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Conserved domains on  [gi|446762751|ref|WP_000840007|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Bacillus]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11482425)

sigma-70 family RNA polymerase sigma factor; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 1-188 2.68e-89

RNA polymerase factor sigma-70; Validated


:

Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 259.49  E-value: 2.68e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   1 MKSNEKNFIKRLQRQKEDALEFVVDTYLPLIKGITHKVLLPIQNDGLIEECINDIFLSIWNNANKFHGEPSDFKKWIAAI 80
Cdd:PRK06811   1 MKINEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKGSFKKWIAAI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  81 AKFKAIDYYRKSTKTVEIIS-DEFHISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLT 159
Cdd:PRK06811  81 SKYKAIDYKRKLTKNNEIDSiDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLT 160

                        170       180
                 ....*....|....*....|....*....
gi 446762751 160 RAAIDNRVYRGKKKLQQNATNISFGGSAI 188
Cdd:PRK06811 161 RSAIDNRLSRGRKKLQKNKLNISLGGEVI 189
 
Name Accession Description Interval E-value
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 1-188 2.68e-89

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 259.49  E-value: 2.68e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   1 MKSNEKNFIKRLQRQKEDALEFVVDTYLPLIKGITHKVLLPIQNDGLIEECINDIFLSIWNNANKFHGEPSDFKKWIAAI 80
Cdd:PRK06811   1 MKINEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKGSFKKWIAAI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  81 AKFKAIDYYRKSTKTVEIIS-DEFHISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLT 159
Cdd:PRK06811  81 SKYKAIDYKRKLTKNNEIDSiDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLT 160

                        170       180
                 ....*....|....*....|....*....
gi 446762751 160 RAAIDNRVYRGKKKLQQNATNISFGGSAI 188
Cdd:PRK06811 161 RSAIDNRLSRGRKKLQKNKLNISLGGEVI 189
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 3-176 3.72e-37

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: 126.65  E-value: 3.72e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   3 SNEKNFIKRLQRQKEDALEFVVDTYLPLIKGITHKVLlpiQNDGLIEECINDIFLSIWNNANKFHGEpSDFKKWIAAIAK 82
Cdd:COG1595    2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLL---GDRADAEDLVQETFLRLWRKLDSFRGR-GSFRAWLYRIAR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  83 FKAIDYYRKSTKTVEIISD--EFHISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTR 160
Cdd:COG1595   78 NLAIDHLRKRRRRRELLDElaEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                        170
                 ....*....|....*.
gi 446762751 161 AAIDNRVYRGKKKLQQ 176
Cdd:COG1595  158 GTVKSRLSRARKKLRE 173
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-176 5.38e-31

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: 110.13  E-value: 5.38e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   18 DALEFVVDTYLPLIKGITHKVLlpiQNDGLIEECINDIFLSIWNNANKFHGEpSDFKKWIAAIAKFKAIDYYRKSTKTVE 97
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYL---GDDADAEDLVQEAFLKLLEALDRFDPE-GSFKAWLFRIARNLILDYLRRKRRLRR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   98 IISDEFHI-STEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQ 176
Cdd:TIGR02937  77 ELDLLEELlDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 121-174 2.06e-13

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: 61.70  E-value: 2.06e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 446762751  121 REELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKL 174
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 121-175 1.59e-08

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: 49.03  E-value: 1.59e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446762751 121 REELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQ 175
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 1-188 2.68e-89

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 259.49  E-value: 2.68e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   1 MKSNEKNFIKRLQRQKEDALEFVVDTYLPLIKGITHKVLLPIQNDGLIEECINDIFLSIWNNANKFHGEPSDFKKWIAAI 80
Cdd:PRK06811   1 MKINEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKGSFKKWIAAI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  81 AKFKAIDYYRKSTKTVEIIS-DEFHISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLT 159
Cdd:PRK06811  81 SKYKAIDYKRKLTKNNEIDSiDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLT 160

                        170       180
                 ....*....|....*....|....*....
gi 446762751 160 RAAIDNRVYRGKKKLQQNATNISFGGSAI 188
Cdd:PRK06811 161 RSAIDNRLSRGRKKLQKNKLNISLGGEVI 189
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 3-176 3.72e-37

