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Conserved domains on  [gi|1829886727|gb|QIX64956|]
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RNA polymerase sigma factor [Parabacteroides distasonis]

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]; ...
 1-166 1.09e-46

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: 150.53  E-value: 1.09e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   1 MDVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSpKASRRD 80
Cdd:COG1595    14 GDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRK-RRRRRE 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  81 NEEALETVLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIR 160
Cdd:COG1595    93 LLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLR 172


                  ....*.
gi 1829886727 161 EKLEKA 166
Cdd:COG1595   173 EALEEE 178
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-166 1.09e-46

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: 150.53  E-value: 1.09e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   1 MDVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSpKASRRD 80
Cdd:COG1595    14 GDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRK-RRRRRE 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  81 NEEALETVLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIR 160
Cdd:COG1595    93 LLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLR 172


                  ....*.
gi 1829886727 161 EKLEKA 166
Cdd:COG1595   173 EALEEE 178
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 2-167 5.35e-36

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 123.16  E-value: 5.35e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   2 DVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRspkasRRDN 81
Cdd:PRK11924   11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLR-----RRRR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  82 E------EALETVLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRA 155
Cdd:PRK11924   86 EkavlsdDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRA 165

                         170
                  ....*....|..
gi 1829886727 156 RKLIREKLEKAS 167
Cdd:PRK11924  166 RQLLRECLEAQW 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 4-163 4.63e-35

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: 120.14  E-value: 4.63e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   4 DVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASRRDNEE 83
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  84 ALEtvLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKL 163
Cdd:TIGR02937  81 LEE--LLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 109-159 8.76e-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: 59.78  E-value: 8.76e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1829886727 109 IQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLI 159
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 106-160 5.08e-12

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: 57.50  E-value: 5.08e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1829886727 106 IRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIR 160
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-166 1.09e-46

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: 150.53  E-value: 1.09e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   1 MDVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSpKASRRD 80
Cdd:COG1595    14 GDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRK-RRRRRE 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  81 NEEALETVLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIR 160
Cdd:COG1595    93 LLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLR 172


                  ....*.
gi 1829886727 161 EKLEKA 166
Cdd:COG1595   173 EALEEE 178
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 2-167 5.35e-36

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 123.16  E-value: 5.35e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   2 DVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRspkasRRDN 81
Cdd:PRK11924   11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLR-----RRRR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  82 E------EALETVLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRA 155
Cdd:PRK11924   86 EkavlsdDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRA 165

                         170
                  ....*....|..
gi 1829886727 156 RKLIREKLEKAS 167
Cdd:PRK11924  166 RQLLRECLEAQW 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 4-163 4.63e-35

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: 120.14  E-value: 4.63e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   4 DVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASRRDNEE 83
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  84 ALEtvLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKL 163
Cdd:TIGR02937  81 LEE--LLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 4-163 2.15e-33

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: 115.74  E-value: 2.15e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   4 DVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASRRDNEE 83
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  84 ALE-TVLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREK 162
Cdd:TIGR02985  81 LAEiEERELSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKE 160


                  .
gi 1829886727 163 L 163
Cdd:TIGR02985 161 L 161
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 1-162 8.75e-27

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 102.31  E-value: 8.75e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   1 MDVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKlWNKRDElGDIQNPEAFSITLVKNLCLDFLRSpkASRRD 80
Cdd:PRK09636    1 MTMADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADR-AQIRDPRAWLTRVVTRLCLDRLRS--ARHRR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  81 NE---EALETVLLTTDSSPEKELEEKEDIRHIQELI-EQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRAR 156
Cdd:PRK09636   77 ETyvgPWLPEPVVEELDDPLEAVVAAEDLSLALMLAlERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRAR 156


                  ....*.
gi 1829886727 157 KLIREK 162
Cdd:PRK09636  157 KHVRAA 162
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 15-165 5.86e-25

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 96.19  E-value: 5.86e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  15 PKLYRIAYALLDNKADAEDILQDAYCKLWNKrdeLGDIQNPEAFS---ITLVKNLCLDFLRspKASRRDN---------- 81
Cdd:PRK11922   41 RRLYRTARAILRNDAEAEDVVQEAYLRAFRA---LGTFRGDASLStwlSRIVLNEALGRLR--RRRRLVNlaemvmasti 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  82 EEALETVLLTTDSSPEKELEEKEdIRHIQE-LIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIR 160
Cdd:PRK11922  116 AGGERTPLADPAEDPERAAARRE-IRALLErAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLR 194


