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Conserved domains on  [gi|1199605673|ref|WP_087339873|]
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sigma-70 family RNA polymerase sigma factor [Flavonifractor sp. An82]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sig70_famx3 super family cl33310
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 11-156 1.04e-37

RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.


The actual alignment was detected with superfamily member TIGR02954:

Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 126.75  E-value: 1.04e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  11 EYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNADS 90
Cdd:TIGR02954  20 SLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECIDLLKKKKKVIPFDPNTSIE 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1199605673  91 PAPASDPA-ERLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:TIGR02954 100 KGECETHAdSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166
 
Name Accession Description Interval E-value
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 11-156 1.04e-37

RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.


Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 126.75  E-value: 1.04e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  11 EYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNADS 90
Cdd:TIGR02954  20 SLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECIDLLKKKKKVIPFDPNTSIE 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1199605673  91 PAPASDPA-ERLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:TIGR02954 100 KGECETHAdSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 6-156 8.69e-37

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 124.72  E-value: 8.69e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   6 RQQLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVS-LE 84
Cdd:COG1595    16 EAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRElLD 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1199605673  85 DSNADSPAPASDPAERL-------DLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:COG1595    96 ELAEELPDEAADPEEALeaeelleALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREA 174
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 16-155 1.77e-25

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 96.03  E-value: 1.77e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  16 HQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNADSP---- 91
Cdd:PRK09652   19 YQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRPPASDVDAEEAedfd 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1199605673  92 ----APASDPAERL--------DLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:PRK09652   99 ladaLRDISTPENEllsaeleqRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 100-154 8.38e-11

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: 54.42  E-value: 8.38e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1199605673 100 RLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLR 154
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 100-153 4.16e-10

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: 52.46  E-value: 4.16e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1199605673 100 RLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRL 153
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
 
Name Accession Description Interval E-value
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 11-156 1.04e-37

RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.


Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 126.75  E-value: 1.04e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  11 EYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNADS 90
Cdd:TIGR02954  20 SLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECIDLLKKKKKVIPFDPNTSIE 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1199605673  91 PAPASDPA-ERLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:TIGR02954 100 KGECETHAdSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 6-156 8.69e-37

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 124.72  E-value: 8.69e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   6 RQQLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVS-LE 84
Cdd:COG1595    16 EAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRElLD 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1199605673  85 DSNADSPAPASDPAERL-------DLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:COG1595    96 ELAEELPDEAADPEEALeaeelleALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 7-156 2.50e-30

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: 107.82  E-value: 2.50e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   7 QQLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDS 86
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1199605673  87 NADSPAPASDP-------AERLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:TIGR02937  81 LEELLDSDPSPeeeleqeEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 6-161 1.23e-27

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: 100.93  E-value: 1.23e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   6 RQQLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSL-- 83
Cdd:TIGR02983   5 EEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLELPtr 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1199605673  84 EDSNADSPAPASDPAERLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELTGEEV 161
Cdd:TIGR02983  85 ELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELLEEPT 162
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 16-155 1.77e-25

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 96.03  E-value: 1.77e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  16 HQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNADSP---- 91
Cdd:PRK09652   19 YQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRPPASDVDAEEAedfd 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1199605673  92 ----APASDPAERL--------DLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:PRK09652   99 ladaLRDISTPENEllsaeleqRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 1-155 6.85e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 89.26  E-value: 6.85e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   1 MDTNIRQQLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRL 80
Cdd:PRK11924    7 DATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRRE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  81 VSLEDSNADSPAPAS---DPAERLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSL 150
Cdd:PRK11924   87 KAVLSDDALEPEFAEtaeTPEAALLakddlarIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166


                  ....*
gi 1199605673 151 RRLRE 155
Cdd:PRK11924  167 QLLRE 171
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 7-161 1.60e-22

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 88.27  E-value: 1.60e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   7 QQLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRR--GKRLVSLE 84
Cdd:PRK09415   16 DLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSwhNKKVIVTE 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  85 DSNADSPAPASDP-------AERLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELT 157
Cdd:PRK09415   96 DIFTYMESQKESVeeeviqnAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175


