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Conserved domains on  [gi|937116721|ref|WP_054554197|]
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MULTISPECIES: RNA polymerase sigma factor [Pseudoalteromonas]

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]; ...
 12-178 3.50e-48

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: 154.77  E-value: 3.50e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  12 QSEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAI 91
Cdd:COG1595    2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  92 SYIRKHKSWFQKVVSFEQSGMD-----EQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSK 166
Cdd:COG1595   82 DHLRKRRRRRELLDELAEELPDeaadpEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVK 161

                        170
                 ....*....|..
gi 937116721 167 SQFHRARQLLKE 178
Cdd:COG1595  162 SRLSRARKKLRE 173
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 12-178 3.50e-48

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: 154.77  E-value: 3.50e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  12 QSEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAI 91
Cdd:COG1595    2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  92 SYIRKHKSWFQKVVSFEQSGMD-----EQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSK 166
Cdd:COG1595   82 DHLRKRRRRRELLDELAEELPDeaadpEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVK 161

                        170
                 ....*....|..
gi 937116721 167 SQFHRARQLLKE 178
Cdd:COG1595  162 SRLSRARKKLRE 173
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 11-179 3.37e-37

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 126.67  E-value: 3.37e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  11 QQSEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIA 90
Cdd:PRK09638   2 QMDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLY 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  91 ISYIRKHK---SWFQKVVSFEQSGMDEQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKS 167
Cdd:PRK09638  82 KDHLRKQKrekLRLQRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKS 161

                        170
                 ....*....|...
gi 937116721 168 QFHRA-RQLLKEW 179
Cdd:PRK09638 162 RVHHGiKQLRKEW 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 27-178 1.08e-34

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: 119.76  E-value: 1.08e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   27 AAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSWFQKVVS 106
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 937116721  107 FEQ----SGMDEQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKE 178
Cdd:TIGR02937  81 LEElldsDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 32-98 1.59e-15

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: 67.61  E-value: 1.59e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 937116721   32 LYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFD-GRSQ-FSTWLHSVTSNIAISYIRKHK 98
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDpERGVsFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 126-177 1.07e-07

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 46.71  E-value: 1.07e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 937116721 126 LDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLK 177
Cdd:cd06171    4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 12-178 3.50e-48

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: 154.77  E-value: 3.50e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  12 QSEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAI 91
Cdd:COG1595    2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  92 SYIRKHKSWFQKVVSFEQSGMD-----EQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSK 166
Cdd:COG1595   82 DHLRKRRRRRELLDELAEELPDeaadpEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVK 161

                        170
                 ....*....|..
gi 937116721 167 SQFHRARQLLKE 178
Cdd:COG1595  162 SRLSRARKKLRE 173
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 11-179 3.37e-37

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 126.67  E-value: 3.37e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  11 QQSEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIA 90
Cdd:PRK09638   2 QMDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLY 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  91 ISYIRKHK---SWFQKVVSFEQSGMDEQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKS 167
Cdd:PRK09638  82 KDHLRKQKrekLRLQRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKS 161

                        170
                 ....*....|...
gi 937116721 168 QFHRA-RQLLKEW 179
Cdd:PRK09638 162 RVHHGiKQLRKEW 174
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 18-178 3.32e-36

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 124.15  E-value: 3.32e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  18 IERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKH 97
Cdd:PRK09652   1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  98 KSWFQKVVSFEQSGMDEQSAADCDGFNGLDKLVLR-------------LPERARMVFVLHAIEGYRHEEIASMLDMAVGS 164
Cdd:PRK09652  81 GRRPPASDVDAEEAEDFDLADALRDISTPENELLSaeleqrvraaiesLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160

                        170
                 ....*....|....
gi 937116721 165 SKSQFHRARQLLKE 178
Cdd:PRK09652 161 VRSRIFRAREALRA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 27-178 1.08e-34

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: 119.76  E-value: 1.08e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   27 AAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSWFQKVVS 106
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 937116721  107 FEQ----SGMDEQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKE 178
Cdd:TIGR02937  81 LEElldsDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 17-177 2.20e-33

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 117.10  E-value: 2.20e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  17 LIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRK 96
Cdd:PRK09641   8 LIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  97 HK-SWFQKVVSFEQSGMDEQSAADCDGFNGLDKLV------------LRLPERARMVFVLHAIEGYRHEEIASMLDMAVG 163
Cdd:PRK09641  88 RKpDYYLDAEVAGTEGLTMYSQLAADDALPEEQVVslelqetiqeaiLQLPEKYRTVIVLKYIEDLSLKEISEILDLPVG 167

                        170
                 ....*....|....
gi 937116721 164 SSKSQFHRARQLLK 177
Cdd:PRK09641 168 TVKTRIHRGREALR 181
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 10-178 9.52e-30