                  ....*
gi 1829886727 161 EKLEK 165
Cdd:PRK11922  195 ESLAR 199
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 2-164 2.38e-24

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 93.33  E-value: 2.38e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   2 DVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKrdeLGDIQNPEAFS---ITLVKNLCLDFLRspKASR 78
Cdd:PRK09652    8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRA---LHSFRGGAAFYtwlYRIARNTAINYLR--KQGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  79 RDNEEALETV---------LLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIR 149
Cdd:PRK09652   83 RPPASDVDAEeaedfdladALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVR 162

                         170
                  ....*....|....*
gi 1829886727 150 TLLSRARKLIREKLE 164
Cdd:PRK09652  163 SRIFRAREALRAKLQ 177
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 2-165 2.28e-22

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 87.70  E-value: 2.28e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   2 DVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDElgDIQNPEAFSITLVKNLCLDFLRSPKASRRDN 81
Cdd:PRK09639    1 SDETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFK--GIENEKGWLIKSARNVAYNYLRSEKRRRARI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  82 EEALETVLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRgIEDCSYEDIEQITGLSSSNIRTLLSRARKLIRE 161
Cdd:PRK09639   79 LGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKKKFRK 157


                  ....
gi 1829886727 162 KLEK 165
Cdd:PRK09639  158 IYEQ 161
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 14-164 1.44e-21

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: 85.52  E-value: 1.44e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  14 HPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASRRDNEEALETVllTTD 93
Cdd:TIGR02983  16 YPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLELPTRELPDAA--APD 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1829886727  94 SSPEKELEEKedirhIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLE 164
Cdd:TIGR02983  94 PAPDVALRAA-----LARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELLE 159
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 16-165 4.05e-19

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 79.74  E-value: 4.05e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  16 KLYRIAYALLDNKADAEDILQDAYCKLWNKRDELgDIQnpEAFSITLVK---NLCLDFLRSPKASRRDNEEALETVLLT- 91
Cdd:PRK09641   30 KIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSY-DIN--RKFSTWLYRiatNLTIDRLRKRKPDYYLDAEVAGTEGLTm 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  92 ------TDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEK 165
Cdd:PRK09641  107 ysqlaaDDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLRH 186
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 2-165 1.98e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 77.94  E-value: 1.98e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   2 DVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELG-DIQNPEAFSITLVKNLCLDFLRSPKASRRD 80
Cdd:PRK12514   17 DRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIARNHAIDRLRARKAVAVD 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  81 NEEALEtvlLTTDS-SPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLI 159
Cdd:PRK12514   97 IDEAHD---LADPSpGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKL 173


                  ....*.
gi 1829886727 160 REKLEK 165
Cdd:PRK12514  174 RECLSR 179
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 18-157 2.08e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 75.48  E-value: 2.08e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  18 YRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSpkasRRDNEEALE--TVLLTTDSS 95
Cdd:PRK12519   43 YGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRSRAIDRLRS----RRSRQRLLErwQQELLGEAS 118

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1829886727  96 PEKELEE---KEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTllsRARK 157
Cdd:PRK12519  119 EDTPLEQaslAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKA---RARQ 180
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 9-161 5.75e-17

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: 73.51  E-value: 5.75e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   9 RFLPFH-PKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASRRD-NEEALE 86
Cdd:TIGR02989   5 RLLTRHeRALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRDRLVfDDDLLE 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1829886727  87 TVLlttDSSPEKELEEKEDIRH-IQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIRE 161
Cdd:TIGR02989  85 ALA---AEAEPTEAERLSDDRQaLEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLRE 157
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 15-164 6.04e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 74.16  E-value: 6.04e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  15 PKLYRIAYALLDNKADAEDILQDAYCKLWNKRdelGDIQNPEAFSIT----LVKNLCLDFLRSPKASRRDNEEALETvll 90
Cdd:PRK12524   37 PRALAVATRVLGDRAEAEDVTQEAMLRLWRIA---PDWRQGEARVSTwlyrVVCNLCTDRLRRRRRASVDLDDAPEP--- 110

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1829886727  91 tTDSSP--EKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLE 164
Cdd:PRK12524  111 -ADAAPgaEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAALLA 185
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 13-164 2.14e-16

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: 71.72  E-value: 2.14e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  13 FHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQ-NPEAFSITlvKNLCLDFLRSPKASRRDNEEALETVLLT 91
Cdd:TIGR02950   4 YMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKDSSiKPWLFRIA--RNAFIDWYRKDKKIQTIDDDAIGDLEQH 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1829886727  92 TDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLE 164
Cdd:TIGR02950  82 PVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLLE 154
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 16-166 4.80e-16