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: 126.65  E-value: 3.72e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   3 SNEKNFIKRLQRQKEDALEFVVDTYLPLIKGITHKVLlpiQNDGLIEECINDIFLSIWNNANKFHGEpSDFKKWIAAIAK 82
Cdd:COG1595    2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLL---GDRADAEDLVQETFLRLWRKLDSFRGR-GSFRAWLYRIAR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  83 FKAIDYYRKSTKTVEIISD--EFHISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTR 160
Cdd:COG1595   78 NLAIDHLRKRRRRRELLDElaEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                        170
                 ....*....|....*.
gi 446762751 161 AAIDNRVYRGKKKLQQ 176
Cdd:COG1595  158 GTVKSRLSRARKKLRE 173
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-176 5.38e-31

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: 110.13  E-value: 5.38e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   18 DALEFVVDTYLPLIKGITHKVLlpiQNDGLIEECINDIFLSIWNNANKFHGEpSDFKKWIAAIAKFKAIDYYRKSTKTVE 97
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYL---GDDADAEDLVQEAFLKLLEALDRFDPE-GSFKAWLFRIARNLILDYLRRKRRLRR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   98 IISDEFHI-STEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQ 176
Cdd:TIGR02937  77 ELDLLEELlDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 14-184 1.45e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 78.47  E-value: 1.45e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  14 RQKEDALEFVVDTYLPLIKGITHKVLlpiQNDGLIEECINDIFLSIWNNANKFHGEPSDfKKWIAAIAKFKAIDYYRKST 93
Cdd:PRK11924   9 TGDKEAFSELFRPHAPDLLRYARRQL---GDRALAEDAVQEAFLRAWRKADLFNGKGSA-RTWLLTIARNVCYDLLRRRR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  94 KTVEIISDEF----HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYR 169
Cdd:PRK11924  85 REKAVLSDDAlepeFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRR 164

                        170
                 ....*....|....*
gi 446762751 170 GKKKLQQNATNISFG 184
Cdd:PRK11924 165 ARQLLRECLEAQWEA 179
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 49-174 2.11e-14

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: 67.20  E-value: 2.11e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   49 EECINDIFLSIWNNANKFHGEPSdFKKWIAAIAKFKAIDYYRKST---KTVEIISDEF-HISTEKSAEDELIVMEDREEL 124
Cdd:TIGR02985  29 EDIVQDVFLKLWENRETLEISES-IKAYLFTIVKNRCLNYLRHKQveeKYQEELAEIEeRELSEADPEEELEAKELEEII 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 446762751  125 LKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKL 174
Cdd:TIGR02985 108 EEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFL 157
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 121-174 2.06e-13

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: 61.70  E-value: 2.06e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 446762751  121 REELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKL 174
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 9-176 4.37e-13

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 64.06  E-value: 4.37e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   9 IKRLQRQKEDALEFVVDTYLPLIKG-ITHKVllpiQNDGLIEECINDIFLSIWNNANKFHGEpSDFKKWIAAIAKFKAID 87
Cdd:PRK09652   1 VERVQRGDRAAFALLVRRYQPRVKRlLSRLT----RDPADAEDLVQETFIKAYRALHSFRGG-AAFYTWLYRIARNTAIN 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  88 YYRK----------STKTVEIISDEFHISTEKSAEDELIVMEDREELLKLINQLePLDQK-VFIMKYLLGMKTEEIGDKL 156
Cdd:PRK09652  76 YLRKqgrrppasdvDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESL-PEELRtAITLREIEGLSYEEIAEIM 154

                        170       180
                 ....*....|....*....|
gi 446762751 157 GLTRAAIDNRVYRGKKKLQQ 176
Cdd:PRK09652 155 GCPIGTVRSRIFRAREALRA 174
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 47-176 3.85e-11