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 108.90  E-value: 9.52e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  10 AQQSEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNI 89
Cdd:PRK11922  13 SAASDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNE 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  90 AISYIRKHK-----------SWFQKVVSFEQSGMDEQ---SAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIA 155
Cdd:PRK11922  93 ALGRLRRRRrlvnlaemvmaSTIAGGERTPLADPAEDperAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETA 172

                        170       180
                 ....*....|....*....|...
gi 937116721 156 SMLDMAVGSSKSQFHRARQLLKE 178
Cdd:PRK11922 173 QALGLPEETVKTRLHRARRLLRE 195
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 17-183 1.38e-26

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 99.41  E-value: 1.38e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  17 LIERVKSGDQAAYATLYELHVKRVYSLcLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIR- 95
Cdd:PRK12518   1 LILRCQRGDRQSFRQLYRRYQQKVRST-LYQLCGRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRq 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  96 --KHKSWFQKVVSFEQsgmdEQSAADCDGFNGLD--KLVLR----LPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKS 167
Cdd:PRK12518  80 faQRPSRIQDDSLNDQ----PSRPSDTPDLMQLHyqDLVQQglqtLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKS 155

                        170
                 ....*....|....*.
gi 937116721 168 QFHRARQLLKEWYENE 183
Cdd:PRK12518 156 RLFYARRQLRKFLQQQ 171
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 23-183 4.95e-26

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 98.12  E-value: 4.95e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  23 SGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHksWFQ 102
Cdd:PRK11924   9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRR--RRE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721 103 KVVsFEQSGMDEQSAADCDG---------FNG-LDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRA 172
Cdd:PRK11924  87 KAV-LSDDALEPEFAETAETpeaallakdDLArIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRA 165

                        170
                 ....*....|.
gi 937116721 173 RQLLKEWYENE 183
Cdd:PRK11924 166 RQLLRECLEAQ 176
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 28-178 1.19e-24

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: 93.78  E-value: 1.19e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   28 AYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRkHKSWFQKVVSF 107
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLR-HKQVEEKYQEE 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 937116721  108 EQSGMDEQSAADC--------DGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKE 178
Cdd:TIGR02985  81 LAEIEERELSEADpeeeleakELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRK 159
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 5-177 2.41e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 93.97  E-value: 2.41e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   5 AEQAFAQQSEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHS 84
Cdd:PRK12519   7 APTSLSSRSDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLT 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  85 VTSNIAISYIRKHKS-------WFQKVVS-------FEQSGMDEQSAAdcdgfngLDKLVLRLPERARMVFVLHAIEGYR 150
Cdd:PRK12519  87 LTRSRAIDRLRSRRSrqrllerWQQELLGeasedtpLEQASLAERSQR-------VQTALAQLPESQRQVLELAYYEGLS 159

                        170       180
                 ....*....|....*....|....*...
gi 937116721 151 HEEIASMLDMAVGSSKSqfhRARQ-LLK 177
Cdd:PRK12519 160 QSEIAKRLGIPLGTVKA---RARQgLLK 184
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 1-178 3.40e-24

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 93.62  E-value: 3.40e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   1 MLIDAEQAFAQQSEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFST 80
Cdd:PRK09643   1 MGYCPAVGFGERSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  81 WLHSVTSNIAISYIRKHKSwfQKVVSFEQSGMDEQSAADCDGFNGLDKLVLR----LPERARMVFVLHAIEGYRHEEIAS 156
Cdd:PRK09643  81 WLHRIVVNACLDRLRRAKA--RPTVPLDDVYPVAQLERDPTARVETALAVQRalmrLPVEQRAALVAVDMQGYSVADAAR 158

                        170       180
                 ....*....|....*....|..
gi 937116721 157 MLDMAVGSSKSQFHRARQLLKE 178
Cdd:PRK09643 159 MLGVAEGTVKSRCARGRARLAE 180
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 22-183 1.89e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 91.33  E-value: 1.89e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  22 KSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSvtsnIAISYIR--KHKS 99
Cdd:PRK12543   2 LSGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIG----LVIKQIHswRRKR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721 100 W-----FQKVVSFEQS-GMDEQSAADCDGFNG-LDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRA 172
Cdd:PRK12543  78 WrrfriFEKAEEQRKPvSIDFSEDVLSKESNQeLIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAA 157

                        170
                 ....*....|.
gi 937116721 173 RQLLKEWYENE 183
Cdd:PRK12543 158 LKKLRQKEQIE 168
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 16-178 2.37e-21

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 85.86  E-value: 2.37e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  16 ALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFD-GRSQFSTWLHSVTSNIAISYI 94
Cdd:PRK05602   9 ELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRpGEARFDTWLHRVVLNLCYDRL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  95 RKhkswfQKVVSFEQS--------GMDEQSAADCDGfNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSK 166
Cdd:PRK05602  89 RR-----RREVPVEDApdvpdpapGPDAGLEARQRA-RRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALE 162