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 71.70  E-value: 4.80e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  16 KLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASRRDNEEALETVLLTTDSS 95
Cdd:PRK09415   28 EVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSWHNKKVIVTEDIFTYMESQKES 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1829886727  96 PEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEKA 166
Cdd:PRK09415  108 VEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEEE 178
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 13-169 2.91e-15

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 69.63  E-value: 2.91e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  13 FHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASrrdneEALETVLLTT 92
Cdd:PRK09637   10 YKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRS-----EELPDDLLFE 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1829886727  93 DSSPEKELEeKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEkASCH 169
Cdd:PRK09637   85 DEEREENAK-KELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE-GCCD 159
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 1-164 7.21e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 68.36  E-value: 7.21e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   1 MDVDVFKQrflpfhpKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRspKASRRD 80
Cdd:PRK12522    7 ELIDIYKQ-------QIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYR--KKKRWK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  81 N-------EEALETVLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLS 153
Cdd:PRK12522   78 DrildlfhKEDGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLN 157

                         170
                  ....*....|.
gi 1829886727 154 RARKLIREKLE 164
Cdd:PRK12522  158 YAKKQMREHLE 168
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 6-163 3.30e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 66.44  E-value: 3.30e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   6 FKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNlclDFLRSPKASRRDNEEAl 85
Cdd:PRK12547    8 FKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRN---EFYSQMRKRGREVQDS- 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1829886727  86 eTVLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKL 163
Cdd:PRK12547   84 -DGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 15-170 3.41e-14

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 66.60  E-value: 3.41e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  15 PKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELgdiQNPEA-FSITL---VKNLCLDFLRSPKAsrRDNEEALETVll 90
Cdd:PRK05602   31 PRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSW---RPGEArFDTWLhrvVLNLCYDRLRRRRE--VPVEDAPDVP-- 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  91 TTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEKASCHG 170
Cdd:PRK05602  104 DPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLADLPGSE 183
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 17-163 5.90e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 66.25  E-value: 5.90e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  17 LYRIAYALLDNKADAEDILQDAYCKLWNKRDElgdiQNPEA-FS---ITLVKNLCLDFLRS---PKASRRDNEEALETvL 89
Cdd:PRK12513   39 LYRFLLRLARDRALAEDIFQETWLRVIRARAQ----YQPRArFRtwlYQIARNLLIDHWRRhgaRQAPSLDADEQLHA-L 113

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1829886727  90 LTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKL 163
Cdd:PRK12513  114 ADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 18-165 9.53e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 66.42  E-value: 9.53e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  18 YRIAYALLDNKADAEDILQDAYCKLWNKRdelGDIQNPEA-FSITL---VKNLCLDFLRSPkasRRDNEEALETVlltTD 93
Cdd:PRK12538   77 YAIALRIVGNRADAEDVVQDTMLKVWTHR---GRWQHGRAkFSTWLyrvVSNRCIDLRRKP---RTENVDAVPEV---AD 147

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1829886727  94 SSPE--KELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEK 165
Cdd:PRK12538  148 GKPDavSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRR 221
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 6-164 2.17e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 64.60  E-value: 2.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   6 FKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNlclDFLRSPKASRRD--NEE 83
Cdd:PRK12516   12 FKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRN---EFYSQMRKRGREvqDTD 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  84 ALETVLLTTDSSPEKELeekeDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKL 163
Cdd:PRK12516   89 GMFTEQLAVHPSQYGTL----DLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164


                  .
gi 1829886727 164 E 164
Cdd:PRK12516  165 Q 165
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 14-161 3.41e-13

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 65.76  E-value: 3.41e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  14 HPKLYRIAYALLDNKADAEDILQDAYCKLwnKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASRRDNEEALET-----V 88
Cdd:PRK09635   15 RAYLVDLAFRMVGDIGVAEDMVQEAFSRL--LRAPVGDIDDERGWLIVVTSRLCLDHIKSASTRRERPQDIAAWhdgdaS 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1829886727  89 LLTTDssPEKELEEKEDIR-HIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIRE 161
Cdd:PRK09635   93 VSSVD--PADRVTLDDEVRlALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINE 164
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 15-161 8.27e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 62.88  E-value: 8.27e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  15 PKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASRRDNEEALEtvlLTTDS 94
Cdd:PRK12511   15 VPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAV---LADAS 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1829886727  95 SPEKElEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIRE 161
Cdd:PRK12511   92 LPAAQ-EHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 109-159 8.76e-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: 59.78  E-value: 8.76e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1829886727 109 IQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLI 159
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 106-160 5.08e-12

