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Conserved domains on  [gi|2501502648|ref|WP_281510276|]
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MULTISPECIES: RNA polymerase sigma factor [Muribaculum]

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]; ...
 5-155 1.39e-34

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: 118.94  E-value: 1.39e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLD-IALENDEAD 83
Cdd:COG1595    26 YRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDeLAEELPDEA 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2501502648  84 DDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYKH 155
Cdd:COG1595   106 ADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEE 177
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 5-155 1.39e-34

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: 118.94  E-value: 1.39e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLD-IALENDEAD 83
Cdd:COG1595    26 YRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDeLAEELPDEA 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2501502648  84 DDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYKH 155
Cdd:COG1595   106 ADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 1-153 3.77e-29

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: 104.35  E-value: 3.77e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   1 MILPHYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIALEND 80
Cdd:TIGR02937   6 LYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELL 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2501502648  81 EADDDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELY 153
Cdd:TIGR02937  86 DSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 2-155 3.94e-25

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 94.65  E-value: 3.94e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   2 ILPHYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIAL---E 78
Cdd:PRK11924   19 FRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDDAlepE 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2501502648  79 NDEADDDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYKH 155
Cdd:PRK11924   99 FAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEA 175
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 96-149 1.11e-09

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: 51.30  E-value: 1.11e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2501502648  96 LEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQL 149
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 96-150 4.62e-09

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: 49.80  E-value: 4.62e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2501502648  96 LEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLK 150
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 5-155 1.39e-34

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: 118.94  E-value: 1.39e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLD-IALENDEAD 83
Cdd:COG1595    26 YRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDeLAEELPDEA 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2501502648  84 DDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYKH 155
Cdd:COG1595   106 ADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 1-153 3.77e-29

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: 104.35  E-value: 3.77e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   1 MILPHYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIALEND 80
Cdd:TIGR02937   6 LYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELL 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2501502648  81 EADDDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELY 153
Cdd:TIGR02937  86 DSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 2-155 3.94e-25

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 94.65  E-value: 3.94e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   2 ILPHYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIAL---E 78
Cdd:PRK11924   19 FRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDDAlepE 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2501502648  79 NDEADDDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYKH 155
Cdd:PRK11924   99 FAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEA 175
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 5-151 9.91e-21

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: 82.99  E-value: 9.91e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIALENDEA-- 82
Cdd:TIGR02985  10 YYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEIEERel 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  83 -DDDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKE 151
Cdd:TIGR02985  90 sEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRK 159
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 5-152 3.36e-19

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: 78.97  E-value: 3.36e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQcidmTRTRYRRNEPLDIALEN--DEA 82
Cdd:TIGR02983  15 RYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNL----ARSRWRRRRLLELPTRElpDAA 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  83 DDDIVKRIDQRDTLekvAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKEL 152
Cdd:TIGR02983  91 APDPAPDVALRAAL---ARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLREL 157
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 5-152 3.74e-15

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 68.91  E-value: 3.74e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREeleGIQSAKGFCMTTIKR----QCIDmtRTRYRRNEPLDIALEND 80
Cdd:PRK05602   29 KLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAP---SWRPGEARFDTWLHRvvlnLCYD--RLRRRREVPVEDAPDVP 103

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2501502648  81 EADDDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKEL 152
Cdd:PRK05602  104 DPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQ 175
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 5-151 2.73e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 64.60  E-value: 2.73e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKreeLEGIQSAKGFcMTTIKRQCIDMTRTRYRRNEPLDIALENDEA-- 82
Cdd:PRK11922   39 HNRRLYRTARAILRNDAEAEDVVQEAYLRAFRA---LGTFRGDASL-STWLSRIVLNEALGRLRRRRRLVNLAEMVMAst 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  83 ------------DDDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLK 150
Cdd:PRK11922  115 iaggertpladpAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLR 194


                  .
gi 2501502648 151 E 151
Cdd:PRK11922  195 E 195
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 4-151 1.13e-12

