e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 38.77  E-value: 3.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  26 VQRHSPDPTEAADYYQECIAIVLEQSRRRAIENPVAYAIRTARNLISKHKRPEQLE----EDDAVSP---APSPEDCYHT 98
Cdd:PRK12525   26 LSRQLGCPHSAEDIASETFLQVLALPDPASIREPRALLTTIARRLMYEGWRRQDLEraylQSLAEAPeavQPSPEEQWMV 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2526794203  99 GQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRAL 152
Cdd:PRK12525  106 IETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAF 159
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 67-152 3.83e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 38.99  E-value: 3.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  67 ARNLISKHKRpEQLEEDDAVSPAPSPE---DCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREA 143
Cdd:PRK12537   87 ALNVLRDTRR-EVVLDDDAEETAQTLHeiiDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGT 165


                  ....*....
gi 2526794203 144 VKKHITRAL 152
Cdd:PRK12537  166 VKAWIKRSL 174
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 52-151 4.61e-04

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 38.64  E-value: 4.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  52 RRRAIENpvAYAIRTArnliskhKRPEQLeeddavspAPSPEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESRE 131
Cdd:PRK09651   77 RRNALEK--AYLEMLA-------LMPEGG--------APSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYS 139

                          90       100
                  ....*....|....*....|
gi 2526794203 132 QIAESMNISREAVKKHITRA 151
Cdd:PRK09651  140 EIAHKLGVSVSSVKKYVAKA 159
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 52-163 9.85e-04

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 37.64  E-value: 9.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  52 RRRAIENPVayairtaRNLISKHKRPEQLEE-------DDAVSPAPSPEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRR 124
Cdd:PRK09047   47 RRQKVRNTW-------VSLFSSFSDDDDDDDfdpletlDSADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRY 119

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2526794203 125 VHGESREQIAESMNISREAVKKHITRALVDIQLHLDKQG 163
Cdd:PRK09047  120 WEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG 158
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 75-150 1.32e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 37.22  E-value: 1.32e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2526794203  75 KRPEQLEEDDAVSPAPSPEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITR 150
Cdd:PRK12541   76 KYKTTTIEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHR 151
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 65-150 1.51e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 37.56  E-value: 1.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  65 RTARNLISKHKRPEQ---LEEDDAVSP---APSPEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMN 138
Cdd:PRK12524   84 RVVCNLCTDRLRRRRrasVDLDDAPEPadaAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVME 163

                          90
                  ....*....|..
gi 2526794203 139 ISREAVKKHITR 150
Cdd:PRK12524  164 IGVEAVESLTAR 175
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 22-76 1.61e-03

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: 35.26  E-value: 1.61e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2526794203  22 IRRYVQRHSPDPTEAADYYQECIAIVLEQSRRRAIE---NPVAYAIRTARNLISKHKR 76
Cdd:pfam04542   9 VYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPErgvSFSTWLYTIIRNAIIDYLR 66
PRK06930 PRK06930
positive control sigma-like factor; Validated
 53-156 1.77e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 37.02  E-value: 1.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2526794203  53 RRAIENPVAYAIRTARN--LISKHKRPEQLEEDDAVSPAP--SPEDcyhtgqrLAQIARVLEDMPPLRRQVFIRRRVHGE 128
Cdd:PRK06930   59 RRGIDRRAAYQREVICDplLIQRYFRSMEDLEWDIEEPESviSEWD-------KIRIEDALSVLTEREKEVYLMHRGYGL 131

                          90       100
                  ....*....|....*....|....*...
gi 2526794203 129 SREQIAESMNISREAVKKHITRALVDIQ 156
Cdd:PRK06930  132 SYSEIADYLNIKKSTVQSMIERAEKKIA 159
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 77-151 2.74e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 36.87  E-value: 2.74e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2526794203  77 PEQLEEDDAVSPAPSPEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRRVHGESREQIAESMNISREAVKKHITRA 151
Cdd:PRK11922  115 IAGGERTPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRA 189
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 82-144 6.67e-03

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 35.80  E-value: 6.67e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2526794203  82 EDDAvspAPSPEDCYHTGQRLAQIARVLEDMPPLRRQVFIRRR--VHGESR--EQIAESMNISREAV 144
Cdd:COG0568   180 EDEE---APSPEEALEEELLREELREALDTLTEREREILRLRFglDDGEPHtlEEIGKEFGVSRERV 243
 
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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