                  ....
gi 1199605673 158 GEEV 161
Cdd:PRK09415  176 EEEV 179
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 16-163 8.43e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 83.97  E-value: 8.43e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  16 HQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNADS----P 91
Cdd:PRK12513   35 HRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRRHGARQAPSLDADEQlhalA 114

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1199605673  92 APASDPAERLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELTGEEVAT 163
Cdd:PRK12513  115 DDGAAPEQQLSlfrdrrrLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEEVAV 193
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 20-155 3.07e-18

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: 76.45  E-value: 3.07e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  20 FYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNADSPAPAS---D 96
Cdd:TIGR02985  14 LCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEIEERELseaD 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1199605673  97 PAERLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:TIGR02985  94 PEEELEakeleeiIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRK 159
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 6-154 1.48e-17

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 75.50  E-value: 1.48e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   6 RQQLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLED 85
Cdd:PRK09641   17 QNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRKPDYYLDA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  86 SNADS---------PAPASDPAERL-------DLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKS 149
Cdd:PRK09641   97 EVAGTegltmysqlAADDALPEEQVvslelqeTIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRG 176


                  ....*
gi 1199605673 150 LRRLR 154
Cdd:PRK09641  177 REALR 181
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 15-161 8.01e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 71.53  E-value: 8.01e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  15 AHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNADS---- 90
Cdd:PRK11922   38 RHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLVNLAEMVMAStiag 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  91 ------PAPASDP--------AERLdLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:PRK11922  118 gertplADPAEDPeraaarreIRAL-LERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLRES 196


                  ....*
gi 1199605673 157 TGEEV 161
Cdd:PRK11922  197 LAREI 201
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 6-156 4.38e-14

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 66.27  E-value: 4.38e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   6 RQQLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGK--RLVSL 83
Cdd:PRK09643   26 RYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRRAKarPTVPL 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1199605673  84 EDsNADSPAPASDPAERLDLY----AAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:PRK09643  106 DD-VYPVAQLERDPTARVETAlavqRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARLAEL 181
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 2-155 6.65e-14

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 65.73  E-value: 6.65e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   2 DTNIRQQLseyIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLV 81
Cdd:PRK09640   24 VTRAYEEL---MRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKR 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  82 SLEDSNADSP--APASDPAERLDLYAAIDR----LGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:PRK09640  101 RLMDALSLDPleEASEEKAPKPEERGGLDRwlvhVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 14-155 1.63e-13

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: 64.26  E-value: 1.63e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  14 VAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRR-GKRLVSLEDSNADSPA 92
Cdd:TIGR02989   8 TRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKlGRDRLVFDDDLLEALA 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  93 PASDP-------AERLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:TIGR02989  88 AEAEPteaerlsDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLRE 157
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 23-160 2.54e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 64.22  E-value: 2.54e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  23 LAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNAdSPAPASDPAE--R 100
Cdd:PRK12516   26 FAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREVQDTDGMF-TEQLAVHPSQygT 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1199605673 101 LDLY---AAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELTGEE 160
Cdd:PRK12516  105 LDLQdfrAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIE 167
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 16-156 4.32e-13

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: 62.86  E-value: 4.32e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  16 HQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQpEYMKTWFYRILLNESMNHYRRGKRLV--------SLEDSN 87
Cdd:TIGR02950   4 YMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD-SSIKPWLFRIARNAFIDWYRKDKKIQtidddaigDLEQHP 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  88 ADSPAPASDPAERLD-LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:TIGR02950  83 VESPEHHLLIKIEQEeITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 15-156 5.19e-13

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 63.47  E-value: 5.19e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  15 AHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDsnaDSPAPA 94
Cdd:PRK09637    9 EYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRSEELPD---DLLFED 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1199605673  95 SDPAERLDLYAA------IDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:PRK09637   86 EEREENAKKELApclrpfIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 11-155 6.28e-13