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 63.79  E-value: 1.13e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   4 PHYEEMYRVAYIILEDRHDAFDAVQEAVVKLwtKREELEGIQSAKGFCMTTIKRQCIDMTRT-RYRRN------------ 70
Cdd:PRK09636   12 PLRPHLLSVAYRMLGSVADAEDIVQEAWLRW--NNADRAQIRDPRAWLTRVVTRLCLDRLRSaRHRREtyvgpwlpepvv 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  71 EPLDIALENDEADDDIvkridqrdtleKVAQL--MDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQ 148
Cdd:PRK09636   90 EELDDPLEAVVAAEDL-----------SLALMlaLERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKH 158


                  ...
gi 2501502648 149 LKE 151
Cdd:PRK09636  159 VRA 161
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 5-152 1.35e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 60.26  E-value: 1.35e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELE-GIQSAKGFCMTTIKRQCIDMTRTRyrRNEPLDIALENDEAD 83
Cdd:PRK12538   72 HIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQhGRAKFSTWLYRVVSNRCIDLRRKP--RTENVDAVPEVADGK 149

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2501502648  84 DDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKEL 152
Cdd:PRK12538  150 PDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDL 218
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 5-156 2.54e-11

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 58.42  E-value: 2.54e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWtkREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIALENDEADD 84
Cdd:PRK09639   12 YYPDVVQQIFYIVKDRTQAEDLAQEVFLRLY--RSDFKGIENEKGWLIKSARNVAYNYLRSEKRRRARILGEFQWQEVDN 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2501502648  85 DIVKRID--QRDTLEKVAQLMDTLPAIQREALRLRaYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYKHL 156
Cdd:PRK09639   90 EPSPEEIwiRKEEITKVQEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM 162
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 8-154 7.24e-11

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 57.45  E-value: 7.24e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   8 EMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRN------EPLDIALENDE 81
Cdd:PRK09415   28 EVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSWHNKKvivtedIFTYMESQKES 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2501502648  82 ADDDIVKRIDQRDTLEKVAQLmdtlPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYK 154
Cdd:PRK09415  108 VEEEVIQNAEDERLASAVMSL----PIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLE 176
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 5-156 1.25e-10

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 57.03  E-value: 1.25e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCID-MTRTRYRRNEPLDialENDEAD 83
Cdd:PRK09643   36 HHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDrLRRAKARPTVPLD---DVYPVA 112

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2501502648  84 DDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYKHL 156
Cdd:PRK09643  113 QLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARLAELLGYL 185
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
21-153 3.21e-10

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 56.87  E-value: 3.21e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  21 HDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIALENDEADDDIVKRID--------- 91
Cdd:PRK08241   44 HDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALEGRARRPLPTDLGAPAADPVDELVERPEvpwlepypd 123

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2501502648  92 ---------------QRDT--LEKVAQLMDtLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELY 153
Cdd:PRK08241  124 alldpaaadpaarvvARESvrLAFVAALQH-LPPRQRAVLILRDVLGWSAAEVAELLDTSVAAVNSALQRARATLAERG 201
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 7-152 3.28e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 55.83  E-value: 3.28e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   7 EEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEG--IQSAKGFCMTTIKRQCIDMTRTRYRRNEPLD-IALENDEAD 83
Cdd:PRK12542   20 QKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSlnTQELKRYILRVAKNKAIDSYRKNKRHETFLEeYERESIEAV 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  84 DDIVKRIDQRDTLE-KVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKEL 152
Cdd:PRK12542  100 DENIEEWEKRKMSEvQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQNM 169
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 96-149 1.11e-09

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: 51.30  E-value: 1.11e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2501502648  96 LEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQL 149
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 10-152 1.25e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 54.51  E-value: 1.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  10 YRVAYIILEDRHDAFDAVQEAVVKLW-TKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIALENDEADDDIVK 88
Cdd:PRK12524   40 LAVATRVLGDRAEAEDVTQEAMLRLWrIAPDWRQGEARVSTWLYRVVCNLCTDRLRRRRRASVDLDDAPEPADAAPGAEE 119