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: 57.50  E-value: 5.08e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1829886727 106 IRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIR 160
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 2-160 7.71e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 60.45  E-value: 7.71e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   2 DVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPE--AFSITLVKNLCLDFLRSPKASRR 79
Cdd:PRK12542    7 DYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQElkRYILRVAKNKAIDSYRKNKRHET 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  80 DNEEALETVLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLI 159
Cdd:PRK12542   87 FLEEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRV 166


                  .
gi 1829886727 160 R 160
Cdd:PRK12542  167 Q 167
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 13-165 7.72e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 60.47  E-value: 7.72e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  13 FHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLvknlcldfLRSPKASRRDNEE----ALETV 88
Cdd:PRK12517   32 LHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITI--------LRRENARRFERKQfdlvDIEDD 103

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1829886727  89 LLTTDSSPEKELEEKEDIrhIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEK 165
Cdd:PRK12517  104 SIEDDASHSSEEEMEQEW--LRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEK 178
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 17-165 1.17e-11

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 59.51  E-value: 1.17e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  17 LYRIAYALLDNKADAEDILQDAYCKLWNKRDELgDIQNPEAFSITLVKNLCLDFLRSPKASRRDNEEALETVLLTtdsSP 96
Cdd:PRK09644   14 VYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDY-DNQKVKPWLFKVAYHTFIDFVRKEKKVSFVGTDEIEAIQAE---ST 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1829886727  97 EKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEK 165
Cdd:PRK09644   90 EEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 13-79 2.15e-11

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: 56.44  E-value: 2.15e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1829886727  13 FHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDEL--GDIQNPEAFSITLVKNLCLDFLRspKASRR 79
Cdd:pfam04542   5 YLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdpERGVSFSTWLYTIIRNAIIDYLR--KQRRT 71
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 11-164 6.13e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 57.93  E-value: 6.13e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  11 LPFH-PKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNlclDFLRSPKASRRDNEEaletvl 89
Cdd:PRK12546   13 LVEHlPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRN---TFYSDRRKHKREVPD------ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  90 ltTDSSPEKELEEKED------IRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKL 163
Cdd:PRK12546   84 --PEGVHAASLAVKPAhdgrlaMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161


                  .
gi 1829886727 164 E 164
Cdd:PRK12546  162 Q 162
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 6-170 6.93e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 58.20  E-value: 6.93e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   6 FKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDEL-GDiqNPEAFSITLVKNLCLdflrSPKASRRDNEEA 84
Cdd:PRK12533   20 FRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFrGD--NARPWLLAIVRHTWY----SEWRRRANAHEV 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  85 LETVLLTTDSS----------PEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSR 154
Cdd:PRK12533   94 AAPDTLDDADSlddwqpagedPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLAR 173

                         170       180
                  ....*....|....*....|
gi 1829886727 155 ARK----LIREKLEKASCHG 170
Cdd:PRK12533  174 ARRrlaaLLGGASAAQAAPG 193
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 2-165 9.72e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 57.76  E-value: 9.72e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   2 DVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELgDIQNPEAFS-ITLV-KNLCLDFLRSPKASRR 79
Cdd:PRK12534   23 DRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQF-DPSRARGLTwLAMIaRNKAIDHLRANAPQRR 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  80 DN--EEALEtvLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARK 157
Cdd:PRK12534  102 NValDDAGE--LRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLA 179


                  ....*...
gi 1829886727 158 LIREKLEK 165
Cdd:PRK12534  180 KLKACLER 187
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 80-165 1.01e-10

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: 58.30  E-value: 1.01e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  80 DNEEALETVlltTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLI 159
Cdd:COG1191   154 DGDDLLDLL---ESGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARL 230


                  ....*.
gi 1829886727 160 REKLEK 165
Cdd:COG1191   231 REYLKE 236
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 16-170 1.53e-10

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 57.10  E-value: 1.53e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  16 KLYRIAYALLDNKADAEDILQDAYCKLWNkrdELGDIQnPEAFS-----ITlvKNLCLDFLRSPKASRRdneEAL-ETV- 88
Cdd:PRK09647   40 RVYRLAYRLSGNQHDAEDLTQETFIRVFR---SLQNYQ-PGTFEgwlhrIT--TNLFLDMVRRRARIRM---EALpEDYd 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  89 -LLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEKAS 167
Cdd:PRK09647  111 rVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHA 190