                        170
                 ....*....|..
gi 937116721 167 SQFHRARQLLKE 178
Cdd:PRK05602 163 SLLARGRRALRA 174
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 4-177 4.64e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 85.71  E-value: 4.64e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   4 DAEQAFAQQSEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANF-DGRSQFSTWL 82
Cdd:PRK12524   3 MPFDALSDVSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWrQGEARVSTWL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  83 HSVTSNIAISYIRKHKSWFQKVVSFEQSGMDEQSAA----DCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASML 158
Cdd:PRK12524  83 YRVVCNLCTDRLRRRRRASVDLDDAPEPADAAPGAEealiEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVM 162

                        170
                 ....*....|....*....
gi 937116721 159 DMAVGSSKSQFHRARQLLK 177
Cdd:PRK12524 163 EIGVEAVESLTARGKRALA 181
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 10-174 1.51e-20

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 84.08  E-value: 1.51e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  10 AQQSEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNI 89
Cdd:PRK11923   3 TQEEDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  90 AISYI--RKHKSwfqkvvsfEQSGMDEQSAADCDGFNGL------DKLVLR-------------LPERARMVFVLHAIEG 148
Cdd:PRK11923  83 AKNHLvsRGRRP--------PDSDVSSEDAEFYDGDHALkdiespERALLRdeiegtvhrtiqqLPEDLRTALTLREFDG 154

                        170       180
                 ....*....|....*....|....*.
gi 937116721 149 YRHEEIASMLDMAVGSSKSQFHRARQ 174
Cdd:PRK11923 155 LSYEDIASVMQCPVGTVRSRIFRARE 180
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 13-178 3.06e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 83.24  E-value: 3.06e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  13 SEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAIS 92
Cdd:PRK12515   8 TDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALS 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  93 YIR--KHKSWFQKVVSFEQSGMD--EQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQ 168
Cdd:PRK12515  88 ALRrrKHEEIDDEAAAAIEDGADtpEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTR 167

                        170
                 ....*....|
gi 937116721 169 FHRARQLLKE 178
Cdd:PRK12515 168 MFYARKKLAE 177
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 5-178 3.69e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 84.14  E-value: 3.69e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   5 AEQAFAQQSEhaLIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLW-HKIANFDGRSQFSTWLH 83
Cdd:PRK12538  43 ADAVFDEDEE--LLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWtHRGRWQHGRAKFSTWLY 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  84 SVTSNIAISYIRKHKSWFQKVVSFEQSGM-DEQSAADCDGFNG-LDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMA 161
Cdd:PRK12538 121 RVVSNRCIDLRRKPRTENVDAVPEVADGKpDAVSVIERNELSDlLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTT 200

                        170
                 ....*....|....*..
gi 937116721 162 VGSSKSQFHRARQLLKE 178
Cdd:PRK12538 201 VAAVESLLKRGRQQLRD 217
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 13-178 1.90e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 81.27  E-value: 1.90e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  13 SEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAIS 92
Cdd:PRK12513  12 SDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLID 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  93 YIRKHKswFQKVVSFEQsgmDEQSAADCDGFNG-------------LDKLVLRLPERARMVFVLHAIEGYRHEEIASMLD 159
Cdd:PRK12513  92 HWRRHG--ARQAPSLDA---DEQLHALADDGAApeqqlslfrdrrrLQAALETLPDEQREVFLLREHGDLELEEIAELTG 166

                        170
                 ....*....|....*....
gi 937116721 160 MAVGSSKSQFHRARQLLKE 178
Cdd:PRK12513 167 VPEETVKSRLRYALQKLRE 185
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 17-181 6.62e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 79.71  E-value: 6.62e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  17 LIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFD-GRSQFSTWLHSVTSNIAISYIR 95
Cdd:PRK12534  15 LLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDpSRARGLTWLAMIARNKAIDHLR 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  96 KHKSWFQKVvsfeqsGMDEQSAADCDGFNGLDKLVLRL-------------PERARMVFVLHaIEGYRHEEIASMLDMAV 162
Cdd:PRK12534  95 ANAPQRRNV------ALDDAGELRAADASPLERTERAStrrridhclaelePPRSELIRTAF-FEGITYEELAARTDTPI 167

                        170
                 ....*....|....*....
gi 937116721 163 GSSKSQFHRARQLLKEWYE 181
Cdd:PRK12534 168 GTVKSWIRRGLAKLKACLE 186
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 11-178 2.10e-18

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 78.44  E-value: 2.10e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  11 QQSEHALIERVKSG---DQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTS 87
Cdd:PRK09640   7 ELNDEELVARVHVElfhVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITY 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  88 NIAISYIRKH--KSWFQKVVSFE-QSGMDEQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGS 164
Cdd:PRK09640  87 NECITQYRKErrKRRLMDALSLDpLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSA 166

                        170
                 ....*....|....
gi 937116721 165 SKSQFHRARQLLKE 178
Cdd:PRK09640 167 TKMRYKRALDKLRE 180
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 32-183 3.14e-18