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2501502648  89 RIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKEL 152
Cdd:PRK12524  120 ALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 6-152 1.37e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 53.92  E-value: 1.37e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   6 YEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQcidmTRTRYRRNEPLDIALENDEADDD 85
Cdd:PRK12517   33 HADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILRRE----NARRFERKQFDLVDIEDDSIEDD 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2501502648  86 IVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKEL 152
Cdd:PRK12517  109 ASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEA 175
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 10-157 1.80e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 53.91  E-value: 1.80e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  10 YRVAYIILEDRHDAFDAVQEAVVKLWTKreelEGIQSAKG----FCMTTIKRQCIDMTRTRYRRNEPLD---IALENDEA 82
Cdd:PRK12519   43 YGLALKILGNSQEAEDLTQEIFLSLWRK----SSYDPKRGslssYLLTLTRSRAIDRLRSRRSRQRLLErwqQELLGEAS 118

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2501502648  83 DDDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDntrTLLSRARR---QLKELYKHLI 157
Cdd:PRK12519  119 EDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLG---TVKARARQgllKLRELLQDLL 193
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 8-154 4.05e-09

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 52.57  E-value: 4.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   8 EMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEgIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIALENDEADDdIV 87
Cdd:PRK09644   13 DVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYD-NQKVKPWLFKVAYHTFIDFVRKEKKVSFVGTDEIEAIQAES-TE 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2501502648  88 KRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYK 154
Cdd:PRK09644   91 EYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 7-156 4.29e-09

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 52.78  E-value: 4.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   7 EEMYRVAYIILEDRHDAFDAVQEAVVKLWTKreeLEGIQSAKGFCmTTIKRQCIDMTRTRYRRNEP---LD--------- 74
Cdd:PRK09641   29 DKIYQLCYRMLGNRHEAEDAAQEAFIRAYVN---IDSYDINRKFS-TWLYRIATNLTIDRLRKRKPdyyLDaevagtegl 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  75 -----IALENDEADDDIVKRIDQRDTLEKVAQLmdtlPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQL 149
Cdd:PRK09641  105 tmysqLAADDALPEEQVVSLELQETIQEAILQL----PEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREAL 180


                  ....*..
gi 2501502648 150 KELYKHL 156
Cdd:PRK09641  181 RKQLRHL 187
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 96-150 4.62e-09

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: 49.80  E-value: 4.62e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2501502648  96 LEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLK 150
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 16-151 8.28e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 51.75  E-value: 8.28e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  16 ILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQ-CIDMTRTRYRRNEPLDIALENDEADDDIVKRIDQRD 94
Cdd:PRK12514   39 VLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNhAIDRLRARKAVAVDIDEAHDLADPSPGPEAEVIAGD 118

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2501502648  95 TLEKVAQLMDTLPAIQREALRlRAYSD-CSVKEISELLGITTDNTRTLLSRARRQLKE 151
Cdd:PRK12514  119 EGQRIDACLEELEKDRAAAVR-RAYLEgLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 11-154 9.63e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 51.89  E-value: 9.63e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  11 RVAYIILEDRHD-AFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLD-IALENDEADDDIVK 88
Cdd:PRK12516   24 RAFAVSLIGRHDrADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREVQDTDgMFTEQLAVHPSQYG 103

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2501502648  89 RIDqrdtLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYK 154
Cdd:PRK12516  104 TLD----LQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 2-151 2.50e-08

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: 50.40  E-value: 2.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   2 ILPHYEEMYRvAYI--ILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIALEN 79
Cdd:TIGR02989   6 LLTRHERALR-AFVrsLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRDRLVFDDDLLE 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2501502648  80 DEADDDIVKRIDQR-DTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKE 151
Cdd:TIGR02989  85 ALAAEAEPTEAERLsDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLRE 157
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 5-136 2.60e-08

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 50.16  E-value: 2.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLwTKREELEGIQSAKGFCMTTIKRQCIDMTR-TRYRRNEPLDiALENDE-- 81
Cdd:PRK12527    4 YYRELVRFLSARLGNRQAAEDVAHDAYLRV-LERSSSAQIEHPRAFLYRTALNLVVDRHRrHRVRQAEPLE-VLDEEErl 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2501502648  82 ADDDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTD 136
Cdd:PRK12527   82 HSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRS 136
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 5-151 2.89e-08