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: 58.62  E-value: 3.85e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   47 LIEECINDIFLSIWNNANKFHGEpsDFKKWIAAIAKFKAIDYYRKSTKTVEIISD---EFHISTEKSAEDELIVMEDREE 123
Cdd:TIGR02950  21 LAEDLLQETFLKAYIHLHSFKDS--SIKPWLFRIARNAFIDWYRKDKKIQTIDDDaigDLEQHPVESPEHHLLIKIEQEE 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446762751  124 LLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQ 176
Cdd:TIGR02950  99 ITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 38-174 5.49e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 58.59  E-value: 5.49e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  38 VLLPIQNDGLIEECINDIFLSIWNNANKFHGEpSDFKKWIAAIAKFKAIDYYRKstKTVEIISDEFHISTEKSAED-ELI 116
Cdd:PRK12515  39 GLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR-SQVSTWLLSIARFKALSALRR--RKHEEIDDEAAAAIEDGADTpEVA 115

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751 117 VMEDR--EELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKL 174
Cdd:PRK12515 116 LQKSDtsAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKL 175
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 49-176 1.30e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 57.25  E-value: 1.30e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  49 EECINDIFLSIWNNANKFHGEpsDFKKWIAAIAKFKAIDYYRKSTKTVEIISDEFHISTEKSAEDELIVMEDREELLKLI 128
Cdd:PRK12541  33 EDLMQETFYRMLVHIDYYKGE--EIRPWLFTIAYNAFIDWYRKEKKYKTTTIEEFHLPNVPSTEHEYFIKHEIASWLDSL 110

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446762751 129 NQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQ 176
Cdd:PRK12541 111 SSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 1-176 6.85e-10

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 55.47  E-value: 6.85e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   1 MKSNEKNFIKRLQRQKEDALEFVVDTYLPLIKGITHKVLlpiQNDGLIEECINDIFLSIWNNANKFHgEPSDFKKWIAAI 80
Cdd:PRK09641   1 MDLLIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRML---GNRHEAEDAAQEAFIRAYVNIDSYD-INRKFSTWLYRI 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  81 AKFKAIDYYRK---------STKTVEIISDEFHI-STEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKTE 150
Cdd:PRK09641  77 ATNLTIDRLRKrkpdyyldaEVAGTEGLTMYSQLaADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLK 156

                        170       180
                 ....*....|....*....|....*.
gi 446762751 151 EIGDKLGLTRAAIDNRVYRGKKKLQQ 176
Cdd:PRK09641 157 EISEILDLPVGTVKTRIHRGREALRK 182
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 42-177 1.27e-09

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 54.99  E-value: 1.27e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  42 IQNDGLIEECINDIFLSIWNNANKFHGEPSdFKKWIAAIAKFKAIDYYRKSTKTVEIISDEFHISTEK--SAEDELIVMe 119
Cdd:PRK09637  22 VSNEADVDDLLQEVLIKTHSNLHSLKDGSS-IKSWLYQIANNTIIDFYRKKNRSEELPDDLLFEDEEReeNAKKELAPC- 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446762751 120 dreeLLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQN 177
Cdd:PRK09637 100 ----LRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 19-182 9.81e-09

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 52.63  E-value: 9.81e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  19 ALEFVVDTYLPLIKGITHKVLlpiQNDGLIEECINDIFLSIWNNANKFHGEpSDFKKWIAAIAKFKAIDYYRKSTKTVEI 98
Cdd:PRK09640  27 AYEELMRRYQRTLFNVCARYL---GNDRDADDVCQEVMLKVLYGLKNFEGK-SKFKTWLYSITYNECITQYRKERRKRRL 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  99 ISDEFHISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQNA 178
Cdd:PRK09640 103 MDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182


                 ....
gi 446762751 179 TNIS 182
Cdd:PRK09640 183 AGLA 186
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 40-185 1.01e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 52.46  E-value: 1.01e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  40 LPIQNDGLIEECINDIFLSIWNNANKFHGEpSDFKKWIAAIAKFKAIDYYRKSTKTV---EIISDEF------------- 103
Cdd:PRK12530  26 LQLKDADLAEDVVQEALVSAYKNADSFKGQ-SALKTWIFAILKNKIIDLIRYRKRFVnesELIEEDSpnsffdekghwkp 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751 104 -HISTEKSAEDELIVMEDREELL--KLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQNATN 180
Cdd:PRK12530 105 eYYEPSEWQEVENTVYKEEFWLIfeACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRARLQLQACLSK 184