                  ...
gi 1829886727 168 CHG 170
Cdd:PRK09647  191 PHA 193
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 15-164 4.42e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 53.20  E-value: 4.42e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  15 PKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRS--------PKASRRDNEEALE 86
Cdd:PRK12520   13 PHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRSgrrevrlsLDDADEQSDDDLF 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  87 TVLLTTD----------SSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRAR 156
Cdd:PRK12520   93 DALFAADghyreppsdwGDPDAALSRREFFEVLQACVDRLPPRTGRVFMMREWLELETEEICQELQITATNAWVLLYRAR 172


                  ....*...
gi 1829886727 157 KLIREKLE 164
Cdd:PRK12520  173 MRLRECLD 180
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 4-163 6.82e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 52.66  E-value: 6.82e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   4 DVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLcldFLRSPKASRRDNEE 83
Cdd:PRK12540    5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNL---FRSDYRKRRREVED 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  84 ALETVLLTTDSSPEKELE-EKEDIRhiqELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREK 162
Cdd:PRK12540   82 ADGSYAKTLKSQPGQNAHlEFEEFR---AALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSAL 158


                  .
gi 1829886727 163 L 163
Cdd:PRK12540  159 L 159
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 2-156 2.45e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 51.34  E-value: 2.45e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   2 DVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKrdelGDIQNPE-----AFSITLVKNLCLDFLRSPKA 76
Cdd:PRK12526   36 DKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRK----AHLYNGDkgaatTWVYTVMRNAAFDMLRKIKA 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  77 SRRDNEE----ALETVLLTTDSSPEKELEEKEDiRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSssnIRTLL 152
Cdd:PRK12526  112 KKEQNLGddiwPIEQALAESQSESEEFSDHLMD-KQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVP---LGTVK 187


                  ....
gi 1829886727 153 SRAR 156
Cdd:PRK12526  188 SRLR 191
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 16-164 2.96e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 50.50  E-value: 2.96e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  16 KLYRIAYALLDNKADAEDILQDAYCKLWNKRDELgDIQNPEAF-----SITLVKNLCLDFLRSPKASRRDNEEALETVLL 90
Cdd:PRK12543   19 EVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKY-DSNRPFRFwliglVIKQIHSWRRKRWRRFRIFEKAEEQRKPVSID 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1829886727  91 TTDSSPEKELEEKedirhIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLE 164
Cdd:PRK12543   98 FSEDVLSKESNQE-----LIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 2-164 3.32e-08

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 50.57  E-value: 3.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   2 DVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKrdeLGDIQNPEAF-------SITLVKNLCLDFLRSP 74
Cdd:PRK11923   18 DKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRA---LGNFRGDSAFytwlyriAINTAKNHLVSRGRRP 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  75 KASRRDNEEAL---ETVLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTL 151
Cdd:PRK11923   95 PDSDVSSEDAEfydGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSR 174

                         170
                  ....*....|...
gi 1829886727 152 LSRARKLIREKLE 164
Cdd:PRK11923  175 IFRAREAIDKALQ 187
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 13-163 3.42e-08

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 50.16  E-value: 3.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  13 FHPKLYRIAYALLDNKADAEDILQDAYCKLWnKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASRRDNEEALETVLLTT 92
Cdd:PRK12527    4 YYRELVRFLSARLGNRQAAEDVAHDAYLRVL-ERSSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDEEERLH 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1829886727  93 DSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKL 163
Cdd:PRK12527   83 SPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 13-164 1.31e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 49.16  E-value: 1.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  13 FHPKLYRIA-YALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASRR--------DNEE 83
Cdd:PRK12532   14 SRKLLLHFArLQLPDHPDLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRKvftllddeLLDE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  84 ALETVLLT-----------TDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLL 152
Cdd:PRK12532   94 AFESHFSQnghwtpegqpqHWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIM 173

                         170
                  ....*....|..
gi 1829886727 153 SRARKLIREKLE 164
Cdd:PRK12532  174 HRARESLRQCLQ 185
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 8-128 1.91e-07

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 48.14  E-value: 1.91e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   8 QRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELgDIQNPEAFSITLVKNLCLDFLRSPKASRR---DNEEA 84
Cdd:PRK07037    2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQD-AVKQPVAYLFRIVRNLAIDHYRRQALENKyhgDEEDG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1829886727  85 LETVllTTDSSPEKELEEKEDIRHIQELIEQLPENQR---QVIRLRG 128
Cdd:PRK07037   81 LDVP--SPEASPEAALINRDTLRHVADALSELPARTRyafEMYRLHG 125
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 30-165 2.06e-07