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 51.51  E-value: 2.89e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLwtKREELEGIQSAKGFCMTTIKRQCIDMTRT-RYRRNEPLDIALENDEad 83
Cdd:PRK09635   14 HRAYLVDLAFRMVGDIGVAEDMVQEAFSRL--LRAPVGDIDDERGWLIVVTSRLCLDHIKSaSTRRERPQDIAAWHDG-- 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2501502648  84 DDIVKRIDQRD--TLEK-----VAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKE 151
Cdd:PRK09635   90 DASVSSVDPADrvTLDDevrlaLLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINE 164
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 17-156 4.65e-08

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 49.58  E-value: 4.65e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  17 LEDRHDAFDAVQEAVVKLWTKReeleGIQSAKGFCMT--TIKRQCI-DMTRTRYRRNEP----LDIALENDEADDDIVKR 89
Cdd:PRK09047    1 VRDDDAALDIVQDAMIKLAEKY----GDRPAAEWPPLfqRILQNRIhDWFRRQKVRNTWvslfSSFSDDDDDDDFDPLET 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  90 ID--------------QRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYKH 155
Cdd:PRK09047   77 LDsadegaespadkleRAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEA 156


                  .
gi 2501502648 156 L 156
Cdd:PRK09047  157 K 157
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 18-152 7.60e-08

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 49.21  E-value: 7.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  18 EDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIAL-ENDEADDDIVKRIDQrdTL 96
Cdd:PRK09637   23 SNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRSEELPDDLLfEDEEREENAKKELAP--CL 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2501502648  97 EKvaqLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKEL 152
Cdd:PRK09637  101 RP---FIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 19-151 9.43e-08

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 49.03  E-value: 9.43e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  19 DRHDAFDAVQEAVVKLWTKREELEGIQSAKGFcMTTIKRQC-IDMTRTRYRRNEPLDIALENDEA--DDDIVKRIDQRDT 95
Cdd:PRK09652   33 DPADAEDLVQETFIKAYRALHSFRGGAAFYTW-LYRIARNTaINYLRKQGRRPPASDVDAEEAEDfdLADALRDISTPEN 111

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2501502648  96 L-------EKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKE 151
Cdd:PRK09652  112 EllsaeleQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 11-151 3.22e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 47.47  E-value: 3.22e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  11 RVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDmtRTRYRRNEPLDIALENDEADDDIVKRI 90
Cdd:PRK12511   19 RYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFID--ELRRRRVEARRADELAVLADASLPAAQ 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2501502648  91 DQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKE 151
Cdd:PRK12511   97 EHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
PRK12544 PRK12544
RNA polymerase factor sigma-70;
7-151 4.10e-07

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 47.49  E-value: 4.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   7 EEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIaLENDEADDDI 86
Cdd:PRK12544   29 KQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKKRHVSASSL-LRDEEEEEDF 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  87 VKRID-----QRDTLEKVAQL-----------------MDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSR 144
Cdd:PRK12544  108 EELFDesghwQKDERPQAWGNpeesleqeqfwrifeacLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYR 187


                  ....*..
gi 2501502648 145 ARRQLKE 151
Cdd:PRK12544  188 ARLRLRE 194
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 11-154 4.63e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 46.79  E-value: 4.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  11 RVAYIILEDRHD-AFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLD-IALENDEADDDIVK 88
Cdd:PRK12547   20 RAFAVSLSSKHDkAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGREVQDSDgVFTARVAVHPAQYG 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2501502648  89 RIDQRDTLEKVAQLmdtlPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYK 154
Cdd:PRK12547  100 SLDLQDFKKALNLL----SADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 5-154 6.04e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 47.03  E-value: 6.04e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGiQSAKGFCMTTIKRqCIDMTRTRYRRNEPLD---IALENDE 81
Cdd:PRK12515   31 HHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEG-RSQVSTWLLSIAR-FKALSALRRRKHEEIDdeaAAAIEDG 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2501502648  82 ADDDIVKrIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYK 154
Cdd:PRK12515  109 ADTPEVA-LQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 12-151 9.09e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 46.31  E-value: 9.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  12 VAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQ-SAKGFCMTTIKRQCIDMTRTRYRrneplDIALENDEADD--DIVK 88
Cdd:PRK12537   39 VARRIVRDRALAEDIVHDAFIKIWTGAASFDPARgSARGWIYSVTRHLALNVLRDTRR-----EVVLDDDAEETaqTLHE 113

