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Conserved domains on  [gi|1525942401|ref|WP_124562163|]
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MULTISPECIES: RNA polymerase sigma factor [unclassified Pedobacter]

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]; ...
 10-157 2.68e-25

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: 95.06  E-value: 2.68e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  10 LEAHKGIIYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLKSSETFNHY 89
Cdd:COG1595    23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEELP 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1525942401  90 FEPP------ELSERADWLYRCIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLLAG 157
Cdd:COG1595   103 DEAAdpeealEAEELLEALLAALERLPPRQREVLVLRyLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEE 177
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 10-157 2.68e-25

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: 95.06  E-value: 2.68e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  10 LEAHKGIIYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLKSSETFNHY 89
Cdd:COG1595    23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEELP 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1525942401  90 FEPP------ELSERADWLYRCIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLLAG 157
Cdd:COG1595   103 DEAAdpeealEAEELLEALLAALERLPPRQREVLVLRyLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 10-155 8.46e-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: 83.17  E-value: 8.46e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  10 LEAHKGIIYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLKSS-----E 84
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLleellD 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1525942401  85 TFNHYFEPPELSERADWLYRCIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLL 155
Cdd:TIGR02937  87 SDPSPEEELEQEEEREALREALEKLPEREREVLVLRyLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 27-156 1.00e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 65.76  E-value: 1.00e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  27 DEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLKSSETFNHYF-----------EPPE- 94
Cdd:PRK11922   53 NDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLVNLAEMVMASTIAggertpladpaEDPEr 132

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1525942401  95 ---LSERADWLYRCIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLLA 156
Cdd:PRK11922  133 aaaRREIRALLERAIDALPDAFRAVFVLRvVEELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 100-151 2.68e-07

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: 45.14  E-value: 2.68e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1525942401 100 DWLYRCIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQL 151
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRyLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 104-151 1.04e-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: 38.24  E-value: 1.04e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1525942401 104 RCIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQL 151
Cdd:cd06171     6 EALDKLPEREREVILLRfGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 10-157 2.68e-25

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: 95.06  E-value: 2.68e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  10 LEAHKGIIYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLKSSETFNHY 89
Cdd:COG1595    23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEELP 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1525942401  90 FEPP------ELSERADWLYRCIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLLAG 157
Cdd:COG1595   103 DEAAdpeealEAEELLEALLAALERLPPRQREVLVLRyLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 10-155 8.46e-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: 83.17  E-value: 8.46e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  10 LEAHKGIIYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLKSS-----E 84
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLleellD 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1525942401  85 TFNHYFEPPELSERADWLYRCIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLL 155
Cdd:TIGR02937  87 SDPSPEEELEQEEEREALREALEKLPEREREVLVLRyLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 27-156 1.00e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 65.76  E-value: 1.00e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  27 DEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLKSSETFNHYF-----------EPPE- 94
Cdd:PRK11922   53 NDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLVNLAEMVMASTIAggertpladpaEDPEr 132

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1525942401  95 ---LSERADWLYRCIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLLA 156
Cdd:PRK11922  133 aaaRREIRALLERAIDALPDAFRAVFVLRvVEELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 33-155 5.87e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 62.81  E-value: 5.87e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  33 DLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLKSSETFNHYFEPPELSE------RADWLYRCI 106
Cdd:PRK12518   39 DLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQFAQRPSRIQDDSLNDQPSRPSDTPdlmqlhYQDLVQQGL 118

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1525942401 107 KQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLL 155
Cdd:PRK12518  119 QTLSLEHRAVLVLHdLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 6-157 1.13e-10

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 56.74  E-value: 1.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401   6 YLDKLeahKGIIYKMVNlyadDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQ-----L 80
Cdd:PRK09652   19 YQPRV---KRLLSRLTR----DPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRPPasdvdA 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  81 KSSETFNHYFEPPELS---------ERADWLYRCIKQLTEIDRSIVML-HLDGFDNTEISEMMGI------SRnhtnvkL 144
Cdd:PRK09652   92 EEAEDFDLADALRDIStpenellsaELEQRVRAAIESLPEELRTAITLrEIEGLSYEEIAEIMGCpigtvrSR------I 165

                         170
                  ....*....|...
gi 1525942401 145 HRIKQQLTTLLAG 157
Cdd:PRK09652  166 FRAREALRAKLQP 178
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 17-155 2.37e-10