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 63.65  E-value: 6.28e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  11 EYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALsKSDSLRQPEYMKTWFYRILLNESMNHYRRGK--RLVSL-EDSN 87
Cdd:PRK09647   32 ELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVF-RSLQNYQPGTFEGWLHRITTNLFLDMVRRRAriRMEALpEDYD 110

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1199605673  88 ---ADSPAPASDPAER---LDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:PRK09647  111 rvpGDEPNPEQIYHDArldPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRA 184
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 2-156 1.21e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 62.40  E-value: 1.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   2 DTNIRQQLSEYIV-AHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMnhyRRGKR- 79
Cdd:PRK12517   17 DMLSKQRRYEALVkALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILRRENA---RRFERk 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  80 ---LVSLED-SNADSPAPASDP-AERLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLR 154
Cdd:PRK12517   94 qfdLVDIEDdSIEDDASHSSEEeMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLK 173


                  ..
gi 1199605673 155 EL 156
Cdd:PRK12517  174 EA 175
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 30-154 2.59e-12

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 61.19  E-value: 2.59e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  30 NRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNADSPAP------ASDPAERLDL 103
Cdd:PRK09638   41 DPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKLRLQRAKEETLRkekweaAIKGAEWSEM 120

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1199605673 104 YAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLR 154
Cdd:PRK09638  121 LDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLR 171
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 24-158 1.79e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 58.73  E-value: 1.79e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  24 AYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLED----SNADSPAPASDPAE 99
Cdd:PRK12547   23 AVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGREVQDSDgvftARVAVHPAQYGSLD 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1199605673 100 RLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELTG 158
Cdd:PRK12547  103 LQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 10-155 2.05e-11

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


Pssm-ID: 274359 [Multi-domain]  Cd Length: 188  Bit Score: 59.01  E-value: 2.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  10 SEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNAD 89
Cdd:TIGR02943   5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGRSALKTWLFAILKNKIIDALRAKGREVKVSDLDDE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  90 --------------------SPAPASDPAERLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTV 142
Cdd:TIGR02943  85 lddeafnalftqnghwaqhgQPQHWNTPEKQLEnkefwevFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTSNC 164

                         170
                  ....*....|...
gi 1199605673 143 KSRLYKSLRRLRE 155
Cdd:TIGR02943 165 HVLLYRARLSLRA 177
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 6-156 2.12e-11

RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).


Pssm-ID: 132004 [Multi-domain]  Cd Length: 170  Bit Score: 58.92  E-value: 2.12e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   6 RQQLSEYIvahqedfyrlaYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLED 85
Cdd:TIGR02959   5 RSELKAFI-----------KSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQKIQSWLYQIARNTIIDFYRSKSRSVELPE 73

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1199605673  86 S--NADSPAPASDPAERLD-LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:TIGR02959  74 SllAADSAREETFVKELSQcIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 8-160 5.41e-11

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 57.58  E-value: 5.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   8 QLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEyMKTWFYRILLNESMNHYRRGKRLV------ 81
Cdd:PRK09644    2 EIEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQK-VKPWLFKVAYHTFIDFVRKEKKVSfvgtde 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  82 --SLEDSNADSPAPASDPAERLDLYaaIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELTGE 159
Cdd:PRK09644   81 ieAIQAESTEEYVVAKNSYEKLIQI--IHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158


                  .
gi 1199605673 160 E 160
Cdd:PRK09644  159 E 159
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 36-155 6.76e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 57.42  E-value: 6.76e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  36 DVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRR-GKRLVSLEDSNA-DSPAPASDPAERLDLY------AAI 107
Cdd:PRK12518   39 DLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQfAQRPSRIQDDSLnDQPSRPSDTPDLMQLHyqdlvqQGL 118

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1199605673 108 DRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:PRK12518  119 QTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 19-161 7.84e-11

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 57.27  E-value: 7.84e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  19 DFYRLAYSYVKNRDAALDVVQESIVRALsKSDsLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNAD----SPAPA 94
Cdd:PRK09639   15 DVVQQIFYIVKDRTQAEDLAQEVFLRLY-RSD-FKGIENEKGWLIKSARNVAYNYLRSEKRRRARILGEFQwqevDNEPS 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1199605673  95 SDPA-----ERLDLYAAIDRLGPKEQAIIRLRfFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELTGEEV 161
Cdd:PRK09639   93 PEEIwirkeEITKVQEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQME 163
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 100-154 8.38e-11