                 ....*
gi 446762751 181 ISFGG 185
Cdd:PRK12530 185 NWFDG 189
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 121-175 1.59e-08

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: 49.03  E-value: 1.59e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446762751 121 REELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQ 175
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 18-175 1.87e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 51.59  E-value: 1.87e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  18 DALEFVVDTYLPLIKGITHKVLLPIQNdglIEECINDIFLSIWNNANKFHG-EPSDFKKWIAAIAKFKAIDYYRKStKTV 96
Cdd:PRK12542   9 EKMEELYELYEQKVYYVAYSILNNIQQ---AEDAVQETFITLYKNLEKLHSlNTQELKRYILRVAKNKAIDSYRKN-KRH 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  97 EIISDEFHISTEKSAEDELIVMEDRE----ELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKK 172
Cdd:PRK12542  85 ETFLEEYERESIEAVDENIEEWEKRKmsevQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARK 164


                 ...
gi 446762751 173 KLQ 175
Cdd:PRK12542 165 RVQ 167
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 69-176 1.02e-07

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 49.49  E-value: 1.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  69 EPSDFKKWIAAIAKFKAIDYYRKSTKTVEIISDEFHISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMK 148
Cdd:PRK09644  47 DNQKVKPWLFKVAYHTFIDFVRKEKKVSFVGTDEIEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELT 126

                         90       100
                 ....*....|....*....|....*...
gi 446762751 149 TEEIGDKLGLTRAAIDNRVYRGKKKLQQ 176
Cdd:PRK09644 127 YEEAASVLDLKLNTYKSHLFRGRKRLKA 154
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 24-95 1.06e-07

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: 47.20  E-value: 1.06e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446762751   24 VDTYLPLIKGITHKVLlpiQNDGLIEECINDIFLSIWNNANKF-HGEPSDFKKWIAAIAKFKAIDYYRKSTKT 95
Cdd:pfam04542   2 VERYLPLVYSLARRYL---GDGADAEDLVQEGFLGLWRAIERFdPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 7-158 2.70e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 48.28  E-value: 2.70e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   7 NFIKRLQRQKEDALEFVVDTYLPLIKGITHKVLlpiQNDGLIEECINDIFLSIWNNANKFHGEPSDFKKWIAAIAKFKAI 86
Cdd:PRK12514   8 KLIVRVSLGDRDAFSSLYDATSAKLFGICLRVL---KDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNHAI 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446762751  87 DYYRKSTKTVEIISDEFHISTEK-SAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGL 158
Cdd:PRK12514  85 DRLRARKAVAVDIDEAHDLADPSpGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDV 157
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 42-176 4.17e-07

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 47.64  E-value: 4.17e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  42 IQNDGLIEECINDIFLSIWNNanKFHGEpSDFKKWIAAIAKFKAIDYYRKSTKTVEIISDEFH---ISTEKSAEDELIVM 118
Cdd:PRK09639  24 VKDRTQAEDLAQEVFLRLYRS--DFKGI-ENEKGWLIKSARNVAYNYLRSEKRRRARILGEFQwqeVDNEPSPEEIWIRK 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446762751 119 EDREELLKLINQLEPLDQKVFIMKYLlGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQ 176
Cdd:PRK09639 101 EEITKVQEVLAKMTERDRTVLLLRFS-GYSYKEIAEALGIKESSVGTTLARAKKKFRK 157
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 19-175 4.40e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 47.74  E-value: 4.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  19 ALEFVVDTYLPLIKGITHKVllpIQNDGLIEECINDIFLSIWNNANKFHGEPSDFKKWIAAIAKFKAIDYYRKSTKTVEI 98
Cdd:PRK12534  26 AFEALYRQTSPKLFGVCLRM---IPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAMIARNKAIDHLRANAPQRRN 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  99 ISDEFHISTEKSAEDELIVMEDREELLKL---INQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQ 175
Cdd:PRK12534 103 VALDDAGELRAADASPLERTERASTRRRIdhcLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKLK 182
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 42-176 9.80e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 46.69  E-value: 9.80e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  42 IQNDGLIEECINDIFLSIWNNANKFHGEPSDFKKWIAAIAKFKAIDYYRKSTKtvEIISDEFHISTEKS---AEDELIVM 118
Cdd:PRK12537  44 VRDRALAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTRHLALNVLRDTRR--EVVLDDDAEETAQTlheIIDDFDLW 121