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 55.73  E-value: 2.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  17 IYKMVNlyadDEEDRKDLYQEiVFqsWQAY-SRFKGNAQFSTWLYKLSLNVSLSFLSKqQKQTQLKSSETFNHYFEPPEL 95
Cdd:PRK09639   20 IFYIVK----DRTQAEDLAQE-VF--LRLYrSDFKGIENEKGWLIKSARNVAYNYLRS-EKRRRARILGEFQWQEVDNEP 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1525942401  96 SERADWL--------YRCIKQLTEIDRSIVMLHLDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLL 155
Cdd:PRK09639   92 SPEEIWIrkeeitkvQEVLAKMTERDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 27-158 6.38e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 55.28  E-value: 6.38e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  27 DEEDRKDLYQEIVFQSWQAYSRFK-GNAQFSTWLYKLSLNvslsfLSKQQKQTQLKSSETFNHYFEPPELS--------- 96
Cdd:PRK12524   49 DRAEAEDVTQEAMLRLWRIAPDWRqGEARVSTWLYRVVCN-----LCTDRLRRRRRASVDLDDAPEPADAApgaeealie 123

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1525942401  97 -ERADWLYRCIKQLTEIDRSIVML-HLDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLLAGK 158
Cdd:PRK12524  124 gDRMRALDAALAALPERQRQAVVLrHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAALLAGQ 187
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 5-155 8.14e-10

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 54.70  E-value: 8.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401   5 SYLDKLEAHKGIIYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQK----QTQL 80
Cdd:PRK09641   19 AFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRKPdyylDAEV 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  81 KSSETFNHYF------EPPE----LSERADWLYRCIKQLTEIDRSIVML-HLDGFDNTEISEMMGISRNHTNVKLHRIKQ 149
Cdd:PRK09641   99 AGTEGLTMYSqlaaddALPEeqvvSLELQETIQEAILQLPEKYRTVIVLkYIEDLSLKEISEILDLPVGTVKTRIHRGRE 178


                  ....*.
gi 1525942401 150 QLTTLL 155
Cdd:PRK09641  179 ALRKQL 184
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 2-158 5.85e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 52.28  E-value: 5.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401   2 IAKSYLDKLeahkgiiYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLK 81
Cdd:PRK11924   18 LFRPHAPDL-------LRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  82 SSET----FNHYFEPPE--LSERADW--LYRCIKQLTEIDR-SIVMLHLDGFDNTEISEMMGISRNHTNVKLHRIKQQLT 152
Cdd:PRK11924   91 SDDAlepeFAETAETPEaaLLAKDDLarIDRCLDALPVKQReVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170


                  ....*.
gi 1525942401 153 TLLAGK 158
Cdd:PRK11924  171 ECLEAQ 176
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 27-157 1.09e-08

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 51.58  E-value: 1.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  27 DEEDRKDLYQEIVFQSWQAYSRFK-GNAQFSTWLYKLSLNVSLSFLSKQQKQTqlksSEtfnhyfEPPEL---------- 95
Cdd:PRK05602   43 DPAEAEDVAQETFLRIWKQAPSWRpGEARFDTWLHRVVLNLCYDRLRRRREVP----VE------DAPDVpdpapgpdag 112

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1525942401  96 ---SERADWLYRCIKQLTEIDR-SIVMLHLDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLLAG 157
Cdd:PRK05602  113 leaRQRARRVEQALAALPERQReAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLAD 178
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 2-157 4.21e-08

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 49.94  E-value: 4.21e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401   2 IAKSYLDKLEAHKGIIYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLK 81
Cdd:PRK09640   24 VTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKRRLM 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  82 SSETFNHYFEP-----PELSERADwLYRCIKQLTEIDRSIVMLHLDG-FDNTEISEMMGISRNHTNVKLHRIKQQLTTLL 155
Cdd:PRK09640  104 DALSLDPLEEAseekaPKPEERGG-LDRWLVHVNPIDREILVLRFVAeLEFQEIADIMHMGLSATKMRYKRALDKLREKF 182


                  ..
gi 1525942401 156 AG 157
Cdd:PRK09640  183 AG 184
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 10-146 7.06e-08

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 49.25  E-value: 7.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  10 LEAHKGIIYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLksSETFNHY 89
Cdd:PRK09638   24 FQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKLR--LQRAKEE 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  90 FEPPELSERA----DW--LYRCIKQLTEIDRSIVML-HLDGFDNTEISEMMGI------SRNHTNVKLHR 146
Cdd:PRK09638  102 TLRKEKWEAAikgaEWseMLDALSKLDPEFRAPVILkHYYGYTYEEIAKMLNIpegtvkSRVHHGIKQLR 171
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 27-157 1.28e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 48.57  E-value: 1.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  27 DEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLsKQQKQTQL--KSSETFNHYFEPPEL----SERAD 100
Cdd:PRK12515   45 DEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSAL-RRRKHEEIddEAAAAIEDGADTPEValqkSDTSA 123