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 77.30  E-value: 3.14e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  32 LYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHkiANFDGRSQFSTWLHSVTSNIAISYIRKHKSWFQKVV-SFEQS 110
Cdd:PRK09639   8 LFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYR--SDFKGIENEKGWLIKSARNVAYNYLRSEKRRRARILgEFQWQ 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 937116721 111 GMDEQSAAD-----CDGFNGLDKLVLRLPERARMVFVLHaIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKEWYENE 183
Cdd:PRK09639  86 EVDNEPSPEeiwirKEEITKVQEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM 162
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 23-183 6.93e-18

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 77.13  E-value: 6.93e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  23 SGDQAAYATLYEL---HVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSqFSTWLHSVTSNIAISYIRKhks 99
Cdd:PRK09647  21 TGDKATMPSWEELvrqHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPGT-FEGWLHRITTNLFLDMVRR--- 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721 100 wfQKVVSFEQSGMD-----------EQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQ 168
Cdd:PRK09647  97 --RARIRMEALPEDydrvpgdepnpEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSR 174

                        170
                 ....*....|....*
gi 937116721 169 FHRARQLLKEWYENE 183
Cdd:PRK09647 175 IHRGRQQLRAALAAH 189
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 33-181 1.72e-17

RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot:


Pssm-ID: 274361 [Multi-domain]  Cd Length: 154  Bit Score: 75.18  E-value: 1.72e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   33 YELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGrSQFSTWLHSVTSNIAISYIRKHK----SWFQKVVSFE 108
Cdd:TIGR02950   1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD-SSIKPWLFRIARNAFIDWYRKDKkiqtIDDDAIGDLE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 937116721  109 QS--GMDEQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKEWYE 181
Cdd:TIGR02950  80 QHpvESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLLE 154
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 15-178 2.80e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 75.20  E-value: 2.80e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  15 HALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFD-GRSQFSTWLHSVTSNIAISY 93
Cdd:PRK12537  11 EACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDpARGSARGWIYSVTRHLALNV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  94 IRKHKswfQKVV----SFEQSGMDEQSAADCDGFNGLDKL--VLRLPERARMVFVLHA-IEGYRHEEIASMLDMAVGSSK 166
Cdd:PRK12537  91 LRDTR---REVVldddAEETAQTLHEIIDDFDLWANSGKIhrCLEQLEPARRNCILHAyVDGCSHAEIAQRLGAPLGTVK 167

                        170
                 ....*....|..
gi 937116721 167 SQFHRARQLLKE 178
Cdd:PRK12537 168 AWIKRSLKALRE 179
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 17-178 3.62e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 74.86  E-value: 3.62e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  17 LIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFD-GRSQFSTWLHSVTSNIAISYIR 95
Cdd:PRK12514   9 LIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIARNHAIDRLR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  96 KHKSwfqkvvsfeqSGMDEQSAAD-CDGFNGLDKLVLRLPERARMVFVL------HA-------IEGYRHEEIASMLDMA 161
Cdd:PRK12514  89 ARKA----------VAVDIDEAHDlADPSPGPEAEVIAGDEGQRIDACLeelekdRAaavrrayLEGLSYKELAERHDVP 158

                        170
                 ....*....|....*..
gi 937116721 162 VGSSKSQFHRARQLLKE 178
Cdd:PRK12514 159 LNTMRTWLRRSLLKLRE 175
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
15-167 3.31e-16

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 72.78  E-value: 3.31e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  15 HALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFD-GRSQFSTWLHSVTSNIAISY 93
Cdd:PRK09646  18 DALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDpARGSALAWLLTLAHRRAVDR 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  94 IRKhkswfqkvvsfEQSGMDEQS---AADCDG-FNGLDKLVLRLPERARMVFVLHAI-------------EGYRHEEIAS 156
Cdd:PRK09646  98 VRS-----------EQAASQREVrygARNVDPaFDQVAEEVEARLERERVRDCLDALtdtqresvtlayyGGLTYREVAE 166

                        170
                 ....*....|.
gi 937116721 157 MLDMAVGSSKS 167
Cdd:PRK09646 167 RLAVPLGTVKT 177
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 13-178 9.76e-16

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 71.10  E-value: 9.76e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  13 SEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFD-GRSQFSTWLHSVTSNIAI 91
Cdd:PRK13919   9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAAV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  92 SYIRKHKSWFQKVVSFEQsgmdEQSAADCDG-----FNGLDKLVLRL------PERARMVFVLHaIEGYRHEEIASMLDM 160
Cdd:PRK13919  89 DHVRRRAARPQPLEPDER----EPEAFDLPGpgldeEGHLDRTRLGRalkalsPEERRVIEVLY-YQGYTHREAAQLLGL 163

                        170
                 ....*....|....*...
gi 937116721 161 AVGSSKSQFHRARQLLKE 178
Cdd:PRK13919 164 PLGTLKTRARRALSRLKE 181
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 32-98 1.59e-15

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: 67.61  E-value: 1.59e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 937116721   32 LYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFD-GRSQ-FSTWLHSVTSNIAISYIRKHK 98
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDpERGVsFSTWLYTIIRNAIIDYLRKQR 69
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 50-183 3.50e-15