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: 54.42  E-value: 8.38e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1199605673 100 RLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLR 154
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 13-160 1.25e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 57.16  E-value: 1.25e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  13 IVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVS-LEDSNADSP 91
Cdd:PRK12546   13 LVEHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKREVPdPEGVHAASL 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1199605673  92 A--PASDPAERL-DLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELTGEE 160
Cdd:PRK12546   93 AvkPAHDGRLAMsDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQLE 164
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 20-156 2.48e-10

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 56.20  E-value: 2.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  20 FYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPE-YMKTWFYRILLNESMNHYRRgKRLVSLEDSnADSPAPASDPA 98
Cdd:PRK05602   33 LLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEaRFDTWLHRVVLNLCYDRLRR-RREVPVEDA-PDVPDPAPGPD 110

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1199605673  99 ERLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:PRK05602  111 AGLEarqrarrVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQ 175
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 9-156 2.79e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 56.13  E-value: 2.79e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   9 LSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVslEDSNA 88
Cdd:PRK12540    7 LRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRREV--EDADG 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1199605673  89 D-SPAPASDPA-----ERLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:PRK12540   85 SyAKTLKSQPGqnahlEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSAL 158
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 100-153 4.16e-10

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: 52.46  E-value: 4.16e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1199605673 100 RLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRL 153
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 7-155 4.78e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 55.26  E-value: 4.78e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   7 QQLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSL--- 83
Cdd:PRK12522    3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKRWKDRild 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  84 -----------EDSNADSPAPASDPAERLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRR 152
Cdd:PRK12522   83 lfhkedggeieFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQ 162


                  ...
gi 1199605673 153 LRE 155
Cdd:PRK12522  163 MRE 165
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
16-154 1.10e-09

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 54.31  E-value: 1.10e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  16 HQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEY-MKTWFYRILLNESMNHYR--RGKRLVSLEDSNADSPA 92
Cdd:PRK09645   18 HAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRsARAWLFTVARNLVIDERRsaRARPVEGGDDVLGVPEQ 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1199605673  93 PASDPAER----LDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLR 154
Cdd:PRK09645   98 SAPDEVDRaldrLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALR 163
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 28-154 1.22e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 54.29  E-value: 1.22e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  28 VKNRDAALDVVQESIVRALSKSDSLrQPEYMK--TWFYRILLNESMNHYRR---GKRLVSLEDSnADSPAPASDPAERLD 102
Cdd:PRK12534   46 IPQRAEAEEVLQDVFTLIWHKAGQF-DPSRARglTWLAMIARNKAIDHLRAnapQRRNVALDDA-GELRAADASPLERTE 123

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1199605673 103 LYAAIDR-------LGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLR 154
Cdd:PRK12534  124 RASTRRRidhclaeLEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKLK 182
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 106-155 4.57e-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. 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: 49.73  E-value: 4.57e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1199605673 106 AIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 22-155 5.34e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 52.48  E-value: 5.34e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  22 RLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRR----GKRLVSLEDSNADSPAPASDP 97
Cdd:PRK12511   19 RYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRrrveARRADELAVLADASLPAAQEH 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1199605673  98 AERL-DLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:PRK12511   99 AVRLaQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 28-155 5.96e-09