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1525942401 101 WLYRCIKQLTEIDRSIVML-HLDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLLAG 157
Cdd:PRK12515  124 ALRACLAKLSPAHREIIDLvYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKA 181
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 26-155 1.31e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 48.77  E-value: 1.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  26 DDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFL---SKQQKQTQLKSSETFNHYFEP---------- 92
Cdd:PRK12532   28 DHPDLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALrqiGRQRKVFTLLDDELLDEAFEShfsqnghwtp 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1525942401  93 ---------PE--LSERADW--LYRCIKQLTE-IDRSIVMLHLDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLL 155
Cdd:PRK12532  108 egqpqhwntPEksLNNNEFQkiLQSCLYNLPEnTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
6-76 1.84e-07

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 49.16  E-value: 1.84e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1525942401   6 YLDKLEAHKGII----YKMVNLYADDEedrkDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQK 76
Cdd:PRK08241   21 FAALVEPHRRELlahcYRMLGSVHDAE----DAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALEGRAR 91
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 100-151 2.68e-07

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: 45.14  E-value: 2.68e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1525942401 100 DWLYRCIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQL 151
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRyLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 17-155 4.03e-07

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 47.05  E-value: 4.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  17 IYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFL-SKQQKQTQLKSSETFNHYFEPPE- 94
Cdd:PRK09415   29 VLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLkSWHNKKVIVTEDIFTYMESQKESv 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1525942401  95 -----LSERADWLYRCIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLL 155
Cdd:PRK09415  109 eeeviQNAEDERLASAVMSLPIKYREVIYLFyYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 13-133 7.28e-07

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 46.72  E-value: 7.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  13 HKgiIYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQ-----TQLKSSETFN 87
Cdd:PRK11923   31 HK--ILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLVSRGRRppdsdVSSEDAEFYD 108

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1525942401  88 HY-----FEPPELSERADWL----YRCIKQLTEIDRSIVML-HLDGFDNTEISEMM 133
Cdd:PRK11923  109 GDhalkdIESPERALLRDEIegtvHRTIQQLPEDLRTALTLrEFDGLSYEDIASVM 164
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 26-136 2.71e-06

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 44.98  E-value: 2.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  26 DDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLKSSETFnhYFEPPELS---ERADWL 102
Cdd:PRK09637   23 SNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRSEELPDDLLF--EDEEREENakkELAPCL 100

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1525942401 103 YRCIKQLTEIDRSIVML-HLDGFDNTEISEMMGIS 136
Cdd:PRK09637  101 RPFIDALPEKYAEALRLtELEGLSQKEIAEKLGLS 135
PRK12545 PRK12545
RNA polymerase factor sigma-70;
27-158 9.74e-06

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 43.79  E-value: 9.74e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  27 DEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLN------------VSLSFLSKQQKQTQLKSSETF--NHYFEP 92
Cdd:PRK12545   31 DADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNklidtlrarqrtVNLSALDAELDGEALLDRELFkdNGHWAA 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  93 ---------PE--LSERADW-LYR-CIKQLTE-IDRSIVMLHLDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLLAGK 158
Cdd:PRK12545  111 hakprpwpkPEtiLQQQQFWtLFEtCLDHLPEqIGRVFMMREFLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEK 190
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 11-76 9.81e-06

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: 41.42  E-value: 9.81e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1525942401  11 EAHKGIIYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRF---KGNAqFSTWLYKLSLNVSLSFLSKQQK 76
Cdd:pfam04542   3 ERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdpeRGVS-FSTWLYTIIRNAIIDYLRKQRR 70
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 13-156 1.68e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 42.75  E-value: 1.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  13 HKGIIYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQ--QKQTQLKSSETFNHYF 90
Cdd:PRK12513   35 HRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRRHgaRQAPSLDADEQLHALA 114

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1525942401  91 EPPELSERA-------DWLYRCIKQLTEIDRSIVMLHLDG-FDNTEISEMMGISRNHTNVKLHRIKQQLTTLLA 156
Cdd:PRK12513  115 DDGAAPEQQlslfrdrRRLQAALETLPDEQREVFLLREHGdLELEEIAELTGVPEETVKSRLRYALQKLRELLA 188
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 15-155 2.86e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 42.54  E-value: 2.86e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  15 GIIYKMVNLYADDEedrkDLYQEIVFQSWQAYSRFK-GNAQFSTWLYKLSLNVSLSFlsKQQKQTqlkssETFNHYFEPP 93
Cdd:PRK12538   78 AIALRIVGNRADAE----DVVQDTMLKVWTHRGRWQhGRAKFSTWLYRVVSNRCIDL--RRKPRT-----ENVDAVPEVA 146