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 69.78  E-value: 3.50e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  50 DKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIrkhKSWFQKVVSFEQSGMD---------EQSAADC 120
Cdd:PRK09415  39 NKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYL---KSWHNKKVIVTEDIFTymesqkesvEEEVIQN 115

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 937116721 121 DGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKEWYENE 183
Cdd:PRK09415 116 AEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEEE 178
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 31-183 5.04e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 69.13  E-value: 5.04e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  31 TLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSWFQKVVSFEQS 110
Cdd:PRK12522   7 ELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKRWKDRILDLFHK 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721 111 GMDEQ------SAADCDGFNGLDKLVLR-----LPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKEW 179
Cdd:PRK12522  87 EDGGEiefaddVNISEEFIQKVEAEMIReviqlLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166


                 ....
gi 937116721 180 YENE 183
Cdd:PRK12522 167 LEGF 170
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
16-178 7.05e-15

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 71.12  E-value: 7.05e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  16 ALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIR 95
Cdd:PRK08241   8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALE 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  96 KHKSWFQKVVSFEQSGMDEQ----------------SAADCDGFNGLDKLVLR-------------LPERARMVFVLHAI 146
Cdd:PRK08241  88 GRARRPLPTDLGAPAADPVDelverpevpwlepypdALLDPAAADPAARVVAResvrlafvaalqhLPPRQRAVLILRDV 167

                        170       180       190
                 ....*....|....*....|....*....|..
gi 937116721 147 EGYRHEEIASMLDMAVGSSKSQFHRARQLLKE 178
Cdd:PRK08241 168 LGWSAAEVAELLDTSVAAVNSALQRARATLAE 199
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 23-178 1.13e-13

RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 65.10  E-value: 1.13e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   23 SGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKhkswfQ 102
Cdd:TIGR02983   2 SATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRR-----R 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  103 KVVSFEQSGMDEQSAADcDGFNGLDKLVL-----RLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLK 177
Cdd:TIGR02983  77 RLLELPTRELPDAAAPD-PAPDVALRAALaralrRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLR 155


                  .
gi 937116721  178 E 178
Cdd:TIGR02983 156 E 156
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 1-177 1.47e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 65.72  E-value: 1.47e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   1 MLIDAEQAFAQQSEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDG-RSQFS 79
Cdd:PRK12531   1 MFNPSPHTFGRQEWLECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGqKSALS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  80 TWLHSVTSNIAISYIRKHKS----------WFQKVV--------SFEQSGMDEQSAadcdgfngldKLVLRLPERARMVF 141
Cdd:PRK12531  81 TWIYTIIRNLCFDLLRKQKGkdlhihaddiWPSDYYppdlvdhySPEQDMLKEQVM----------KFLDRLPKAQRDVL 150

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 937116721 142 VLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLK 177
Cdd:PRK12531 151 QAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLR 186
SigX4 TIGR02957
RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of ...
 32-178 4.22e-12

RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.


Pssm-ID: 132002 [Multi-domain]  Cd Length: 281  Bit Score: 62.76  E-value: 4.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   32 LYELHVKRVYSLCLRLLADKEHAEDATQEVFVQlWHKIAnfdgRSQFST---WLHSVTSNIAISYIR----KHKS----W 100
Cdd:TIGR02957   2 EFEALRPLLFSLAYRMLGSVADAEDIVQETFLR-WQEAD----RAQIENpkaYLTKVVTRRCIDVLRsaraRREVyvgpW 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 937116721  101 FQKVVsFEQSGMDEQSAADCDGFNGLDKLVL-RLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKE 178
Cdd:TIGR02957  77 LPEPL-LTTSADPAESVELAESLSMAYLLLLeRLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHLDA 154
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 126-176 5.46e-12

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: 57.85  E-value: 5.46e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 937116721  126 LDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLL 176
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 31-183 3.79e-11

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 58.74  E-value: 3.79e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  31 TLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDgRSQFSTWLHSVTSNIAISYIRKHKswfqKVVSFEQS 110
Cdd:PRK09644   5 EIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYD-NQKVKPWLFKVAYHTFIDFVRKEK----KVSFVGTD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721 111 GMD-------EQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKEWYENE 183
Cdd:PRK09644  80 EIEaiqaestEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE 159
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 26-181 2.28e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 56.48  E-value: 2.28e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  26 QAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRsQFSTWLHSVTSNIAISYIRKHKSWfqKVV 105
Cdd:PRK12541   4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKKY--KTT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721 106 SFEQSGMDEQSAADCDGF------NGLDKLVLRLPERaRMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKEW 179
Cdd:PRK12541  81 TIEEFHLPNVPSTEHEYFikheiaSWLDSLSSLPLER-RNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159


                 ..
gi 937116721 180 YE 181
Cdd:PRK12541 160 KE 161
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 28-178 4.15e-10

RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 55.79  E-value: 4.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   28 AYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSwfQKVVSF 107
Cdd:TIGR02989   2 AFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGR--DRLVFD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  108 EQ----------SGMDEQSAADcdgFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLK 177
Cdd:TIGR02989  80 DDllealaaeaePTEAERLSDD---RQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLR 156


                  .
gi 937116721  178 E 178
Cdd:TIGR02989 157 E 157
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 16-173 8.24e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 55.67  E-value: 8.24e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  16 ALIERVKSGDQAAYATLYELHVKRVYSLcLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIR 95
Cdd:PRK12535  14 DLALAAGRGDRAALTEFIRETQDDVWRL-LAHLGGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIR 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  96 KHKSWFQK-VVSFEQSGMDEQSAADCDGFN---GLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHR 171
Cdd:PRK12535  93 HDMARPRKsATEYEDAAATTASNETTGSWSewiDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVAR 172


                 ..
gi 937116721 172 AR 173
Cdd:PRK12535 173 AR 174
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 13-183 1.39e-09

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 54.56  E-value: 1.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  13 SEHALIERVKSGDQAAYATLYELHVKRVYSLCLRLL---ADKEHAEDATQEVFVQLWHKIANFDG-RSQFSTWLHSVTSN 88
Cdd:PRK06811   4 NEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLgtvNYSQLIEECVNDIFLSIWNNIDKFDEeKGSFKKWIAAISKY 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  89 IAISYIRK-HKSwfQKVVSFEQSGMDEQSAADCDGF-----NGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAV 162
Cdd:PRK06811  84 KAIDYKRKlTKN--NEIDSIDEFILISEESIENEIIlkenkEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTR 161

                        170       180
                 ....*....|....*....|.
gi 937116721 163 GSSKSQFHRARQLLKEWYENE 183
Cdd:PRK06811 162 SAIDNRLSRGRKKLQKNKLNI 182
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 42-178 2.26e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 54.20  E-value: 2.26e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  42 SLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSWFQkvvsfEQSGM-DEQSAADC 120
Cdd:PRK12516  25 AFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREVQ-----DTDGMfTEQLAVHP 99

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 937116721 121 DGFNGLD-----KLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKE 178
Cdd:PRK12516 100 SQYGTLDlqdfrAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQE 162
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 20-174 2.34e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 54.29  E-value: 2.34e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  20 RVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRS--QFSTWLHSVTSNIAISYIRKH 97
Cdd:PRK12542   2 KVTNNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNtqELKRYILRVAKNKAIDSYRKN 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  98 KSWFQKVVSFEQSGMD------EQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHR 171
Cdd:PRK12542  82 KRHETFLEEYERESIEavdeniEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFER 161


                 ...
gi 937116721 172 ARQ 174
Cdd:PRK12542 162 ARK 164
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 36-178 3.21e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 53.69  E-value: 3.21e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  36 HVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSWFQKVVSFEQSGMDEQ 115
Cdd:PRK12546  16 HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKREVPDPEGVHAASLAVK 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 937116721 116 SAADCD-GFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKE 178
Cdd:PRK12546  96 PAHDGRlAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAE 159
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 48-182 4.09e-09

RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.


Pssm-ID: 274359 [Multi-domain]  Cd Length: 188  Bit Score: 53.62  E-value: 4.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721   48 LADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSwfQKVVS--------------FEQSG-- 111
Cdd:TIGR02943  23 LRDRDLAEDAVQETLLAALSHRDSFAGRSALKTWLFAILKNKIIDALRAKGR--EVKVSdlddelddeafnalFTQNGhw 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  112 ----------MDEQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKEWYE 181
Cdd:TIGR02943 101 aqhgqpqhwnTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTSNCHVLLYRARLSLRACLS 180


                  .
gi 937116721  182 N 182
Cdd:TIGR02943 181 I 181
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
25-177 4.66e-09

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 53.16  E-value: 4.66e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  25 DQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLW-HKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSWFQK 103
Cdd:PRK09645   7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWqHPEVLADTGRSARAWLFTVARNLVIDERRSARARPVE 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 937116721 104 VVSfEQSGMDEQSAADcDGFNGLDKLVLR-----LPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLK 177
Cdd:PRK09645  87 GGD-DVLGVPEQSAPD-EVDRALDRLLVAdalaqLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALR 163
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 36-178 7.85e-08

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 50.74  E-value: 7.85e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  36 HVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANF--DGRSqfstWLHSVTSNIAISYIRKHKSWFQK--VVSFEQSG 111
Cdd:PRK09635  14 HRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDidDERG----WLIVVTSRLCLDHIKSASTRRERpqDIAAWHDG 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 937116721 112 MDEQSAADCDGFNGLD--------KLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKE 178
Cdd:PRK09635  90 DASVSSVDPADRVTLDdevrlallIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINE 164
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 126-177 1.07e-07