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 48.04  E-value: 2.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  30 DAEDILQDAYCKLWNKRDELGDIQNPEAFSITLvKNLCLDFLRSPK---------ASRRDNEEA-----LETVLLTTDS- 94
Cdd:PRK09047    6 AALDIVQDAMIKLAEKYGDRPAAEWPPLFQRIL-QNRIHDWFRRQKvrntwvslfSSFSDDDDDddfdpLETLDSADEGa 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1829886727  95 -SPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEK 165
Cdd:PRK09047   85 eSPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEA 156
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 2-164 2.28e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 48.39  E-value: 2.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   2 DVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRdELGDIQNP--EAFSITLVKNLCLDFLRSPKAsrR 79
Cdd:PRK12531   25 DKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKA-HLFDGQKSalSTWIYTIIRNLCFDLLRKQKG--K 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  80 DNEEALETVL--------LTTDSSPEKELEEKEDIRhiqeLIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTL 151
Cdd:PRK12531  102 DLHIHADDIWpsdyyppdLVDHYSPEQDMLKEQVMK----FLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSR 177

                         170
                  ....*....|...
gi 1829886727 152 LSRARKLIREKLE 164
Cdd:PRK12531  178 LRLAVEKLRHSMD 190
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 31-155 3.19e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 47.54  E-value: 3.19e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  31 AEDILQDAYCKLWNkRDELGDIQNPEAFSITLVKNLCLDFLRspkasRRDNEEA-LETVLLTTDS---SPEKELEEKEDI 106
Cdd:PRK12523   37 AEDLSQDTFVRLLG-RPELPTPREPRAFLAAVAKGLMFDHFR-----RAALEQAyLAELALVPEAeqpSPEEQHLILEDL 110

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1829886727 107 RHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRA 155
Cdd:PRK12523  111 KAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQG 159
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 25-155 9.78e-07

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 46.34  E-value: 9.78e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  25 LDNKADAEDILQDAYCKLWNKrDELGDIQNPEAFSITLVKNLCLDFLRSpKASRRDNEEALETVLLTTDSSPEKELEEKE 104
Cdd:PRK09651   31 LQSAFDADDIAQDTFLRVMVS-ETLSTIRDPRSFLCTIAKRVMVDLFRR-NALEKAYLEMLALMPEGGAPSPEERESQLE 108

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1829886727 105 DIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRA 155
Cdd:PRK09651  109 TLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 159
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 112-161 1.07e-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: 43.57  E-value: 1.07e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1829886727 112 LIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIRE 161
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 17-164 1.27e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 46.08  E-value: 1.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  17 LYRIAYALLDNKADAEDILQDAYCKLWNKRDEL-GDIQNPEAFSITLvkNLCLDFLRspKASRRDNEEaLETVLLTTDSS 95
Cdd:PRK12541   18 LFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYkGEEIRPWLFTIAY--NAFIDWYR--KEKKYKTTT-IEEFHLPNVPS 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1829886727  96 PEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLE 164
Cdd:PRK12541   93 TEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIKE 161
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 18-164 3.67e-06

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 44.93  E-value: 3.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  18 YRIAYALLD---NKADAEDILQDAYCKLWNKRDEL-GDIQNPEAFSITLVKNLCLDFLRspKASRRDNEEALETVLLTTD 93
Cdd:PRK06811   32 KKIVHKVLGtvnYSQLIEECVNDIFLSIWNNIDKFdEEKGSFKKWIAAISKYKAIDYKR--KLTKNNEIDSIDEFILISE 109

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1829886727  94 SSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLE 164
Cdd:PRK06811  110 ESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 2-166 3.89e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 44.71  E-value: 3.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   2 DVDVFKQRFLPFHPKLYRIAYALLDNKAdAEDILQDAYCKLWNKrdeLGDIQNPEAFSITLVK---NLCLDFLRS--PKA 76
Cdd:PRK12518    9 DRQSFRQLYRRYQQKVRSTLYQLCGREL-LDDLVQEVFLRVWKG---LPKLRNPAYFSTWLYRitwNVATDARRQfaQRP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  77 SRRDNEEALETVLLTTDSSPEKELeekedirHIQELIEQ----LPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLL 152
Cdd:PRK12518   85 SRIQDDSLNDQPSRPSDTPDLMQL-------HYQDLVQQglqtLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRL 157

                         170
                  ....*....|....
gi 1829886727 153 SRARKLIREKLEKA 166
Cdd:PRK12518  158 FYARRQLRKFLQQQ 171
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 2-164 6.67e-06