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2501502648  89 RIDQRDTLEKVAQLMDTLPAIQ--REALRLRAYSD-CSVKEISELLGITTDNTRTLLSRARRQLKE 151
Cdd:PRK12537  114 IIDDFDLWANSGKIHRCLEQLEpaRRNCILHAYVDgCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
5-150 9.58e-07

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 46.23  E-value: 9.58e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGI-QSAKGFCMTTIKRQCIDMTRT-RYRRNEPLDIALENDE- 81
Cdd:PRK09645   18 HAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTgRSARAWLFTVARNLVIDERRSaRARPVEGGDDVLGVPEq 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  82 -ADDDIVKRIDQRDtlekVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLK 150
Cdd:PRK09645   98 sAPDEVDRALDRLL----VADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALR 163
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 25-156 2.13e-06

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 45.29  E-value: 2.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  25 DAVQEAVVKLWTKREELEGIQ-SAKGFCMTTIKRQCIDMTRTRYRRNEPLDIALENDEADDDIVKRIDQRDTLE--KVAQ 101
Cdd:PRK13919   52 DVVQEVFIRVWKKAKEFDPRRgSARAWLLALAHHAAVDHVRRRAARPQPLEPDEREPEAFDLPGPGLDEEGHLDrtRLGR 131

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2501502648 102 LMDTLPAIQREALRLRAYSDCSVKEISELLGITTDntrTLLSRARRQLKELYKHL 156
Cdd:PRK13919  132 ALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLG---TLKTRARRALSRLKEVL 183
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 1-154 2.55e-06

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 45.31  E-value: 2.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   1 MILPHYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRT-RYRRNEPLDIALEN 79
Cdd:PRK09640   31 LMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKeRRKRRLMDALSLDP 110

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2501502648  80 -DEADDDIVKRIDQRDTLEKvaqLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYK 154
Cdd:PRK09640  111 lEEASEEKAPKPEERGGLDR---WLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKFA 183
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 1-152 4.43e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 44.72  E-value: 4.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   1 MILPHYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGiQSAKGFCMTTIKRQCIdmtrTRYRRNEPLDIALEND 80
Cdd:PRK12533   23 LVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRG-DNARPWLLAIVRHTWY----SEWRRRANAHEVAAPD 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  81 EADDDIVKRIDQRDTLEKVAQLM---DT---------LPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQ 148
Cdd:PRK12533   98 TLDDADSLDDWQPAGEDPLALLLraeDVrlvnaalakLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRR 177


                  ....
gi 2501502648 149 LKEL 152
Cdd:PRK12533  178 LAAL 181
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 102-151 7.66e-06

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 40.87  E-value: 7.66e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2501502648 102 LMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKE 151
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 5-151 7.95e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 43.95  E-value: 7.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRT--RYRRNEPLDIALENDEA 82
Cdd:PRK12520   11 LRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRSgrREVRLSLDDADEQSDDD 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  83 DDDIVKRID------------------QRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSR 144
Cdd:PRK12520   91 LFDALFAADghyreppsdwgdpdaalsRREFFEVLQACVDRLPPRTGRVFMMREWLELETEEICQELQITATNAWVLLYR 170


                  ....*..
gi 2501502648 145 ARRQLKE 151
Cdd:PRK12520  171 ARMRLRE 177
PRK12545 PRK12545
RNA polymerase factor sigma-70;
8-150 1.24e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 43.41  E-value: 1.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   8 EMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYR--RNEPLDIALENDEADD- 84
Cdd:PRK12545   20 DLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRARQRtvNLSALDAELDGEALLDr 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  85 ---------------------DIVKRIDQRDTLEKVAqlMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLS 143
Cdd:PRK12545  100 elfkdnghwaahakprpwpkpETILQQQQFWTLFETC--LDHLPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLY 177