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 46.71  E-value: 1.07e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 937116721 126 LDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLK 177
Cdd:cd06171    4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 39-178 2.24e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 48.33  E-value: 2.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  39 RVYSLCLRLLADKehAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSWFQKV--VSFEQSGMDEQS 116
Cdd:PRK12547  20 RAFAVSLSSKHDK--AEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGREVQDSdgVFTARVAVHPAQ 97

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 937116721 117 AADCDgFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKE 178
Cdd:PRK12547  98 YGSLD-LQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 49-182 2.94e-07

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 48.06  E-value: 2.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  49 ADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHK---------SWFQKVVsfEQSGMDEqsAAD 119
Cdd:PRK09637  23 SNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNrseelpddlLFEDEER--EENAKKE--LAP 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 937116721 120 CdgfngLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKEWYEN 182
Cdd:PRK09637  99 C-----LRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 48-176 3.14e-07

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 48.11  E-value: 3.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  48 LADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSwfQKVVSFeqsGMDEQSAADCD----GF 123
Cdd:PRK09649  44 LSDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHVRS--RPRTTR---GARPEHLIDGDrharGF 118

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 937116721 124 NGL---DKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLL 176
Cdd:PRK09649 119 EDLvevTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174
PRK09642 PRK09642
RNA polymerase sigma factor;
40-183 3.66e-07

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 47.79  E-value: 3.66e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  40 VYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDGRSqFSTWLHSVTSNIAISYIRKHKSWFQKVVSFEQSGMDEQSAAD 119
Cdd:PRK09642   8 IFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFRG-LKTWMARIATNHAIDYKRKKARENEELSLCKETEENIKSSHN 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 937116721 120 CDGF--NGLDKLVL-----RLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKEWYENE 183
Cdd:PRK09642  87 IEDLllTKEQKLLIaqklrELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE 157
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 39-178 1.02e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 46.88  E-value: 1.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  39 RVYSLCLRLLADKehAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHK-------SWFQKVVsfeQSG 111
Cdd:PRK12540  19 RAFAISLSGNGDR--ADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRrevedadGSYAKTL---KSQ 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 937116721 112 MDEQSAADCDGFN-GLDKLvlrlPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKE 178
Cdd:PRK12540  94 PGQNAHLEFEEFRaALDKL----PQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSA 157
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 54-182 1.57e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 46.46  E-value: 1.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  54 AEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSWFQKVVSFEQSGMDE------------------- 114
Cdd:PRK12532  33 AEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRKVFTLLDDELLDEafeshfsqnghwtpegqpq 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 937116721 115 -----QSAADCDGFNGLDKLVL-RLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKEWYEN 182
Cdd:PRK12532 113 hwntpEKSLNNNEFQKILQSCLyNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQI 186
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 24-173 4.87e-06

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 45.30  E-value: 4.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  24 GDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQlWHKIANFDGRSQfSTWLHSVTSNIAISYIR--KHK--- 98
Cdd:PRK09636   1 MTMADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQIRDP-RAWLTRVVTRLCLDRLRsaRHRret 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  99 ---SWF-QKVVSFEQSGMDEQSAADCDGFNGLdkLVL-RLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRAR 173
Cdd:PRK09636  79 yvgPWLpEPVVEELDDPLEAVVAAEDLSLALM--LALeRLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRAR 156
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 23-172 6.88e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 44.16  E-value: 6.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  23 SGDQAAYATLY-ELHVKRVYSLCLRLLA-DKEHAEDATQEVFVQLW--HKIANFDGRSQFSTWLHSVTSNIAISYIRKH- 97
Cdd:PRK12529   9 SADRDKVATLYrENHAWLRNWLAYRLRSwGRGVADDLAHDIFLRILasRDGGQREAIRQPRAYLARIANCVLVSWRRRQs 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  98 --KSWFQKVVSF---EQSGMDEQSAAdCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRA 172
Cdd:PRK12529  89 leLAWLEALATLpepLHPSPEQQSVI-LETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQA 167
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 47-183 1.60e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 43.24  E-value: 1.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  47 LLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSWFQKVVSFEQSGmDEQSAADCDGFNGL 126
Cdd:PRK12511  24 LTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLA-DASLPAAQEHAVRL 102

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721 127 DKL---VLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKEWYENE 183
Cdd:PRK12511 103 AQIrdaFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT 162
PRK12544 PRK12544
RNA polymerase factor sigma-70;
48-182 2.84e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 42.87  E-value: 2.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  48 LADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHK------SWFQKVVS-------FEQSG--- 111
Cdd:PRK12544  39 LSDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKKrhvsasSLLRDEEEeedfeelFDESGhwq 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721 112 ---------MDEQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKEWYEN 182
Cdd:PRK12544 119 kderpqawgNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRARLRLRECLEN 198
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 34-178 5.70e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 42.03  E-value: 5.70e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  34 ELHVKRVYSLCL-RL-LADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHkswfQKVVSFEQSG 111
Cdd:PRK12520   7 QLEALRPHLLRFaRLqLRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRSG----RREVRLSLDD 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721 112 MDEQSAADC-------DG---------------------FNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVG 163
Cdd:PRK12520  83 ADEQSDDDLfdalfaaDGhyreppsdwgdpdaalsrrefFEVLQACVDRLPPRTGRVFMMREWLELETEEICQELQITAT 162