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446762751 119 EDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQ 176
Cdd:PRK12537 122 ANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 40-176 1.86e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 46.26  E-value: 1.86e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  40 LPIQNDGLIEECINDIFLSIWNNANKFHGEpSDFKKWIAAIAKFKAIDYYRKSTKTVEIISDEFHISTEKSAEDELI--- 116
Cdd:PRK12520  21 LQLRDPALAEDAVSETLLAVLEHPERFAGQ-SSLKTYLVGILKHKIIDAIRSGRREVRLSLDDADEQSDDDLFDALFaad 99

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446762751 117 ---------------VMEDRE--ELLKL-INQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQ 176
Cdd:PRK12520 100 ghyreppsdwgdpdaALSRREffEVLQAcVDRLPPRTGRVFMMREWLELETEEICQELQITATNAWVLLYRARMRLRE 177
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 14-176 2.29e-06

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 46.06  E-value: 2.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  14 RQKEDALEFVVDTYLPLIKGITHKVLLpiqNDGLIEECINDIFLSIWNNANKFHGEPSDFKKWIAAIAKFKAIDYYRK-S 92
Cdd:PRK13919  19 RGEEEALRALFRRYAGAFLALARRMGL---DGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALAHHAAVDHVRRrA 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  93 TKTVEIISDE-----FHISTEKSAEDELIvmeDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRV 167
Cdd:PRK13919  96 ARPQPLEPDErepeaFDLPGPGLDEEGHL---DRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRA 172


                 ....*....
gi 446762751 168 YRGKKKLQQ 176
Cdd:PRK13919 173 RRALSRLKE 181
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 47-176 2.51e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 45.69  E-value: 2.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  47 LIEECINDIFLSIWNNANKFHGEpSDFKKWIAAIAKFKAIDYYRKSTKTVEIIS-------DE-----FHISTEKSAEDE 114
Cdd:PRK12532  32 LAEDLVQETLLSAYSAGDSFQGR-ALVNSWLFAILKNKIIDALRQIGRQRKVFTllddellDEafeshFSQNGHWTPEGQ 110

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446762751 115 LIVMEDREELLK----------LINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQ 176
Cdd:PRK12532 111 PQHWNTPEKSLNnnefqkilqsCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLRQ 182
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
76-174 3.14e-06

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 45.49  E-value: 3.14e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  76 WIAAIAKFKAIDYYRK---STKTVEIisDEFHistEKSAEDELIVMEDREELLKLINQL-EPLDQKVFIMKyLLGMKTEE 151
Cdd:PRK12539  79 WVYAIARYKLIDHLRRtraSLADVPI--DDAD---ELVAHDDHAAVESTLDLGRLLARLpEKMRLAIQAVK-LEGLSVAE 152

                         90       100
                 ....*....|....*....|...
gi 446762751 152 IGDKLGLTRAAIDNRVYRGKKKL 174
Cdd:PRK12539 153 AATRSGMSESAVKVSVHRGLKAL 175
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 96-160 3.47e-06

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


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 45.81  E-value: 3.47e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446762751  96 VEIISDEfhisTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT----EEIGDKLGLTR 160
Cdd:COG0568  176 GDLLEDE----EAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEphtlEEIGKEFGVSR 240
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 48-174 5.79e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 44.66  E-value: 5.79e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  48 IEECINDIFLSIWNNANKFH-GEPsdFKKWIAAIAKFKAIDYYRKSTKTvEIISDEFHISTEKSAEDELIVMEDREELLK 126
Cdd:PRK12536  49 VEDLVQEILLAVHNARHTYRaDQP--LTAWVHAIARYKLMDFLRSRARR-EALHDPLDDESELFATSDDEAAEARRDLGK 125