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 51.89  E-value: 5.96e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  28 VKNRDAALDVVQESIVRaLSKSDSLRQPEYMKTWFYRILLNESMNHYRRGK---RLVSL----------EDSN-----AD 89
Cdd:PRK09047    1 VRDDDAALDIVQDAMIK-LAEKYGDRPAAEWPPLFQRILQNRIHDWFRRQKvrnTWVSLfssfsdddddDDFDpletlDS 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1199605673  90 SPAPASDPAERLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:PRK09047   80 ADEGAESPADKLEraqvlqlIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAK 152
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 6-156 1.53e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 51.09  E-value: 1.53e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   6 RQQLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEyMKTWFYRILLNESMNHYRRGKRLVSLED 85
Cdd:PRK12541    4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKKYKTTTI 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1199605673  86 SNADSPAPASDPAE---RLDLYAAIDRLG---PKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:PRK12541   83 EEFHLPNVPSTEHEyfiKHEIASWLDSLSslpLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 6-162 3.45e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 50.88  E-value: 3.45e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   6 RQQLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQpEYMKTWFYRILLNESMNHYRRGK--RLVSL 83
Cdd:PRK12533   17 GERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRG-DNARPWLLAIVRHTWYSEWRRRAnaHEVAA 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  84 EDSNADSPAP------ASDPAERL-------DLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSL 150
Cdd:PRK12533   96 PDTLDDADSLddwqpaGEDPLALLlraedvrLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARAR 175

                         170
                  ....*....|..
gi 1199605673 151 RRLRELTGEEVA 162
Cdd:PRK12533  176 RRLAALLGGASA 187
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 9-155 8.25e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 49.34  E-value: 8.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   9 LSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSN- 87
Cdd:PRK12520    4 APAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRSGRREVRLSLDDa 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  88 -------------------ADSPAPASDPAERLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISR---VTGTN 138
Cdd:PRK12520   84 deqsdddlfdalfaadghyREPPSDWGDPDAALSrreffevLQACVDRLPPRTGRVFMMREWLELETEEICQelqITATN 163

                         170
                  ....*....|....*..
gi 1199605673 139 LNTVksrLYKSLRRLRE 155
Cdd:PRK12520  164 AWVL---LYRARMRLRE 177
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 1-160 1.13e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 49.03  E-value: 1.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   1 MDTNIRQQLSEYI--VAHQED---------FY-----RLAYSYVKNRDAALDVVQESIVRALSKSdSLRQPE--YMKTWF 62
Cdd:PRK12526   16 TDEQVPTELSQWLilVAISRDkqafthlfqFFapkikRFGIKQLGNEAQANELVQETMSNVWRKA-HLYNGDkgAATTWV 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  63 YRILLNESMNHYRR---------GKRLVSLEDSNADS---PAPASDPAERLDLYAAIDRLGPKEQAIIRLRFFEDMKLEE 130
Cdd:PRK12526   95 YTVMRNAAFDMLRKikakkeqnlGDDIWPIEQALAESqseSEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQ 174

                         170       180       190
                  ....*....|....*....|....*....|
gi 1199605673 131 ISRVTGTNLNTVKSRLYKSLRRLRELTGEE 160
Cdd:PRK12526  175 LAQQLNVPLGTVKSRLRLALAKLKVQMGEQ 204
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 13-149 1.36e-07

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 49.03  E-value: 1.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  13 IVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHY-RRGKRL----VSLED-- 85
Cdd:PRK11923   26 VLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLvSRGRRPpdsdVSSEDae 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1199605673  86 --------SNADSPAPA--SDPAERLdLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKS 149
Cdd:PRK11923  106 fydgdhalKDIESPERAllRDEIEGT-VHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRA 178
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 21-156 1.82e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 48.73  E-value: 1.82e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  21 YRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPE-YMKTWFYRILLNESMNHYRRGKRLVSLEDSNADSPAPASDPAE 99
Cdd:PRK12524   40 LAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEaRVSTWLYRVVCNLCTDRLRRRRRASVDLDDAPEPADAAPGAEE 119

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1199605673 100 RLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:PRK12524  120 ALIegdrmraLDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 28-91 1.87e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 48.22  E-value: 1.87e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1199605673  28 VKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLED-SNADSP 91
Cdd:PRK12530   28 LKDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRKRFVNESElIEEDSP 92
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 13-79 5.60e-07