                  ....*..
gi 2501502648 144 RARRQLK 150
Cdd:PRK12545  178 RARTRLR 184
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 1-69 1.35e-05

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


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 41.03  E-value: 1.35e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2501502648   1 MILPHYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQ--SAKGFCMTTIKRQCIDMTRTRYRR 69
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERgvSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 1-151 1.80e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 42.55  E-value: 1.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   1 MILPHYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFcMTTIkrqCIDMTRTRYRRNEP-LDIALE- 78
Cdd:PRK12522    8 LIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKW-ITTI---CVRTFYDFYRKKKRwKDRILDl 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  79 ---------NDEADDDIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQL 149
Cdd:PRK12522   84 fhkedggeiEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQM 163


                  ..
gi 2501502648 150 KE 151
Cdd:PRK12522  164 RE 165
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 6-151 5.02e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 41.26  E-value: 5.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   6 YEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEpldiALENDEADDD 85
Cdd:PRK12543   17 IQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRWRRFR----IFEKAEEQRK 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2501502648  86 IVKRIDQRDTLEK-----VAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKE 151
Cdd:PRK12543   93 PVSIDFSEDVLSKesnqeLIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 2-152 7.62e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 40.98  E-value: 7.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   2 ILPHYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRrnepldialENDE 81
Cdd:PRK12546   13 LVEHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKR---------EVPD 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2501502648  82 ADDDIVKRI------DQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKEL 152
Cdd:PRK12546   84 PEGVHAASLavkpahDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAEL 160
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 8-150 8.90e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 40.90  E-value: 8.90e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   8 EMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIALENDEA---DD 84
Cdd:PRK12530   19 QMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRKRFVNESELIEEDSPNsffDE 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  85 DIVKRID--QRDTLEKVAQL-------------MDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQL 149
Cdd:PRK12530   99 KGHWKPEyyEPSEWQEVENTvykeefwlifeacLNHLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRARLQL 178


                  .
gi 2501502648 150 K 150
Cdd:PRK12530  179 Q 179
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 19-152 1.40e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 40.44  E-value: 1.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  19 DRHDAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDIALENDEADDDIVKRIDQRDTLEK 98
Cdd:PRK12513   49 DRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRRHGARQAPSLDADEQLHALADDGAAPEQQLSLFR 128

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2501502648  99 VAQLMD----TLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKEL 152
Cdd:PRK12513  129 DRRRLQaaleTLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 8-151 1.45e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 40.30  E-value: 1.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   8 EMYRVAYIILEDRHD-AFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNEPLDiaLENDEADD-- 84
Cdd:PRK12532   17 LLLHFARLQLPDHPDlAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRKVFT--LLDDELLDea 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  85 ---------------------DIVKRIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLS 143
Cdd:PRK12532   95 feshfsqnghwtpegqpqhwnTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMH 174


                  ....*...
gi 2501502648 144 RARRQLKE 151
Cdd:PRK12532  175 RARESLRQ 182
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 23-150 1.53e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 40.30  E-value: 1.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  23 AFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQ-CIDMTRTRYRRNEPL--DIALENDEADDDIVKRID-QRDTL-E 97
Cdd:PRK12531   54 AMEMVQETMSTVWQKAHLFDGQKSALSTWIYTIIRNlCFDLLRKQKGKDLHIhaDDIWPSDYYPPDLVDHYSpEQDMLkE 133

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2501502648  98 KVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLK 150
Cdd:PRK12531  134 QVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLR 186
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 73-156 2.71e-04

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 39.81  E-value: 2.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  73 LDIALENDEADDDIVK------RIDQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTdntrtllSRAR 146
Cdd:COG1191   148 LDEPLEDGDDLLDLLEsgdpeeELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSE-------SRVS 220