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446762751 127 LINQLePLDQKVFIMKYLL-GMKTEEIGDKLGLTRAAIDNRVYRGKKKL 174
Cdd:PRK12536 126 LLEQL-PDRQRLPIVHVKLeGLSVAETAQLTGLSESAVKVGIHRGLKAL 173
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 48-180 4.77e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 42.03  E-value: 4.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  48 IEECINDIFLSIWNNANKFHGEPSdFKKWIAAIAKFKAIDYYRKSTKTVEIISDEFHISTEKSAED--ELIVMEDREELL 125
Cdd:PRK12543  34 VDDVVNEIYIQLWESLRKYDSNRP-FRFWLIGLVIKQIHSWRRKRWRRFRIFEKAEEQRKPVSIDFseDVLSKESNQELI 112

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446762751 126 KLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQNATN 180
Cdd:PRK12543 113 ELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQI 167
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 42-177 6.07e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 42.26  E-value: 6.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  42 IQNDGLIEECINDIFLSIWNNANKFHGEpSDFKKWIAAIAKFKAIDYYRKSTKTVEIISDE-----------FHISTEKS 110
Cdd:PRK11922  51 LRNDAEAEDVVQEAYLRAFRALGTFRGD-ASLSTWLSRIVLNEALGRLRRRRRLVNLAEMVmastiaggertPLADPAED 129

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446762751 111 AEDELIVMEDREELLKLINQLePLD-QKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQN 177
Cdd:PRK11922 130 PERAAARREIRALLERAIDAL-PDAfRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLRES 196
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 2-175 6.52e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 41.84  E-value: 6.52e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   2 KSNEKNFIKRLQRQKEDALEFVVDTYLPLIKGITHKvllPIQNDGLIEECINDIFLSIWNNANKFHGEPSDFKKWIAAIA 81
Cdd:PRK12531  11 RQEWLECMEKVKSRDKQAFALVFSYYAPKLKQFAMK---HVGNEQVAMEMVQETMSTVWQKAHLFDGQKSALSTWIYTII 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  82 KFKAIDYYRKST-KTVEIISDEFHIS--------TEKSAEDELIvmedREELLKLINQLEPLDQKVFIMKYLLGMKTEEI 152
Cdd:PRK12531  88 RNLCFDLLRKQKgKDLHIHADDIWPSdyyppdlvDHYSPEQDML----KEQVMKFLDRLPKAQRDVLQAVYLEELPHQQV 163

                        170       180
                 ....*....|....*....|...
gi 446762751 153 GDKLGLTRAAIDNRVYRGKKKLQ 175
Cdd:PRK12531 164 AEMFDIPLGTVKSRLRLAVEKLR 186
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 69-159 9.60e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 40.99  E-value: 9.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  69 EPSDFKKWIAAIAKFKAIDYYRKSTKTVEIISDEFHI--STEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLG 146
Cdd:PRK12523  56 TPREPRAFLAAVAKGLMFDHFRRAALEQAYLAELALVpeAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDG 135

                         90
                 ....*....|...
gi 446762751 147 MKTEEIGDKLGLT 159
Cdd:PRK12523 136 MGHAEIAERLGVS 148
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 5-176 2.13e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 40.61  E-value: 2.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751   5 EKNFIKRLQRQKEDALEFVVDTYLPLIKGITHKVLlpiQNDGLIEECINDIFLSIWNNANKFHGEPSDFKKWIAAIAKFK 84
Cdd:PRK12538  50 DEELLDRLATDDEAAFRLLVERHIDRAYAIALRIV---GNRADAEDVVQDTMLKVWTHRGRWQHGRAKFSTWLYRVVSNR 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  85 AIDYYRK-STKTVEIISDefhisTEKSAEDELIVMEDRE--ELLKLINQLEPLDQKV-FIMKYLLGMKTEEIGDKLGLTR 160
Cdd:PRK12538 127 CIDLRRKpRTENVDAVPE-----VADGKPDAVSVIERNElsDLLEAAMQRLPEQQRIaVILSYHENMSNGEIAEVMDTTV 201