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 44.31  E-value: 6.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   2 DVDVFKQRFLPFHPKLYRIAYALLDNKADAEDILQDAYCKLWNKRdelGDIQNPEAFSITL---VKNLCLDFLRSPKASR 78
Cdd:PRK09643   25 DRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAA---GSFRGDAAVSSWLhriVVNACLDRLRRAKARP 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  79 rdnEEALETVlLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKL 158
Cdd:PRK09643  102 ---TVPLDDV-YPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRAR 177


                  ....*.
gi 1829886727 159 IREKLE 164
Cdd:PRK09643  178 LAELLG 183
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 14-166 6.79e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 44.34  E-value: 6.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  14 HPKLYRIAYALLDNKADAEDILQDAYCKLWNKRDEL-GDIQ-NPEAFSITLVKNLCLdfLRSPKASRRDNEEALEtvLLT 91
Cdd:PRK12515   32 HVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFeGRSQvSTWLLSIARFKALSA--LRRRKHEEIDDEAAAA--IED 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1829886727  92 TDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEKA 166
Cdd:PRK12515  108 GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKAA 182
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
95-165 1.16e-05

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 43.88  E-value: 1.16e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1829886727  95 SPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEK 165
Cdd:PRK07670  181 TPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLEK 251
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 23-156 2.75e-05

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 42.34  E-value: 2.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  23 ALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASRRDNEEALETVLLTTDsspeKELEE 102
Cdd:PRK09649   42 AYLSDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHVRSRPRTTRGARPEHLIDGD----RHARG 117

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1829886727 103 KEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRAR 156
Cdd:PRK09649  118 FEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARAR 171
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 15-161 3.81e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 42.07  E-value: 3.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  15 PKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELgDIQNPEA----FSITlvKNLCLDFLRSpkaSRR------DNEEA 84
Cdd:PRK12537   34 ARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASF-DPARGSArgwiYSVT--RHLALNVLRD---TRRevvlddDAEET 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1829886727  85 LETVLLTTDsspekELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIRE 161
Cdd:PRK12537  108 AQTLHEIID-----DFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179
PRK12544 PRK12544
RNA polymerase factor sigma-70;
14-164 3.99e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 42.10  E-value: 3.99e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  14 HPKLYRIAYALLDNKADAEDILQDAYcklwnkrdeLGDIQNPEAFS---------ITLVKNLCLDFLRSPK----AS--- 77
Cdd:PRK12544   28 RKQMIKFATLQLSDLHLAEDAVQEAL---------IGALKNADSFAgraafktwvFAILKNKIIDLLRQKKrhvsASsll 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  78 RRDNEEALETVLLTTDS------------SPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSS 145
Cdd:PRK12544   99 RDEEEEEDFEELFDESGhwqkderpqawgNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLSV 178

                         170
                  ....*....|....*....
gi 1829886727 146 SNIRTLLSRARKLIREKLE 164
Cdd:PRK12544  179 SNLNVLLYRARLRLRECLE 197
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 91-166 5.55e-05

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: 41.96  E-value: 5.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  91 TTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLR----GIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEKA 166
Cdd:COG0568   182 EEAPSPEEALEEELLREELREALDTLTEREREILRLRfgldDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSR 261
PRK12545 PRK12545
RNA polymerase factor sigma-70;
17-160 6.15e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 41.48  E-value: 6.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  17 LYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRspkASRR-----------DNEEAL 85
Cdd:PRK12545   21 LLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLR---ARQRtvnlsaldaelDGEALL 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  86 ETVLLTTDS------------SPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLS 153
Cdd:PRK12545   98 DRELFKDNGhwaahakprpwpKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLY 177


                  ....*..
gi 1829886727 154 RARKLIR 160
Cdd:PRK12545  178 RARTRLR 184
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 29-163 1.83e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 40.03  E-value: 1.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  29 ADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSpkASRRDN-----EEALEtVLLTTDSSPEkeleek 103
Cdd:PRK12536   47 DEVEDLVQEILLAVHNARHTYRADQPLTAWVHAIARYKLMDFLRS--RARREAlhdplDDESE-LFATSDDEAA------ 117

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727 104 EDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKL 163
Cdd:PRK12536  118 EARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
1-165 1.12e-03

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 38.08  E-value: 1.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727   1 MDVDVFKQRFLPFH-PKLYRIAYALLDNKADAEDILQDAYCKLWNKRDElgdiqnpEAFSITLV----KNLCLDFLRSPK 75
Cdd:PRK06704   13 IDMNHSNINFLIEQyGELKRYCTFLTKNKWDGEDLAQETVCKVLQKYSN-------KDICMTLVykiaRNRWLDQIKSKS 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  76 ASRRDNEEaletvllTTDSSPEKELEEKEDIrhIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRA 155
Cdd:PRK06704   86 VHEKIRDQ-------ITFEEPHEKIADLHEM--VGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRS 156