                          90
                  ....*....|
gi 2501502648 147 RQLKELYKHL 156
Cdd:COG1191   221 RLHKKALARL 230
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
2-150 8.11e-04

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 38.47  E-value: 8.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   2 ILPHYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREElegiqsaKGFCMTTI----KRQCIDMTRTRyRRNEPLDIAL 77
Cdd:PRK06704   23 LIEQYGELKRYCTFLTKNKWDGEDLAQETVCKVLQKYSN-------KDICMTLVykiaRNRWLDQIKSK-SVHEKIRDQI 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2501502648  78 ENDEADDDIVkridqrDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLK 150
Cdd:PRK06704   95 TFEEPHEKIA------DLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLK 161
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
16-152 2.07e-03

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 36.96  E-value: 2.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  16 ILEDRHDAFDAVQEAVVKLWTKREELEGIQ-SAKGFCMTTIKRQCIDMTR------TRYRRNEPLDIALENDEADDDIVK 88
Cdd:PRK09646   50 VLRDPGYSEETTQEVYLEVWRTASRFDPARgSALAWLLTLAHRRAVDRVRseqaasQREVRYGARNVDPAFDQVAEEVEA 129

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2501502648  89 RIDQrdtlEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGIttdNTRTLLSRARRQLKEL 152
Cdd:PRK09646  130 RLER----ERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAV---PLGTVKTRMRDGLIRL 186
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 75-155 3.83e-03

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 36.36  E-value: 3.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  75 IALENDEADDDIVKRIDQRDTLEKVAQLMDTLPaiQREALRLRAYSD--CSVKEISELLGITTDNTRTLLSRARRQLKEL 152
Cdd:PRK06986  154 ILVTEDHQDEDPLQQLEDEELREALVEAIESLP--EREQLVLSLYYQeeLNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231


                  ...
gi 2501502648 153 YKH 155
Cdd:PRK06986  232 LGE 234
PRK09191 PRK09191
two-component response regulator; Provisional
 91-149 3.85e-03

two-component response regulator; Provisional


Pssm-ID: 236402 [Multi-domain]  Cd Length: 261  Bit Score: 36.36  E-value: 3.85e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2501502648  91 DQRDTLEKVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQL 149
Cdd:PRK09191   74 PGSPFEARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEI 132
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 22-154 5.10e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 35.83  E-value: 5.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  22 DAFDAVQEAVVKLWTKREELEGIQSAKGFCMTTIKRQCIDMTRTRYRRNE-PLDIALENDEADDdivkridQRDTLE--K 98
Cdd:PRK12512   52 QAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLIDALRRRGRRVFvDIDDFAETLPAEP-------ATETLPagD 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2501502648  99 VAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYK 154
Cdd:PRK12512  125 VGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 17-155 7.81e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 35.08  E-value: 7.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648  17 LEDRHDAFDAVQEAVVKLWTKREELEGiqsaKGFCMTTIKR----QCIDMTRTRYRRNEPLDIALENDEA----DDDIVK 88
Cdd:PRK12518   31 LCGRELLDDLVQEVFLRVWKGLPKLRN----PAYFSTWLYRitwnVATDARRQFAQRPSRIQDDSLNDQPsrpsDTPDLM 106

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2501502648  89 RIDQRDTlekVAQLMDTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKELYKH 155
Cdd:PRK12518  107 QLHYQDL---VQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQ 170
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 5-152 8.76e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 34.91  E-value: 8.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2501502648   5 HYEEMYRVAYIILEDRHDAFDAVQEAVVKLWTKREELEGiQSAKGFCMTTIKRQCIDMTRT--RYRRNEPLDIALEN-DE 81
Cdd:PRK12541   14 HMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKG-EEIRPWLFTIAYNAFIDWYRKekKYKTTTIEEFHLPNvPS 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2501502648  82 ADDDIVKRIDQRDTLEKVAqlmdTLPAIQREALRLRAYSDCSVKEISELLGITTDNTRTLLSRARRQLKEL 152
Cdd:PRK12541   93 TEHEYFIKHEIASWLDSLS----SLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159
 
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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