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1525942401  94 ----------ELSERADWLYRCIKQLTEIDRSIVML-HLDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLL 155
Cdd:PRK12538  147 dgkpdavsviERNELSDLLEAAMQRLPEQQRIAVILsYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 104-151 1.04e-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: 38.24  E-value: 1.04e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1525942401 104 RCIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQL 151
Cdd:cd06171     6 EALDKLPEREREVILLRfGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 27-151 1.62e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 39.92  E-value: 1.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  27 DEEDRKDLYQEIVFQSWQAYSRFKGNaQFSTWLYKLSLNVSLSFLSKQQKQTQLKSSE--------TFNHYFEPPELser 98
Cdd:PRK12541   28 DSHFAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKKYKTTTIEEfhlpnvpsTEHEYFIKHEI--- 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1525942401  99 ADWLYRcIKQLTEIDRSIVMLH-LDGFDNTEISEMMGISRNHTNVKLHRIKQQL 151
Cdd:PRK12541  104 ASWLDS-LSSLPLERRNVLLLRdYYGFSYKEIAEMTGLSLAKVKIELHRGRKET 156
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 24-136 2.07e-04

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 39.64  E-value: 2.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  24 YADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLyklsLNVSLSFLSKQQKQTQLKSSETFNHYfepPELSERADWLY 103
Cdd:PRK09649   43 YLSDVGSADDLTQETFLRAIGAIPRFSARSSARTWL----LAIARHVVADHIRHVRSRPRTTRGAR---PEHLIDGDRHA 115

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1525942401 104 RCIKQLTEIDRSIVMLHLDGFDNTEISEMMGIS 136
Cdd:PRK09649  116 RGFEDLVEVTTMIADLTTDQREALLLTQLLGLS 148
PRK12544 PRK12544
RNA polymerase factor sigma-70;
33-158 2.23e-04

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 39.78  E-value: 2.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  33 DLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLKS-------SETFNHYFE-------------- 91
Cdd:PRK12544   47 DAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKKRHVSASSllrdeeeEEDFEELFDesghwqkderpqaw 126

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1525942401  92 --PPELSERAD-WLY--RCIKQL-TEIDRSIVMLHLDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLLAGK 158
Cdd:PRK12544  127 gnPEESLEQEQfWRIfeACLDGLpAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRARLRLRECLENK 199
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 17-150 2.51e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 39.33  E-value: 2.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  17 IYKMVNLYADDEEDRKDLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQL----KSSETFNHYFEP 92
Cdd:PRK12543   20 VYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRWRRFRIfekaEEQRKPVSIDFS 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1525942401  93 PEL--SERADWLYRCIKQLTEIDRS-IVMLHLDGFDNTEISEMMGI------SRNHTNVKlhRIKQQ 150
Cdd:PRK12543  100 EDVlsKESNQELIELIHKLPYKLRQvIILRYLHDYSQEEIAQLLQIpigtvkSRIHAALK--KLRQK 164
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 33-155 1.36e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 37.51  E-value: 1.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  33 DLYQEIVFQSWQAYSRFKGNAQFSTWLYKLSLNVSLSFLSKQQKQTQLKSSETFNHYFEPPELSERADW--LYRCIKQLT 110
Cdd:PRK12546   36 DLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKREVPDPEGVHAASLAVKPAHDGRLAMsdFRAAFAQLP 115

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1525942401 111 EIDRSIVML-HLDGFDNTEISEMMGISRNHTNVKLHRIKQQLTTLL 155
Cdd:PRK12546  116 DEQREALILvGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
108-151 1.78e-03

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 37.04  E-value: 1.78e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1525942401 108 QLTEIDRSIVMLHLDGFDNTEISEMMGISRNHTNVKLHRIKQQL 151
Cdd:COG2771   127 GLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
36-135 2.51e-03

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 36.57  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  36 QEIVFQSWQAYSRF---KGNAqfSTWLYKLSLNVSLSFLSKQQKQTQLKSSE-------TFNHYFEPPELSERADWLYRC 105
Cdd:PRK09646   62 QEVYLEVWRTASRFdpaRGSA--LAWLLTLAHRRAVDRVRSEQAASQREVRYgarnvdpAFDQVAEEVEARLERERVRDC 139

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1525942401 106 IKQLTEIDR-SIVMLHLDGFDNTEISEMMGI 135
Cdd:PRK09646  140 LDALTDTQReSVTLAYYGGLTYREVAERLAV 170
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 14-98 7.49e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 35.29  E-value: 7.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942401  14 KGIIYKMVNlyadDEEDRKDLYQEIVFQSWQAYSRFKGN-AQFSTWLYKLSLNVSLSFLSKQQ-KQTQLKSSETFNHYFE 91
Cdd:PRK12531   41 KQFAMKHVG----NEQVAMEMVQETMSTVWQKAHLFDGQkSALSTWIYTIIRNLCFDLLRKQKgKDLHIHADDIWPSDYY 116


                  ....*..
gi 1525942401  92 PPELSER 98
Cdd:PRK12531  117 PPDLVDH 123
 
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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