                         170
                  ....*....|
gi 1829886727 156 RKLIREKLEK 165
Cdd:PRK06704  157 RNRLKTVSEE 166
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 25-156 1.28e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 37.82  E-value: 1.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  25 LDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSPK----ASRRDNEEALETVLLTT-----DSS 95
Cdd:PRK12530   28 LKDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRKrfvnESELIEEDSPNSFFDEKghwkpEYY 107

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1829886727  96 PEKELEEKEDIRHIQEL-------IEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRAR 156
Cdd:PRK12530  108 EPSEWQEVENTVYKEEFwlifeacLNHLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRAR 175
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 73-164 1.62e-03

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 37.83  E-value: 1.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  73 SPKASRRDNEEALETVLLTTDSspekELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLL 152
Cdd:PRK07122  177 SGGGSGDDDARAIADTLGDVDA----GLDQIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLL 252

                          90
                  ....*....|..
gi 1829886727 153 SRARKLIREKLE 164
Cdd:PRK07122  253 AKTLARLRDQLE 264
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 79-164 2.92e-03

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 37.16  E-value: 2.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  79 RDNEEALETVLLTTDSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLR-GIEDC---SYEDIEQITGLSSSNIRTLLSR 154
Cdd:PRK07598  314 KDKDTELGDLLETDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRfGLADGhtySLAEIGRALDLSRERVRQIESK 393

                          90
                  ....*....|....*....
gi 1829886727 155 A---------RKLIREKLE 164
Cdd:PRK07598  394 AlqklrqpkrRNRIRDYLE 412
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 93-165 3.59e-03

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 36.86  E-value: 3.59e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1829886727  93 DSSPEKELEEKEDIRHIQELIEQLPENQRQVIR----LRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKLEK 165
Cdd:PRK05657  240 ENGPEDTTQDDDMKQSIVKWLFELNDKQREVLArrfgLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQT 316
PRK09191 PRK09191
two-component response regulator; Provisional
 115-163 3.82e-03

two-component response regulator; Provisional


Pssm-ID: 236402 [Multi-domain]  Cd Length: 261  Bit Score: 36.75  E-value: 3.82e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1829886727 115 QLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIREKL 163
Cdd:PRK09191   88 GLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEIARQV 136
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 23-157 3.85e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 36.41  E-value: 3.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  23 ALLDNKADAEDILQDAYCKLWNKRDELGDIQNPEAFSITLVKNLCLDFLRSPKASRRDNEEALETVLlTTDSSPEKELEE 102
Cdd:PRK12535   43 AHLGGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIRHDMARPRKSATEYEDAA-ATTASNETTGSW 121

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1829886727 103 KEDIrHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARK 157
Cdd:PRK12535  122 SEWI-DVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARA 175
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
93-159 3.93e-03

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 36.10  E-value: 3.93e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1829886727  93 DSSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTL----LSRARKLI 159
Cdd:PRK09648  117 DAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAqhraLARLRAEI 187
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
15-125 4.99e-03

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 35.82  E-value: 4.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  15 PKLYRIAYALLDNKADAEDILQDAYCKLWNKRDELGDIQNP-EAFSITLVKNLCLDFLRSPKASRrdnEEALETVLLTTD 93
Cdd:PRK09645   20 APLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSaRAWLFTVARNLVIDERRSARARP---VEGGDDVLGVPE 96

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1829886727  94 SSPEKELEEKEDIRHIQELIEQLPENQRQVIR 125
Cdd:PRK09645   97 QSAPDEVDRALDRLLVADALAQLSPEHRAVLV 128
PRK09642 PRK09642
RNA polymerase sigma factor;
17-161 6.35e-03

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 35.46  E-value: 6.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1829886727  17 LYRIAYALLDNKADAEDILQDAYCKLWNKRDELgDIQNPEAFSITLVKNLCLDFLRspKASRRDNEEAL---ETVLLTTD 93
Cdd:PRK09642    8 IFQVIFSILRHEEDAKDVTQEVFVKIHASLPNY-QFRGLKTWMARIATNHAIDYKR--KKARENEELSLckeTEENIKSS 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1829886727  94 SSPEKELEEKEDIRHIQELIEQLPENQRQVIRLRGIEDCSYEDIEQITGLSSSNIRTLLSRARKLIRE 161
Cdd:PRK09642   85 HNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKK 152
 
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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