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


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 44.89  E-value: 5.60e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1199605673  13 IVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMK--TWFYRILLNESMNHYRRGKR 79
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSfsTWLYTIIRNAIIDYLRKQRR 70
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 6-163 7.64e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 46.81  E-value: 7.64e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   6 RQQLSEYIVAHQEDFYRLaYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFY---RILLNESMNH--YRRGKRL 80
Cdd:PRK12535   24 RAALTEFIRETQDDVWRL-LAHLGGHDIADDLTQETYLRVMSALPRFAARSSARTWLLslaRRVWVDNIRHdmARPRKSA 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  81 VSLEDSNADSPAPASDP--AERLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELTG 158
Cdd:PRK12535  103 TEYEDAAATTASNETTGswSEWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADLIAATA 182


                  ....*
gi 1199605673 159 EEVAT 163
Cdd:PRK12535  183 TGQAS 187
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 21-161 7.85e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 46.59  E-value: 7.85e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  21 YRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTwfYRILLNES--MNHYR-RGKRLVSLE--DSNADSPAPAS 95
Cdd:PRK12519   43 YGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSS--YLLTLTRSraIDRLRsRRSRQRLLErwQQELLGEASED 120

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1199605673  96 DPAERLDL-------YAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELTGEEV 161
Cdd:PRK12519  121 TPLEQASLaersqrvQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQDLL 193
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 67-155 1.70e-06

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: 45.97  E-value: 1.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  67 LNESMNHYR------RGKRLVSLEDS-----------NADSPAPASDPAE-RLDLYAAIDRLGPKEQAIIRLRFFEDMKL 128
Cdd:COG1191   126 LGISLEEVQealeaaNAYQLLSLDEPledgddlldllESGDPEEELEHEElREALAEAIEQLPERERLVLSLYYFEELTL 205

                          90       100
                  ....*....|....*....|....*...
gi 1199605673 129 EEISRVTGTNLNTVkSRLYK-SLRRLRE 155
Cdd:COG1191   206 KEIAEVLGVSESRV-SRLHKkALARLRE 232
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 16-156 1.93e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 45.49  E-value: 1.93e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  16 HQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRgKRLVSLEDSNADS-PAPA 94
Cdd:PRK12515   31 HHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRR-RKHEEIDDEAAAAiEDGA 109

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1199605673  95 SDPAERLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:PRK12515  110 DTPEVALQksdtsaaLRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAEL 178
PRK12544 PRK12544
RNA polymerase factor sigma-70;
22-155 3.06e-06

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 45.18  E-value: 3.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  22 RLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSL------EDSNAD------ 89
Cdd:PRK12544   33 KFATLQLSDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKKRHVSAssllrdEEEEEDfeelfd 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  90 ---------SPAPASDPAERLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISR---VTGTNLNTVksrLYKSL 150
Cdd:PRK12544  113 esghwqkdeRPQAWGNPEESLEqeqfwriFEACLDGLPAKYARVFMMREFIELETNEICHavdLSVSNLNVL---LYRAR 189


                  ....*
gi 1199605673 151 RRLRE 155
Cdd:PRK12544  190 LRLRE 194
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 22-154 3.71e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 44.92  E-value: 3.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  22 RLAYSYVKNRDAALDVVQESIVRALSKSDSLR-QPEYMKTWFYRILLNESMNHYRR--GKRLVSLedsnADSPAPaSD-- 96
Cdd:PRK12531   42 QFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDgQKSALSTWIYTIIRNLCFDLLRKqkGKDLHIH----ADDIWP-SDyy 116

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  97 PAERLDLYAA------------IDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLR 154
Cdd:PRK12531  117 PPDLVDHYSPeqdmlkeqvmkfLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLR 186
PRK12545 PRK12545
RNA polymerase factor sigma-70;
12-160 4.87e-06

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 44.56  E-value: 4.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  12 YIVAHQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNAD-- 89
Cdd:PRK12545   13 YLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRARQRTVNLSALDAEld 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  90 --------------------SPAPASDPAERLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTV 142
Cdd:PRK12545   93 gealldrelfkdnghwaahaKPRPWPKPETILQqqqfwtlFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTANHC 172