                        170
                 ....*....|....*.
gi 446762751 161 AAIDNRVYRGKKKLQQ 176
Cdd:PRK12538 202 AAVESLLKRGRQQLRD 217
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 127-176 5.99e-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: 36.25  E-value: 5.99e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 446762751  127 LINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQQ 176
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 44-175 7.03e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 38.90  E-value: 7.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  44 NDGLIEECINDIFLSIWNNANKFHGEPSdFKKWIAAIAKFKAIDYYRKStKTVEIISDEFHISTEKSAED------ELIV 117
Cdd:PRK12513  49 DRALAEDIFQETWLRVIRARAQYQPRAR-FRTWLYQIARNLLIDHWRRH-GARQAPSLDADEQLHALADDgaapeqQLSL 126

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446762751 118 MEDREELLKLINQLePLDQK-VFIMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKLQ 175
Cdd:PRK12513 127 FRDRRRLQAALETL-PDEQReVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLR 184
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
49-168 7.52e-04

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 38.52  E-value: 7.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  49 EECINDIFLSIWNNANKFHGEPSDFKKWIAAIAKFKAIDYYRKSTKTVEIISDEFHISTEKSAEDELIVMEDREELLKLI 128
Cdd:PRK09645  37 EDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSARARPVEGGDDVLGVPEQSAPDEVDRALDRLLVADAL 116

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446762751 129 NQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVY 168
Cdd:PRK09645 117 AQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLH 156
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
103-174 1.15e-03

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 38.35  E-value: 1.15e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446762751 103 FHISTEKSA--EDELIVMEDREELL-KLINQLEPLDQKVFiMKYLLGMKTEEIGDKLGLTRAAIDNRVYRGKKKL 174
Cdd:PRK08295 125 DVISEAKVTdpEELIISKEELEDIEeKIEELLSELEKEVL-ELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKL 198
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 17-181 1.99e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 37.16  E-value: 1.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  17 EDALEFVVDTYLPLIKGITHKVllpIQNDGLIEECINDIFLSIWNNANKFHGEPSdFKKWIAAIAKFKAIDYYRKSTKTV 96
Cdd:PRK12522   2 EEKVEELIDIYKQQIYSLCYKL---AKTKEDAEDIFQETWIKVFSSRHQLSYVEN-YKKWITTICVRTFYDFYRKKKRWK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  97 EIISDEFH--------ISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKTEEIGDKLGLTRAAIDNRVY 168
Cdd:PRK12522  78 DRILDLFHkedggeieFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLN 157

                        170
                 ....*....|...
gi 446762751 169 RGKKKLQQNATNI 181
Cdd:PRK12522 158 YAKKQMREHLEGF 170
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 90-174 2.55e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 36.97  E-value: 2.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  90 RKSTKTVEI----ISDEFHISTEKSAEDELIvmedREELLKL-INQLEPLdqkvfIMKYLLGMKTEEIGDKLGLTRAAID 164
Cdd:PRK12517  92 RKQFDLVDIeddsIEDDASHSSEEEMEQEWL----RRQIAKLdPEYREPL-----LLQVIGGFSGEEIAEILDLNKNTVM 162

                         90
                 ....*....|
gi 446762751 165 NRVYRGKKKL 174
Cdd:PRK12517 163 TRLFRARNQL 172
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 73-174 4.15e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 36.60  E-value: 4.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446762751  73 FKKWIAAIAKFKAIDYYRKSTKTVEIISDEF--HISTEKSAEDelivmEDREELLKLINQLEPLDQKVFIMKYLLGMKTE 150
Cdd:PRK12512  77 FAPWLFAIARNKLIDALRRRGRRVFVDIDDFaeTLPAEPATET-----LPAGDVGRHLETLPPRQRDVVQSISVEGASIK 151

                         90       100
                 ....*....|....*....|....
gi 446762751 151 EIGDKLGLTRAAIDNRVYRGKKKL 174
Cdd:PRK12512 152 ETAAKLSMSEGAVRVALHRGLAAL 175
 
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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