                        170
                 ....*....|....*
gi 937116721 164 SSKSQFHRARQLLKE 178
Cdd:PRK12520 163 NAWVLLYRARMRLRE 177
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 26-178 5.86e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 41.60  E-value: 5.86e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  26 QAAYATLYELhvkrVYSLClrllADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLhsvtsniaISYIRKHKSW-FQKV 104
Cdd:PRK12517  30 KALHADIYRY----AYWLC----KDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWL--------ITILRRENARrFERK 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721 105 vSFEQSGMDEQSAADCDGFNG--------LDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLL 176
Cdd:PRK12517  94 -QFDLVDIEDDSIEDDASHSSeeemeqewLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQL 172


                 ..
gi 937116721 177 KE 178
Cdd:PRK12517 173 KE 174
PRK12545 PRK12545
RNA polymerase factor sigma-70;
25-128 7.53e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 41.48  E-value: 7.53e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  25 DQAAYATLYELHVKRVYSLCLRllaDKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHkswfQKV 104
Cdd:PRK12545   9 DDPAYLAQLRHDLLRFARLQLR---DADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRAR----QRT 81

                         90       100
                 ....*....|....*....|....
gi 937116721 105 VSFeqSGMDeqsaADCDGFNGLDK 128
Cdd:PRK12545  82 VNL--SALD----AELDGEALLDR 99
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
114-177 1.90e-04

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 40.34  E-value: 1.90e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 937116721 114 EQSAADCDGFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLK 177
Cdd:PRK09648 121 EERALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARLR 184
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 132-178 2.71e-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. 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: 37.41  E-value: 2.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 937116721  132 RLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRARQLLKE 178
Cdd:pfam04545   4 SLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 48-98 4.69e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 39.36  E-value: 4.69e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937116721  48 LADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHK 98
Cdd:PRK12530  28 LKDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRK 78
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 21-178 1.19e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 37.91  E-value: 1.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  21 VKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWhkianfdGRSQFST------WLHSVTSNIAISYI 94
Cdd:PRK12523   4 AQSPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLL-------GRPELPTprepraFLAAVAKGLMFDHF 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  95 RK------HKSWFQKVVSFEQSGMDEQSAADCDgFNGLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGssksq 168
Cdd:PRK12523  77 RRaaleqaYLAELALVPEAEQPSPEEQHLILED-LKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVS----- 150

                        170
                 ....*....|
gi 937116721 169 fhRARQLLKE 178
Cdd:PRK12523 151 --RVRQYLAQ 158
PRK06930 PRK06930
positive control sigma-like factor; Validated
 133-173 1.44e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 37.79  E-value: 1.44e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 937116721 133 LPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRAR 173
Cdd:PRK06930 115 LTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAE 155
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 16-178 2.46e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 37.09  E-value: 2.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  16 ALIERVKSGDQAAYATLYELHVKRVYSLCLRLLADKEHAEDATQEVFVQLWHKIANFDG-RSQFSTWLHSVTSNIAISYI 94
Cdd:PRK12526  27 WLILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGdKGAATTWVYTVMRNAAFDML 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  95 RKHKSWFQKVVS-----FEQSGMDEQSAADCDGFNGLDKLVLR----LPERARMVFVLHAIEGYRHEEIASMLDMAVGSS 165
Cdd:PRK12526 107 RKIKAKKEQNLGddiwpIEQALAESQSESEEFSDHLMDKQILSyiekLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTV 186

                        170
                 ....*....|...
gi 937116721 166 KSQFHRARQLLKE 178
Cdd:PRK12526 187 KSRLRLALAKLKV 199
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 24-172 3.71e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 36.60  E-value: 3.71e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  24 GDQAAYATLyelhVKRVYSL--------CLRLLADKEHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIR 95
Cdd:PRK12512  19 GDAAAYRRL----LKAVTPVlraaarrgLARAGQPADQAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLIDALR 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 937116721  96 KH-KSWFQKVVSFEQSGMDEQSAADCDGFNgLDKLVLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHRA 172
Cdd:PRK12512  95 RRgRRVFVDIDDFAETLPAEPATETLPAGD-VGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRG 171
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
52-171 6.98e-03

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 35.86  E-value: 6.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937116721  52 EHAEDATQEVFVQLWHKIANFDGRSQFSTWLHSVTSNIAISYIRKHKSwFQKVVSFEQSG--MDEQSAADCDGFNGLDKL 129
Cdd:PRK12539  50 EEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARYKLIDHLRRTRA-SLADVPIDDADelVAHDDHAAVESTLDLGRL 128

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 937116721 130 VLRLPERARMVFVLHAIEGYRHEEIASMLDMAVGSSKSQFHR 171
Cdd:PRK12539 129 LARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHR 170
 
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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