                         170
                  ....*....|....*...
gi 1199605673 143 KSRLYKSLRRLRELTGEE 160
Cdd:PRK12545  173 SVLLYRARTRLRTCLSEK 190
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 18-155 7.61e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 43.95  E-value: 7.61e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  18 EDFYRLAYSYVKNRDAALDVVQE---SIVRALSKSDSLRQpeyMKTWFYRILLNEsMNHYRRG----------KRLVSLE 84
Cdd:PRK12543   18 QEVYKTVHFLVEDKQDVDDVVNEiyiQLWESLRKYDSNRP---FRFWLIGLVIKQ-IHSWRRKrwrrfrifekAEEQRKP 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1199605673  85 DSNADSPAPASDPAeRLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:PRK12543   94 VSIDFSEDVLSKES-NQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 33-159 8.05e-06

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 43.75  E-value: 8.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  33 AALDVVQESIVRALSKSDSLR-QPEYMKTWFYRILLNESMNHYRR-GKRLVSLEDSNA-----DSPAPASDPAERLD--- 102
Cdd:PRK13919   49 AAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAAVDHVRRrAARPQPLEPDERepeafDLPGPGLDEEGHLDrtr 128

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1199605673 103 LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELTGE 159
Cdd:PRK13919  129 LGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLRE 185
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 7-158 8.75e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 43.89  E-value: 8.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   7 QQLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIV---RALSKSDSLRQPEyMKTWFYRILLNESMNHYRRGKRLVS- 82
Cdd:PRK12542    9 EKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFItlyKNLEKLHSLNTQE-LKRYILRVAKNKAIDSYRKNKRHETf 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  83 LEDSNADSPAPASDPAE--------RLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLR 154
Cdd:PRK12542   88 LEEYERESIEAVDENIEewekrkmsEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQ 167


                  ....
gi 1199605673 155 ELTG 158
Cdd:PRK12542  168 NMIG 171
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 16-156 1.73e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 43.31  E-value: 1.73e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  16 HQEDFYRLAYSYVKNRDAALDVVQESIVRALSKSDSLRQPEY-MKTWFYRILLNESMNHYRRGK-RLVSLEDSNADSPAP 93
Cdd:PRK12538   72 HIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAkFSTWLYRVVSNRCIDLRRKPRtENVDAVPEVADGKPD 151

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1199605673  94 ASDPAERLD----LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLREL 156
Cdd:PRK12538  152 AVSVIERNElsdlLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDL 218
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 16-158 2.71e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 42.46  E-value: 2.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  16 HQEDFYRL---AYSYVKNRDAALDVVQESIVRALSKSDSLRQPE-YMKTWFYRILLNESMNHYRRGKRLVSLEDSNADS- 90
Cdd:PRK12537   29 YQQESARLlgvARRIVRDRALAEDIVHDAFIKIWTGAASFDPARgSARGWIYSVTRHLALNVLRDTRREVVLDDDAEETa 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1199605673  91 --PAPASDPAERLDLYAAIDR----LGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELTG 158
Cdd:PRK12537  109 qtLHEIIDDFDLWANSGKIHRcleqLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRECMG 182
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 18-154 8.80e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 40.53  E-value: 8.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  18 EDFYRLAYSYVK----NRDAALDVVQESIVRALSKSDSlRQPEYMKTWFYRILLNESMNHYRR--GKRLVSLEDSNADSP 91
Cdd:PRK12527    2 ENYYRELVRFLSarlgNRQAAEDVAHDAYLRVLERSSS-AQIEHPRAFLYRTALNLVVDRHRRhrVRQAEPLEVLDEEER 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  92 APASDPAERLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLR 154
Cdd:PRK12527   81 LHSPSPQTRLDlgqrlalLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCR 150
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 28-155 1.95e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 39.80  E-value: 1.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  28 VKNRDAALDVVQESIVRALSKSDSLRQPEYMK-TWFYRILLNESMNHYRRGKR----LVSLEDSNADSPAP-----ASDP 97
Cdd:PRK12514   40 LKDRSEAEEALQDVYVKIWTKADRFAVSGLSPmTWLITIARNHAIDRLRARKAvavdIDEAHDLADPSPGPeaeviAGDE 119

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1199605673  98 AERLDlyAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:PRK12514  120 GQRID--ACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 32-155 2.49e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 39.53  E-value: 2.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  32 DAALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLV---SLEDSN------------------ADS 90
Cdd:PRK12532   31 DLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRkvfTLLDDElldeafeshfsqnghwtpEGQ 110

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1199605673  91 PAPASDPAERLD-------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISR---VTGTNLNTVKSRLYKSLRRLRE 155
Cdd:PRK12532  111 PQHWNTPEKSLNnnefqkiLQSCLYNLPENTARVFTLKEILGFSSDEIQQmcgISTSNYHTIMHRARESLRQCLQ 185
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 83-133 7.68e-04

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: 38.50  E-value: 7.68e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1199605673  83 LEDSNADSPAP-ASDPAERLDLYAAIDRLGPKEQAIIRLRFF----EDMKLEEISR 133
Cdd:COG0568   179 LEDEEAPSPEEaLEEELLREELREALDTLTEREREILRLRFGlddgEPHTLEEIGK 234
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 65-154 7.86e-04

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 38.51  E-value: 7.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  65 ILLNESMNHYRRGKRLV---SLEDSNADSPAPASDPAE-RLDLYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLN 140
Cdd:PRK06288  164 VSLNDLWFGGDEGDEVSlmdTLESPAALNPDEIAEREEiKRVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTES 243

                          90
                  ....*....|....
gi 1199605673 141 TVKSRLYKSLRRLR 154
Cdd:PRK06288  244 RISQLHTKAVLQLR 257
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
34-122 1.49e-03

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 37.99  E-value: 1.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  34 ALDVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKRLVSLEDSNADSPAPASDPAERL---------DLY 104
Cdd:PRK08241   46 AEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALEGRARRPLPTDLGAPAADPVDELVERPevpwlepypDAL 125

                          90       100
                  ....*....|....*....|..
gi 1199605673 105 AAIDRLGPKEQAI----IRLRF 122
Cdd:PRK08241  126 LDPAAADPAARVVaresVRLAF 147
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 103-161 1.55e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 37.23  E-value: 1.55e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1199605673 103 LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRELTGEEV 161
Cdd:PRK06811  125 ILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKLNIS 183
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 8-155 1.66e-03

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 37.64  E-value: 1.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673   8 QLSEYIVAHQEDFYRLAYSYVKNRDAALDVVQESIVR-ALSKSDSLRQPeymKTWFY----RILLNESMNHYRRGKRLVS 82
Cdd:PRK09635    6 PVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRlLRAPVGDIDDE---RGWLIvvtsRLCLDHIKSASTRRERPQD 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  83 LEDSNADSPAPAS-DPAER--LD------LYAAIDRLGPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRL 153
Cdd:PRK09635   83 IAAWHDGDASVSSvDPADRvtLDdevrlaLLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKI 162


                  ..
gi 1199605673 154 RE 155
Cdd:PRK09635  163 NE 164
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 36-153 8.82e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 35.03  E-value: 8.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  36 DVVQESIVRALSKSDSLRQPEYMKTWFYRILLNESMNHYRRGKR----LVSLEDSNADSPAPASDPAE-RLDLYAAIDRL 110
Cdd:PRK12536   51 DLVQEILLAVHNARHTYRADQPLTAWVHAIARYKLMDFLRSRARrealHDPLDDESELFATSDDEAAEaRRDLGKLLEQL 130

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1199605673 111 GPKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRL 153
Cdd:PRK12536  131 PDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLKAL 173
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 33-155 8.84e-03

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 35.52  E-value: 8.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1199605673  33 AALDVVQESIVRALSKSDSlrqpeymktwfYRIL-LNESMNHYRRGKRlvSLEDSNADSPAPASDPAERLDLYAAIDRLG 111
Cdd:PRK07122  151 AELGMDREEVVEGLVAGSA-----------YNTLsIDSGGGSGDDDAR--AIADTLGDVDAGLDQIENREALRPLLAALP 217

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1199605673 112 PKEQAIIRLRFFEDMKLEEISRVTGTNLNTVKSRLYKSLRRLRE 155
Cdd:PRK07122  218 ERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261
 
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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